@article{xie_li_liu_zhao_li_ingvarsson_zhang_2019, title={Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants}, volume={31}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.18.00601}, abstractNote={A multifaceted approach combining RNA-seq, genomics, and molecular biology allows systematic comparative analysis of pseudogenes in seven plant species. Pseudogenes (Ψs), nonfunctional relatives of functional genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Evolutionary analysis provides clues to Ψ origins and effects on gene regulation. However, few systematic studies of plant Ψs have been conducted, hampering comparative analyses. Here, we examined the origin, evolution, and expression patterns of Ψs and their relationships with noncoding sequences in seven angiosperm plants. We identified ∼250,000 Ψs, most of which are more lineage specific than protein-coding genes. The distribution of Ψs on the chromosome indicates that genome recombination may contribute to Ψ elimination. Most Ψs evolve rapidly in terms of sequence and expression levels, showing tissue- or stage-specific expression patterns. We found that a surprisingly large fraction of nontransposable element regulatory noncoding RNAs (microRNAs and long noncoding RNAs) originate from transcription of Ψ proximal upstream regions. We also found that transcription factor binding sites preferentially occur in putative Ψ proximal upstream regions compared with random intergenic regions, suggesting that Ψs have conditioned genome evolution by providing transcription factor binding sites that serve as promoters and enhancers. We therefore propose that rapid rewiring of Ψ transcriptional regulatory regions is a major mechanism driving the origin of novel regulatory modules.}, number={3}, journal={PLANT CELL}, author={Xie, Jianbo and Li, Ying and Liu, Xiaomin and Zhao, Yiyang and Li, Bailian and Ingvarsson, Par K. and Zhang, Deqiang}, year={2019}, month={Mar}, pages={563–578} }
 @article{zhang_wang_qi_dong_wang_li_chen_li_zhang_2019, title={Ploidy and hybridity effects on leaf size, cell size and related genes expression in triploids, diploids and their parents in Populus}, volume={249}, ISSN={["1432-2048"]}, DOI={10.1007/s00425-018-3029-0}, abstractNote={Cell-size enlargement plays a pivotal role in increasing the leaf size of triploid poplar, and polyploidization could change leaf shape. ABP1 was highly expressed in triploid plants and positively related to cell size. In the plant kingdom, the leaf is the most important energy production organ, and polyploidy often exhibits a "Gigas" effect on leaf size, which benefits agriculture and forestry. However, little is known regarding the cellular and molecular mechanisms underlying the leaf size superiority of polyploid woody plants. In the present study, the leaf area and abaxial epidermal cells of diploid and triploid full-sib groups and their parents were measured at three different positions. We measured the expression of several genes related to cell division and cell expansion. The results showed that the leaf area of triploids was significantly larger than that of diploids, and the triploid group showed transgressive variation compared to their full-sib diploid group. Cell size but not cell number was the main reason for leaf size variation. Cell expansion was in accordance with leaf enlargement. In addition, the leaf shape changes in triploids primarily resulted from a significant decrease in the leaf ratio of length to -width. Auxin-binding protein 1 (ABP1) was highly expressed in triploids and positively related to leaf size. These results enhanced the current understanding that giant leaf is affected by polyploidy vigor. However, significant heterosis is not exhibited in diploid offspring. Overall, polyploid breeding is an effective strategy to enhance leaf size, and Populus, as an ideal material, plays an important role in studying the leaf morphological variations of polyploid woody plants.}, number={3}, journal={PLANTA}, author={Zhang, Yan and Wang, Beibei and Qi, Shuaizheng and Dong, Mingliang and Wang, Zewei and Li, Yixuan and Chen, Siyuan and Li, Bailian and Zhang, Jinfeng}, year={2019}, month={Mar}, pages={635–646} }
 @article{du_yang_xie_quan_xiao_lu_tian_gong_chen_li_et al._2019, title={Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus}, volume={17}, ISSN={["1467-7652"]}, DOI={10.1111/pbi.13002}, abstractNote={SummaryIn perennial woody plants, the coordinated increase of stem height and diameter during juvenile growth improves competitiveness (i.e. access to light); however, the factors underlying variation in stem growth remain unknown in trees. Here, we used linkage‐linkage disequilibrium (linkage‐LD) mapping to decipher the genetic architecture underlying three growth traits during juvenile stem growth. We used two Populus populations: a linkage mapping population comprising a full‐sib family of 1,200 progeny and an association mapping panel comprising 435 unrelated individuals from nearly the entire natural range of Populus tomentosa. We mapped 311 quantitative trait loci (QTL) for three growth traits at 12 timepoints to 42 regions in 17 linkage groups. Of these, 28 regions encompassing 233 QTL were annotated as 27 segmental homology regions (SHRs). Using SNPs identified by whole‐genome re‐sequencing of the 435‐member association mapping panel, we identified significant SNPs (P ≤ 9.4 × 10−7) within 27 SHRs that affect stem growth at nine timepoints with diverse additive and dominance patterns, and these SNPs exhibited complex allelic epistasis over the juvenile growth period. Nineteen genes linked to potential causative alleles that have time‐specific or pleiotropic effects, and mostly overlapped with significant signatures of selection within SHRs between climatic regions represented by the association mapping panel. Five genes with potential time‐specific effects showed species‐specific temporal expression profiles during the juvenile stages of stem growth in five representative Populus species. Our observations revealed the importance of considering temporal genetic basis of complex traits, which will facilitate the molecular design of tree ideotypes.}, number={3}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Du, Qingzhang and Yang, Xiaohui and Xie, Jianbo and Quan, Mingyang and Xiao, Liang and Lu, Wenjie and Tian, Jiaxing and Gong, Chenrui and Chen, Jinhui and Li, Bailian and et al.}, year={2019}, month={Mar}, pages={608–624} }
 @article{zhang_wang_guo_xu_wang_li_zhang_2018, title={Factors influencing direct shoot regeneration from leaves, petioles, and plantlet roots of triploid hybrid Populus sect. Tacamahaca}, volume={29}, ISSN={["1993-0607"]}, DOI={10.1007/s11676-017-0559-4}, number={6}, journal={JOURNAL OF FORESTRY RESEARCH}, author={Zhang, Yan and Wang, Beibei and Guo, Liqin and Xu, Wenting and Wang, Zewei and Li, Bailian and Zhang, Jinfeng}, year={2018}, month={Nov}, pages={1533–1545} }
 @article{zhang_wang_qi_wang_zhao_zhang_li_zhang_liu_yuan_2017, title={In Vitro Tetraploid Induction from Leaf and Petiole Explants of Hybrid Sweetgum (Liquidambar styraciflua x Liquidambar formosana)}, volume={8}, ISSN={["1999-4907"]}, DOI={10.3390/f8080264}, abstractNote={Liquidambar is an important forestry species used to generate many commercial wood products, such as plywood. Inducing artificial polyploidy is an effective method to encourage genetic enhancements in forestry breeding. This report presents the first in vitro protocol for the induction of genus Liquidambar tetraploids based on the established in vitro regeneration system of hybrid sweetgum (Liquidambar styraciflua × Liquidambar formosana). The leaves and petioles from three genotypes were pre-cultured in woody plant medium (WPM) supplemented with 0.1 mg/L thidiazuron (TDZ), 0.8 mg/L benzyladenine (BA), and 0.1 mg/L α-naphthalene acetic acid (NAA) for a variable number of days (4, 6 or 8 days), and exposed to varying concentrations of colchicine (120, 160, 200 mg/L) for 3, 4 or 5 days; the four factors were investigated using an orthogonal experimental design. Adventitious shoots were rooted in 1/2 WPM medium supplemented with 2.0 mg/L indole butyric acid (IBA) and 0.1 mg/L NAA. The ploidy level was assessed using flow cytometry and chromosome counting. Four tetraploids and nine mixoploids were obtained from the leaves. Pre-treatment of the leaves for 8 days and exposure to 200 mg/L colchicine for 3 days led to the most efficient tetraploid induction. Producing 11 tetraploids and five mixoploids from petioles, the best tetraploid induction treatment for petioles was almost the same as that with the leaves, except that pre-culturing was required for only 6 days. In total, 15 tetraploids were obtained with these treatments. This study described a technique for the induction of tetraploid sweetgum from the leaves or petioles of parental material. Based on the success of polyploid breeding in other tree species, the production of hybrid sweetgum allotetraploids constitutes a promising strategy for the promotion of future forestry breeding.}, number={8}, journal={FORESTS}, author={Zhang, Yan and Wang, Zewei and Qi, Shuaizheng and Wang, Xiaoqi and Zhao, Jian and Zhang, Jinfeng and Li, Bailian and Zhang, Yadong and Liu, Xuezeng and Yuan, Wei}, year={2017}, month={Aug} }
 @article{xie_tian_du_chen_li_yang_li_zhang_2016, title={Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis}, volume={67}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erw151}, abstractNote={Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits.}, number={11}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Xie, Jianbo and Tian, Jiaxing and Du, Qingzhang and Chen, Jinhui and Li, Ying and Yang, Xiaohui and Li, Bailian and Zhang, Deqiang}, year={2016}, month={May}, pages={3325–3338} }
 @article{tian_chen_li_zhang_2016, title={Association genetics in Populus reveals the interactions between Pto-miR160a and its target Pto-ARF16}, volume={291}, ISSN={1617-4615 1617-4623}, url={http://dx.doi.org/10.1007/S00438-015-1165-9}, DOI={10.1007/S00438-015-1165-9}, abstractNote={MicroRNAs (miRNAs) play important roles in the regulation of gene expression in various biological processes. However, the interactions between miRNAs and their targets are largely unknown in plants. As a powerful tool for identification of variation associated with traits, association genetics provides another strategy for exploration of interactions between miRNAs and their targets. Here, we conducted expression analysis and association mapping to evaluate the interaction between Pto-miR160a and its target Pto-ARF16 in Populus tomentosa. By examining the expression patterns of Pto-MIR160a and Pto-ARF16, we identified a significant, negative correlation between their expression levels, indicating that Pto-miR160a may affect the expression of Pto-ARF16. Among the single nucleotide polymorphisms (SNPs) identified in this study, one common SNP in the pre-miRNA region of Pto-miR160a altered its predicted secondary structure while another common SNP in the predicted miRNA target site changed the binding affinity of Pto-miR160a. Linkage disequilibrium (LD) analysis revealed low LD levels of Pto-MIR160a and Pto-ARF16, indicating that they are suitable for candidate gene-based association analysis. Single SNP-based association analysis identified 19 SNPs (false discovery rate Q < 0.05) in Pto-MIR160a and Pto-ARF16 associated with three phenotypic traits. Epistasis analysis further identified 36 SNP-SNP interactions between SNPs in Pto-MIR160a and SNPs in Pto-ARF16, reflecting the possible genetic interaction of Pto-miR160a and Pto-ARF16. Taking these results together, our study identified SNPs in Pto-MIR160a and Pto-ARF16 associated with tree growth and wood properties, providing SNPs with potential applications in marker-assisted breeding and evidence for the genetic interaction of Pto-miR160a and Pto-ARF16.}, number={3}, journal={Molecular Genetics and Genomics}, publisher={Springer Science and Business Media LLC}, author={Tian, Jiaxing and Chen, Jinhui and Li, Bailian and Zhang, Deqiang}, year={2016}, month={Jan}, pages={1069–1082} }
 @article{chen_du_chen_yang_tian_li_zhang_2016, title={Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus}, volume={117}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/HDY.2016.26}, DOI={10.1038/HDY.2016.26}, abstractNote={MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.}, number={2}, journal={Heredity}, publisher={Springer Nature}, author={Chen, B and Du, Q and Chen, J and Yang, X and Tian, J and Li, B and Zhang, D}, year={2016}, month={Apr}, pages={73–83} }
 @article{chen_xie_chen_quan_li_li_zhang_2016, title={Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus}, volume={212}, ISSN={["1469-8137"]}, DOI={10.1111/nph.14040}, abstractNote={Summary


Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized.

We investigated the associations and interactions of single‐nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus.

We used RNA‐seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA–target pairs showed significant co‐expression. Gene ontology (GO) term analysis showed that most of the genes in the co‐regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single‐SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA–target pairs associated with the same traits. Multi‐SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co‐expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood.

This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis.

}, number={1}, journal={NEW PHYTOLOGIST}, author={Chen, Jinhui and Xie, Jianbo and Chen, Beibei and Quan, Mingyang and Li, Ying and Li, Bailian and Zhang, Deqiang}, year={2016}, month={Oct}, pages={150–160} }
 @article{du_gong_wang_zhou_yang_pan_li_zhang_2016, title={Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies}, volume={209}, ISSN={["1469-8137"]}, DOI={10.1111/nph.13695}, abstractNote={Summary


Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker‐assisted breeding. Recent advances in high‐throughput sequencing have enabled strategies that integrate linkage–linkage disequilibrium (LD) mapping in Populus.

We used an integrated method of quantitative trait locus (QTL) dissection with a high‐resolution linkage map and multi‐gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals).

Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) ≥ 2.5), and explained 2.7–18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi‐gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P ≤ 0.0001; FDR ≤ 0.10) that exhibited reproducible associations with additive/dominant effects, and further determined 11 top‐ranked genes tightly linked to the QTLs. Epistasis analysis uncovered a uniquely interconnected gene–gene network for each trait.

This study opens up opportunities to uncover the causal networks of interacting genes in plants using an integrated linkage–LD mapping approach.

}, number={3}, journal={NEW PHYTOLOGIST}, author={Du, Qingzhang and Gong, Chenrui and Wang, Qingshi and Zhou, Daling and Yang, Haijiao and Pan, Wei and Li, Bailian and Zhang, Deqiang}, year={2016}, month={Feb}, pages={1067–1082} }
 @article{yang_li_li_zhang_2014, title={Genome-wide transcriptional profiling reveals molecular signatures of secondary xylem differentiation in Populus tomentosa}, volume={13}, ISSN={["1676-5680"]}, DOI={10.4238/2014.november.11.14}, abstractNote={Wood formation occurs via cell division, primary cell wall and secondary wall formation, and programmed cell death in the vascular cambium. Transcriptional profiling of secondary xylem differentiation is essential for understanding the molecular mechanisms underlying wood formation. Differential gene expression in secondary xylem differentiation of Populus has been previously investigated using cDNA microarray analysis. However, little is known about the molecular mechanisms from a genome-wide perspective. In this study, the Affymetrix poplar genome chips containing 61,413 probes were used to investigate the changes in the transcriptome during secondary xylem differentiation in Chinese white poplar (Populus tomentosa). Two xylem tissues (newly formed and lignified) were sampled for genome-wide transcriptional profiling. In total, 6843 genes (~11%) were identified with differential expression in the two xylem tissues. Many genes involved in cell division, primary wall modification, and cellulose synthesis were preferentially expressed in the newly formed xylem. In contrast, many genes, including 4-coumarate:cinnamate-4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and caffeoyl CoA 3-O-methyltransferase (CCoAOMT), associated with lignin biosynthesis were more transcribed in the lignified xylem. The two xylem tissues also showed differential expression of genes related to various hormones; thus, the secondary xylem differentiation could be regulated by hormone signaling. Furthermore, many transcription factor genes were preferentially expressed in the lignified xylem, suggesting that wood lignification involves extensive transcription regulation. The genome-wide transcriptional profiling of secondary xylem differentiation could provide additional insights into the molecular basis of wood formation in poplar species.}, number={4}, journal={GENETICS AND MOLECULAR RESEARCH}, author={Yang, X. H. and Li, X. G. and Li, B. L. and Zhang, D. Q.}, year={2014}, pages={9489–9504} }
 @article{du_tian_yang_pan_xu_li_ingvarsson_zhang_2015, title={Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa}, volume={22}, ISSN={["1756-1663"]}, DOI={10.1093/dnares/dsu040}, abstractNote={Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene–gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.}, number={1}, journal={DNA RESEARCH}, author={Du, Qingzhang and Tian, Jiaxing and Yang, Xiaohui and Pan, Wei and Xu, Baohua and Li, Bailian and Ingvarsson, Par K. and Zhang, Deqiang}, year={2015}, month={Feb}, pages={53–67} }
 @article{xi_guo_xu_zhang_li_2014, title={Megasporogenesis, megagametogenesis, and induction of 2n eggs with colchicine in poplar section Aigeiros}, volume={29}, ISSN={["1651-1891"]}, DOI={10.1080/02827581.2014.935472}, abstractNote={Triploid breeding through 2n eggs induction has become one of the most powerful approaches for the improvement of the genus Populus. To enhance the efficiency of triploid production in section Aigeiros, female buds (catkins) of P. × euramericana (Dode) Guinier at different developmental stages were exposed to colchicine for 2n eggs induction. The relationship between flower bud morphological characteristics (or time after pollination) and female meiotic stage (or embryo sac development) was established to guide colchicine treatments. In the resulting progeny, three triploid seedlings were obtained via embryo rescue and identified by flow cytometric analyses. Cytological observation revealed that the leptotene to pachytene stage of meiosis and 12 h after pollination might be the suitable period for 2n eggs induction with colchicine in P. × euramericana. Results and protocols related to 2n eggs induction, effective methodologies for embryo rescue, and ploidy evaluation in this study might be applicable in polyploidy breeding in section Aigeiros.}, number={6}, journal={SCANDINAVIAN JOURNAL OF FOREST RESEARCH}, author={Xi, Xiaojun and Guo, Liqin and Xu, Wenting and Zhang, Jinfeng and Li, Bailian}, year={2014}, pages={527–536} }
 @article{du_xu_gong_yang_pan_tian_li_zhang_2014, title={Variation in growth, leaf, and wood property traits of Chinese white poplar (Populus tomentosa), a major industrial tree species in Northern China}, volume={44}, ISSN={["1208-6037"]}, DOI={10.1139/cjfr-2013-0416}, abstractNote={The natural phenotypic variation in Chinese white poplar (Populus tomentosa Carr.), which is distributed across a wide geographical area of northern China (30°N–40°N, 105°E–125°E), is a potential source of beneficial variation for poplar breeding. Thirteen traits related to growth, leaf, and wood properties were quantified in 460 P. tomentosa individuals grown in a common garden plot. There was considerable range-wide phenotypic variation in all traits across individuals according to the patterns of ANOVA among hierarchical groups (populations and regions, respectively). A clear sexual dimorphism for seven traits was examined. In total, 32 trait–trait phenotypic correlations (P ≤ 0.05), 10 trait–geographical factor correlations (P ≤ 0.05), and a highly interrelated structure network were identified, which was further supported by principal component analysis (PCA). These associations can be used in multiple-trait selective breeding programs for advantageous phenotypic traits. A hierarchical cluster analysis was used to classify four groups (southeastern, central, northeastern, and southwestern populations) among the natural populations using these 13 phenotypic traits. This study provides important perspectives into the use of direct breeding to potentially improve economic traits and provides a starting point for genome-wide association studies in P. tomentosa in the near future.}, number={4}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Du, Qingzhang and Xu, Baohua and Gong, Chenrui and Yang, Xiaohui and Pan, Wei and Tian, Jiaxing and Li, Bailian and Zhang, Deqiang}, year={2014}, month={Apr}, pages={326–339} }
 @article{du_xu_pan_gong_wang_tian_li_zhang_2013, title={Allelic Variation in a Cellulose Synthase Gene (PtoCesA4) Associated with Growth and Wood Properties in Populus tomentosa}, volume={3}, ISSN={["2160-1836"]}, DOI={10.1534/g3.113.007724}, abstractNote={Abstract
               Lignocellulosic biomass from trees provides a renewable feedstock for biofuels, lumber, pulp, paper, and other uses. Dissecting the mechanism underlying natural variation of the complex traits controlling growth and lignocellulose biosynthesis in trees can enable marker-assisted breeding to improve wood quality and yield. Here, we combined linkage disequilibrium (LD)-based association analysis with traditional linkage analysis to detect the genetic effect of a Populus tomentosa cellulose synthase gene, PtoCesA4. PtoCesA4 is strongly expressed in developing xylem and leaves. Nucleotide diversity and LD in PtoCesA4, sampled from the P. tomentosa natural distribution, revealed that PtoCesA4 harbors high single nucleotide polymorphism (SNP) diversity (πT = 0.0080 and θw = 0.0098) and low LD (r2 ≥ 0.1, within 1400 bp), demonstrating that the potential of a candidate-gene-based LD approach in understanding the molecular basis underlying quantitative variation in this species. By combining single SNP, multi-SNP, and haplotype-based associations in an association population of 460 individuals with single SNP linkage analysis in a family-based linkage populations (1200 individuals), we identified three strong associations (false discovery rate Q < 0.05) in both populations. These include two nonsynonymous markers (SNP49 associated with α-cellulose content and SNP59 associated with fiber width) and a noncoding marker (SNP18 associated with α-cellulose content). Variation in RNA transcript abundance among genotypic classes of SNP49 was confirmed in these two populations. Therefore, combining different methods allowed us to examine functional PtoCesA4 allelic variation underlying natural variation in complex quantitative traits related to growth and lignocellulosic biosynthesis.}, number={11}, journal={G3-GENES GENOMES GENETICS}, author={Du, Qingzhang and Xu, Baohua and Pan, Wei and Gong, Chenrui and Wang, Qingshi and Tian, Jiaxing and Li, Bailian and Zhang, Deqiang}, year={2013}, month={Nov}, pages={2069–2084} }
 @article{yang_li_li_zhang_2014, title={Identification of Genes Differentially Expressed in Shoot Apical Meristems and in Mature Xylem of Populus tomentosa}, volume={32}, ISSN={["1572-9818"]}, DOI={10.1007/s11105-013-0660-6}, number={2}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Yang, Xiaohui and Li, Xinguo and Li, Bailian and Zhang, Deqiang}, year={2014}, month={Apr}, pages={452–464} }
 @article{tian_du_li_zhang_2014, title={Single-nucleotide polymorphisms in the 5′ UTR of UDP-glucose dehydrogenase (PtUGDH) associate with wood properties in Populus tomentosa}, volume={10}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-013-0689-6}, DOI={10.1007/S11295-013-0689-6}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Tian, Jiaxing and Du, Qingzhang and Li, Bailian and Zhang, Deqiang}, year={2014}, month={Apr}, pages={339–354} }
 @article{xi_li_xu_guo_zhang_li_2012, title={2n egg formation in Populus × euramericana (Dode) Guinier}, volume={8}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-012-0510-Y}, DOI={10.1007/S11295-012-0510-Y}, number={6}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Xi, Xiaojun and Li, Dan and Xu, Wenting and Guo, Liqin and Zhang, Jinfeng and Li, Bailian}, year={2012}, month={May}, pages={1237–1245} }
 @article{wei_du_zhang_li_zhang_2013, title={Genetic Diversity and Population Structure in Chinese Indigenous Poplar (Populus simonii) Populations Using Microsatellite Markers}, volume={31}, ISSN={0735-9640 1572-9818}, url={http://dx.doi.org/10.1007/S11105-012-0527-2}, DOI={10.1007/S11105-012-0527-2}, number={3}, journal={Plant Molecular Biology Reporter}, publisher={Springer Science and Business Media LLC}, author={Wei, Zunzheng and Du, Qingzhang and Zhang, Jinfeng and Li, Bailian and Zhang, Deqiang}, year={2013}, pages={620–632} }
 @article{ma_song_jiang_zhang_li_zhang_2012, title={Photosynthetic response to genome methylation affects the growth of Chinese white poplar}, volume={8}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-012-0527-2}, DOI={10.1007/S11295-012-0527-2}, number={6}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Ma, Kaifeng and Song, Yuepeng and Jiang, Xibing and Zhang, Zhiyi and Li, Bailian and Zhang, Deqiang}, year={2012}, month={Jun}, pages={1407–1421} }
 @article{du_pan_xu_li_zhang_2013, title={Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa}, volume={197}, ISSN={["1469-8137"]}, DOI={10.1111/nph.12072}, abstractNote={Summary


Chinese white poplar (Populus tomentosa), an important commercial tree species for timber and pulp production in northern China, has been used to examine the individual genes and allelic diversity responsible for complex traits controlling growth and lignocellulosic biosynthesis. Taking advantage of the low degree of linkage disequilibrium (LD) within P. tomentosa association populations, we examined associations between 15 cellulose synthase (PtoCesA) genes and traits including growth and wood properties.

Thirty‐six novel simple sequence repeat (SSR) markers within PtoCesA genes were detected by re‐sequencing and genotyped in an association population (460 individuals). Single‐marker and haplotype‐based LD approaches were used to identify significant marker–trait associations. Family‐based linkage studies and real‐time PCR testing were conducted to validate the functional significance of SSR variation.

Fifteen single‐marker associations from seven PtoCesA genes and nine haplotype‐based associations within six genes were identified in the association population (false discovery rate Q < 0.05). Next, five SSR marker–trait associations (Q < 0.05) from four PtoCesA genes were successfully validated in a linkage mapping population (1200 individuals).

The results imply a functional role for these genes in mediating wood properties, demonstrating the potential of combining single‐marker and haplotype‐based LD approaches to detect functional allelic variation underlying quantitative traits in a low‐LD population.

}, number={3}, journal={NEW PHYTOLOGIST}, author={Du, Qingzhang and Pan, Wei and Xu, Baohua and Li, Bailian and Zhang, Deqiang}, year={2013}, month={Feb}, pages={763–776} }
 @article{cumbie_isik_li_goldfarb_2011, title={Effects of propagule type on genetic parameters of wood density and growth in a loblolly pine progeny test at ages 10 and 11 years}, volume={7}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/s11295-011-0402-6}, DOI={10.1007/s11295-011-0402-6}, number={6}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Cumbie, W. Patrick and Isik, Fikret and Li, Bailian and Goldfarb, Barry}, year={2011}, month={Jul}, pages={1147–1158} }
 @article{xi_jiang_li_guo_zhang_wei_li_2011, title={Induction of 2n pollen by colchicine in Populus X popularis and its triploids breeding}, volume={60}, ISSN={["2509-8934"]}, DOI={10.1515/sg-2011-0021}, abstractNote={AbstractInduction of 2n pollen is a required technique for cultivating polyploid via sexual polyploidy. Orthogonal design or Taguchi Design was applied to select the best treatment process of 2n pollen induction inPopulus×popularisfrom different levels of the meiosis stage of male flower buds, colchicine concentration, times of injection, and interval between injections. Flow cytometry and chromosome counting were used to identify the triploids from the offspring ofP.×euramericana. (Dode) Guinier pollinated with induced pollen ofP.×popularis. The results showed that high 2n pollen rate can be achieved by selecting the flower buds during diakinesis stage in meiosis, and then injecting 0.6% colchicine 4 times with 2 hours interval. The 2n pollen rate reached 62.10% by this process, and two triploids were obtained, which indicates that it is possible for cultivating triploids via 2n pollen induction by colchicine treatment in poplar. Results and protocol related to 2n pollen induction, polyploid identification and effect of 2n pollen in this study might be applicable in polyploidy breeding in sectionAigeirosandTacamahacaof poplar.}, number={3-4}, journal={SILVAE GENETICA}, author={Xi, X. J. and Jiang, X. B. and Li, D. and Guo, L. Q. and Zhang, J. F. and Wei, Z. Z. and Li, B. L.}, year={2011}, pages={155–160} }
 @article{aspinwall_li_mckeand_isik_gumpertz_2010, title={Prediction of whole-stem alpha-cellulose yield, lignin content, and wood density in juvenile and mature loblolly pine}, volume={34}, number={2}, journal={Southern Journal of Applied Forestry}, author={Aspinwall, M. J. and Li, B. L. and McKeand, S. E. and Isik, F. and Gumpertz, M. L.}, year={2010}, pages={84–90} }
 @article{eckard_isik_bullock_li_gumpertz_2010, title={Selection efficiency for solid wood traits in pinus taeda using time-of-flight acoustic and micro-drill resistance methods}, volume={56}, number={3}, journal={Forest Science}, author={Eckard, J. T. and Isik, F. and Bullock, B. and Li, B. L. and Gumpertz, M.}, year={2010}, pages={233–241} }
 @article{zhang_du_xu_zhang_li_2010, title={The actin multigene family in Populus: organization, expression and phylogenetic analysis}, volume={284}, ISSN={1617-4615 1617-4623}, url={http://dx.doi.org/10.1007/S00438-010-0552-5}, DOI={10.1007/S00438-010-0552-5}, abstractNote={Despite the significance of actin in plant growth and development, little is known of the structure, expression and evolution of the actin gene family in woody plants. In this study, we systematically examined the diversification of the actin gene family in Populus by integrating genomic organization, expression, and phylogeny data. Genome-wide analysis of the Populus genome indicated that actin is a multigene family consisting of eight members, all predicted to encode 377-amino acid polypeptides that share high sequence homology ranging from 94.2 to 100% identity. Microarray and real-time PCR expression analysis showed that the PtrACT family members are differentially expressed in different tissues, exhibiting overlapping and unique expression patterns. Of particular interest, all PtrACT genes have been found to be preferentially expressed in the stem phloem and xylem, suggesting that poplar PtrACTs are involved in the wood formation. Gene structural and phylogenetic analyses revealed that the PtrACT family is composed of two main subgroups that share an ancient common ancestor. Extremely high intraspecies synonymous nucleotide diversity of pi(syn) = 0.01205 was detected, and the pi(non-syn)/pi(syn) ratio was significantly less than 1; therefore, the PtACT1 appears to be evolving in Populus, primarily under purifying selection. We demonstrated that the actin gene family in Populus is divided into two distinct subgroups, suggesting functional divergence. The results reported here will be useful in conducting future functional genomics studies to understand the detailed function of actin genes in tree growth and development.}, number={2}, journal={Molecular Genetics and Genomics}, publisher={Springer Science and Business Media LLC}, author={Zhang, Deqiang and Du, Qingzhang and Xu, Baohua and Zhang, Zhiyi and Li, Bailian}, year={2010}, month={Jun}, pages={105–119} }
 @article{zhang_xu_yang_zhang_li_2011, title={The sucrose synthase gene family in Populus: structure, expression, and evolution}, volume={7}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-010-0346-2}, DOI={10.1007/S11295-010-0346-2}, number={3}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Zhang, Deqiang and Xu, Baohua and Yang, Xiaohui and Zhang, Zhiyi and Li, Bailian}, year={2011}, pages={443–456} }
 @article{zhang_yang_zhang_li_2010, title={Expression and nucleotide diversity of the poplar COBL gene}, volume={6}, ISSN={["1614-2942"]}, DOI={10.1007/s11295-009-0252-7}, number={2}, journal={TREE GENETICS & GENOMES}, author={Zhang, Deqiang and Yang, Xiaohui and Zhang, Zhiyi and Li, Bailian}, year={2010}, month={Feb}, pages={331–344} }
 @article{zhang_wei_li_li_2009, title={Using SSR markers to study the mechanism of 2n pollen formation in Populus x euramericana (Dode) Guinier and P. x popularis}, volume={66}, ISSN={["1297-966X"]}, DOI={10.1051/forest/2009032}, abstractNote={Abstract• Using cytological methods and SSR DNA marker analysis, this study revealed the formation mechanisms and the genetic constitutions of the 2n pollen in Populus × euramericana (Dode) Guinier and P. × popularis.• In P. × euramericana (Dode) Guinier, four abnormalities in microsporogenesis were observed: parallel spindle, fused spindle, tripolar spindle and premature cytokinesis. The first three can lead to first-division restitution (FDR) 2n pollen formation and the last one can form second-division restitution (SDR) 2n pollen. The SSR marker analysis results of parents and their tetraploidy filial generation confirmed that the genetic constitution of 2n pollen produced by P. × euramericana (Dode) Guinier was FDR.• In P. × popularis, three of these abnormalities were observed: parallel spindle, fused spindle and premature cytokinesis. The SSR marker analysis results showed the genetic constitution of 2n pollen produced by P. × popularis was SDR. Natural 2n female gametes in P. × euramericana (Dode) Guinier are reported for the first time. SSR analysis indicated that natural 2n female gametes of P. × euramericana (Dode) Guinier did exist and were fertile, which could be FDR genetic constitution.• The results from this study showed a great potential for using 2n gametes to produce polyploid poplar clones, which can be used effectively for polyploid breeding for poplar species in the section Aigeiros.Résumé• En utilisant des méthodes cytologiques et des analyses avec des marqueurs SSR, cette étude a révélé les mécanismes de formation et la constitution génétique du pollen 2n chez Populus × euramericana (Dode) Guinier et P. × popularis.• Chez P. × euramericana (Dode) Guinier, quatre anomalies dans la microsporogénèse ont été observées : en parallèle broche, broche fusion,tripolaire broche et une cytokinèse prématurée. Les trois premiers peuvent entraîner une première division restitution (FDR) de formation du pollen 2n et le dernier peut former une deuxième division de restitution (SDR) du pollen 2n. Les résultats de l’analyse des marqueurs SSR des parents et de leur descendanta tetraploides ont confirmé que la constitution génétique du pollen 2n produit par P. × euramericana (Dode) Guinier a été FDR.• Dans P. × popularis, trois de ces anomalies ont été observées : en parallèle broche, broche fusion et cytokinèse prématurée. Les résultats de l’analyse de marqueurs SSR ont montré que la constitution génétique du pollen 2n produit par P. × popularis a été SDR. Les gamètes naturelles femelles 2n chez P. × euramericana (Dode) Guinier ont été signalés pour la première fois. Les analyses SSR ont montré que les gamètes naturels femelles 2n de P. × euramericana (Dode) Guinier existaient et étaient fertiles, cela pourrait être la constitution génétique FDR.• Les résultats de cette étude ont montré le grand potentiel de l’utilisation des gamètes 2n pour produire des clones de peuplier polyploïdes, cela peut être utilisé efficacement pour la sélection de polyploïdes pour des espèces de peuplier de la section Aigeiros.}, number={5}, journal={ANNALS OF FOREST SCIENCE}, author={Zhang, Jin-Feng and Wei, Zun-Zheng and Li, Dan and Li, Bailian}, year={2009} }
 @article{isik_gumpertz_li_goldfarb_sun_2008, title={Analysis of cellulose microfibril angle using a linear mixed model in Pinus taeda clones}, volume={38}, ISSN={["1208-6037"]}, DOI={10.1139/X08-010}, abstractNote={ Variation in microfibril angle (MFA) (degrees) among loblolly pine ( Pinus taeda L.) full-sib families and clones was investigated using 43 clones from nine full-sib crosses tested at two locations. When the experiments were 12 years old, a total of 316 trees were drilled and 12 mm thick wood increment cores were collected. MFA for each growth ring in the wood core was measured using the SilviScan-2 tool. A quadratic mixed model was fitted to evaluate the MFA variation over different rings. Among the error covariance structures tested in the model, autoregressive order 1 was the best model for producing MFA estimates with the smallest errors. Estimated MFA was about 33° in the pith (ring 1) of the trees and decreased to 18° in the outer wood (ring 11). Full-sib crosses and clones within crosses explained about 12.5% of the total phenotypic variation. Repeatability of full-sib family means (H2f = 0.46) was moderate but repeatability of clone means was high (H2c = 0.79). Although it is possible to improve (decrease) MFA with recurrent selection in tree improvement programs to improve lumber quality, cost efficient and rapid methods for measuring MFA are needed. }, number={6}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, publisher={Canadian Science Publishing}, author={Isik, Fikret and Gumpertz, Marcia and Li, Bailian and Goldfarb, Barry and Sun, Xuan}, year={2008}, month={Jun}, pages={1676–1689} }
 @article{mckeand_li_grissom_isik_jayawickrama_2008, title={Genetic parameter estimates for growth traits from diallel tests of loblolly pine throughout the southeastern United States}, volume={57}, ISSN={["2509-8934"]}, DOI={10.1515/sg-2008-0016}, abstractNote={Abstract
                Variation in heritability and in genetic correlation estimates were evaluated for juvenile tree height and volume for six testing areas of loblolly pine (Pinus taeda L.) in the southeastern United States. Variance components and their functions (heritability and type B genetic correlations) were estimated from 265 six-parent disconnected diallel series, tested in almost 1000 trials (4 tests per diallel series). Original data were collected at age 6 years from about one million trees (265 diallel series x 30 crosses x 36 trees per cross/site x 4 sites) planted in field tests. Genetic tests were from the second cycle of breeding in the North Carolina State University - Industry Cooperative Tree Improvement Program. The overall unbiased individual-tree narrow-sense heritability for height was 0.19 and for volume was 0.16. The broad-sense heritabilities for height (0.24) and for volume (0.22) were higher than narrow-sense heritabilities due to the presence of non-additive genetic variance. There were moderate regional differences in these estimates, with tests in the Lower Gulf Coastal Plain tending to have the highest heritabilities for growth traits. There was very little association between site index and heritability, but heritabilities were higher on sites with the highest survival and highest test precision. Genotype x environment interactions were generally low both for half-sib and full-sib families, indicating that families can be operationally deployed to different sites with little concern about unpredictable performance.}, number={3}, journal={SILVAE GENETICA}, author={McKeand, S. E. and Li, B. and Grissom, J. E. and Isik, F. and Jayawickrama, K. J. S.}, year={2008}, pages={101–110} }
 @article{isik_li_goldfarb_mckeand_2008, title={Prediction of wood density breeding values of Pinus taeda elite parents from unbalanced data: A method for adjustment of site and age effects using common checklots}, volume={65}, ISSN={["1286-4560"]}, DOI={10.1051/forest:2008018}, abstractNote={Abstract• Wood density of elite parents of loblolly pine (Pinus taeda L.) was investigated in 6 to 18 year-old progeny trials. The sampling was carried out separately in seven testing regions in the southeastern US. A checklot was the only connection between elite parents planted at different trials in a testing region.• We used a data normalization method suggested for unbalanced designs in cDNA microarray experiments to remove confounding site and age effects using the checklot as a reference sample. Wood density breeding values of parents were predicted by fitting a linear mixed model to the normalized data.• Using the reference samples to remove site and age effects appears to be an effective method for analysis of unbalanced progeny tests data. In general, wood density (kg/m3) decreased from coastal to inland plantings and from the southern to the northern planting. Considerable genetic variation for wood density was detected among these fast-growing elite parents in six of seven testing regions, with half-sib family mean heritabilities ranging from 0.71 to 0.97 within a testing region. With the exception of two regions, checklots were stable across trials in a region, based on regressing the checklot means on trial means.Résumé• La densité du bois de parents d’élite de Pinus taeda L. a été étudiée dans des essais de descendance âgés de 6 à 18 ans. L’échantillonnage a été mené à bonne fin séparément dans sept régions tests du Sud des États-Unis. Le lot a été le seul lien entre parents d’élite plantés dans différents essais dans la région de test.• Nous avons utilisé une méthode de normalisation des données proposée pour des effectifs non équilibrés de puces à CDNA pour éliminer les effets confondus du site et de l’âge, en utilisant le lot comme échantillon de référence. Les valeurs de la densité du bois des parents ont été prédites par ajustement d’un modèle linéaire mixte aux données normalisées.• Utiliser les échantillons références pour enlever les effets de site et de l’âge apparaît être une méthode efficace pour analyser les données non équilibrées d’un test de descendances. En général, la densité du bois (kg/m3) décroît depuis les plantations côtières jusqu’aux plantations des régions intérieures et depuis les plantations du sud jusqu’aux plantations plus au nord. Une variabilité génétique considérable de la densité du bois a été détectée entre ces parents à croissance rapide dans six des sept régions de test, avec des héritabilités moyennes variant de 0,71 à 0,97 dans une région de test. Sur la base d’une régression entre moyennes des lots de référence et moyennes des essais, il a été déterminé qu’à l’exception de deux régions, les lots ont été stables à travers les essais dans une région déterminée.}, number={4}, journal={ANNALS OF FOREST SCIENCE}, publisher={Springer Nature}, author={Isik, Fikret and Li, Bailian and Goldfarb, Barry and McKeand, Steve}, year={2008}, month={Jun} }
 @article{isik_amerson_whetten_garcia_li_mckeand_2008, title={Resistance of <i>Pinus taeda</i> families under artificial inoculations with diverse fusiform rust pathogen populations and comparison with field trials}, volume={38}, ISSN={0045-5067 1208-6037}, url={http://dx.doi.org/10.1139/x08-111}, DOI={10.1139/X08-111}, abstractNote={ Controlled inoculations with 10 bulk inocula of Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme were carried out on open-pollinated progeny of 25 fast-growing Pinus taeda L. parents. The parents had a range of breeding values for resistance to fusiform rust in progeny field trials. There were highly significant differences among the half-sib families in response to inoculations, and these differences were very reproducible; the half-sib family-mean heritability of resistance to controlled inoculation was 0.97. All of the families that were susceptible in the field were susceptible in controlled inoculations, and most (12 of 17) of the field-resistant families were resistant in response to controlled inoculations. Significant pathogenic variability was observed among the different bulk inocula, although this accounted for only 1.9% of the total variation. Genetic differences among families within field-resistant or field-susceptible groups accounted for 13.7% of the total variation. The family by inocula interaction was highly significant, but a single field-resistant family contributed 44% of the total family by inocula interaction variance, and two other field-resistant families also showed significant interactions. }, number={10}, journal={Canadian Journal of Forest Research}, publisher={Canadian Science Publishing}, author={Isik, Fikret and Amerson, Henry V. and Whetten, Ross W. and Garcia, Saul A. and Li, Bailian and McKeand, Steven E.}, year={2008}, month={Oct}, pages={2687–2696} }
 @article{isik_amerson_whetten_garcia_li_mckeand_2008, title={Resistance of Pinus taeda families under artificial inoculations with diverse fusiform rust pathogen populations and comparison with field trials (vol 38, pg 2687, 2008)}, volume={38}, ISSN={["0045-5067"]}, DOI={10.1139/x08-910}, number={12}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={Isik, Fikret and Amerson, Henry V. and Whetten, Ross W. and Garcia, Saul A. and Li, Bailian and McKeand, Steven E.}, year={2008}, month={Dec}, pages={3151–3151} }
 @article{chen_hu_chang_li_2007, title={Micro analytical methods for determination of compression wood content in loblolly pine}, volume={27}, ISSN={["1532-2319"]}, DOI={10.1080/02773810701700810}, abstractNote={Abstract All loblolly pine trees, especially the juvenile portion, contain various amounts of compression wood. The morphological, chemical, and papermaking properties of compression wood are distinctively different from those of normal juvenile wood and mature wood. Compression wood has higher lignin and galactan, but lower cellulose and mannan content, shorter average fiber length, lower fiber width but thicker cell wall, higher fiber coarseness and higher microfibril angles as compared with the corresponding normal wood. Micro analytical methods have been developed to quantitatively determine the percentage of compression wood in an incremental core so as to eliminate the effects of compression wood on the aforementioned properties. This enables accurate quantitative genetic analyses of these properties for tree breeding programs.}, number={3-4}, journal={JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY}, author={Chen, Qing-min and Hu, Zhoujian and Chang, Hou-min and Li, Bailian}, year={2007}, pages={169–178} }
 @article{hu_li_2006, title={Additive genetic variation and the distribution of QTN effects among sites}, volume={243}, ISSN={["0022-5193"]}, DOI={10.1016/j.jtbi.2006.06.009}, abstractNote={Early quantitative genetic theories emphasize the distribution of gene effects at individual loci or the distribution of mutant effects in maintaining quantitative genetic variation, but infrequently stress the distribution of gene effects among loci. In this study, we analyse the effects of the distribution of quantitative trait nucleotides (QTN) effects among sites under artificial and stabilizing selection. Wright's formula is applied to describing the density distribution of allele frequencies of multiple diallelic QTN at the equilibrium of mutation-drift-selection. Our results demonstrate that the distribution of QTN effects among sites can affect additive genetic variation in terms of total additive variance, average gene diversity, per-class contribution of QTN effects and per-QTN contribution. When the distribution of QTN effects among sites is changed from L-shaped to bell-shaped or to be a flatter, both the total additive variance and the average gene diversity are changed. Per-class and per-QTN contributions exhibit different distribution patterns. The L-shaped distribution indicates the predominant role of the aggregative effects from the QTN of small finite effects. The bell-shaped or flatter distributions indicate the predominance of the QTN of intermediate and large effects. These predictions highlight the significance of the distribution of QTN effects among sites in interpreting the maintenance of quantitative genetic variation at the fine genome scale.}, number={1}, journal={JOURNAL OF THEORETICAL BIOLOGY}, author={Hu, Xin-Sheng and Li, Bailian}, year={2006}, month={Nov}, pages={76–85} }
 @article{yu_li_nelson_mckeand_batista_mullin_2006, title={Association of the cad-n1 allele with increased stem growth and wood density in full-sib families of loblolly pine}, volume={2}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-005-0032-y}, number={2}, journal={TREE GENETICS & GENOMES}, author={Yu, Q. and Li, B. and Nelson, C. D. and McKeand, S. E. and Batista, V. B. and Mullin, T. J.}, year={2006}, month={Apr}, pages={98–108} }
 @article{alizoti_li_mckeand_2006, title={Early evaluation of intra- and inter-provenance hybrids of loblolly pine for planting in piedmont regions of the southern United States}, volume={52}, number={5}, journal={Forest Science}, author={Alizoti, P. G. and Li, B. L. and McKeand, S. E.}, year={2006}, pages={557–567} }
 @article{li_amerson_li_2006, title={Genetic models of host-pathogen gene interaction based on inoculation of loblolly pine seedlings with the fusiform rust fungus}, volume={31}, ISSN={["1573-5095"]}, DOI={10.1007/s11056-005-6576-8}, number={2}, journal={NEW FORESTS}, author={Li, H and Amerson, H and Li, BL}, year={2006}, month={Mar}, pages={245–252} }
 @article{sykes_li_isik_kadla_chang_2006, title={Genetic variation and genotype by environment interactions of juvenile wood chemical properties in Pinus taeda L.}, volume={63}, ISSN={["1286-4560"]}, DOI={10.1051/forest:2006073}, abstractNote={Genetic variation and genotype by environment interaction (G×E) were studied in several juvenile wood traits of 11 year-old loblolly pine trees (Pinus taeda L.). Wafer thin (200 µm) samples from juvenile (ring 3) and transition (ring 8) wood of 12 mm increment cores were analyzed. Transition wood had higher α-cellulose content (46.1%), longer fiber (1.98 mm), and higher coarseness (0.34), but lower lignin (29.7%) than juvenile wood (cellulose 40.9%, fiber length 1.4 mm, coarseness 0.28 and lignin 30.3%). General combining ability variance for the traits explained 2% to 10% of the total variance, whereas the specific combining ability variance was negligible, except for α-cellulose content in transition wood (2%). Specific combining ability by site interaction variance explained from 5% (fiber length) to 37% (lignin) of the total variance. Weak individual-tree heritabilities were found for all the traits, except coarseness, which was moderately high in both juvenile (0.39) and transition wood (0.30). Full-sib and half-sib family heritabilities of traits ranged 0.29 to 0.72. Genetic correlations of wood quality traits with volume and stem straightness were weak, while favorable genetic correlations of lignin with cellulose, coarseness and fiber length were observed. Implications on forest tree improvement programs were discussed. heritability / genetic correlation / α-cellulose / coarseness / lignin}, number={8}, journal={ANNALS OF FOREST SCIENCE}, publisher={EDP Sciences}, author={Sykes, Robert and Li, Bailian and Isik, Fikret and Kadla, John and Chang, H. -M.}, year={2006}, month={Dec}, pages={897–904} }
 @article{li_ghosh_amerson_li_2006, title={Major gene detection for fusiform rust resistance using Bayesian complex segregation analysis in loblolly pine}, volume={113}, ISSN={["0040-5752"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33747640613&partnerID=MN8TOARS}, DOI={10.1007/s00122-006-0351-x}, abstractNote={The presence of major genes affecting rust resistance of loblolly pine was investigated in a progeny population that was generated with a half-diallel mating of six parents. A Bayesian complex segregation analysis was used to make inference about a mixed inheritance model (MIM) that included polygenic effects and a single major gene effect. Marginalizations were achieved by using Gibbs sampler. A parent block sampling by which genotypes of a parent and its offspring were sampled jointly was implemented to improve mixing. The MIM was compared with a pure polygenic model (PM) using Bayes factor. Results showed that the MIM was a better model to explain the inheritance of rust resistance than the pure PM in the diallel population. A large major gene variance component estimate (> 50% of total variance), indicated the existence of major genes for rust resistance in the studied loblolly pine population. Based on estimations of parental genotypes, it appears that there may be two or more major genes affecting disease phenotypes in this diallel population.}, number={5}, journal={THEORETICAL AND APPLIED GENETICS}, author={Li, Hua and Ghosh, Sujit and Amerson, Henry and Li, Bailian}, year={2006}, month={Sep}, pages={921–929} }
 @inproceedings{isik_mckeand_li_amerson_2006, title={Marker aided selection of loblolly pine clones}, booktitle={Consortium for Plant Biotechnology Symposium}, author={Isik, F. and McKeand, S. and Li, B. and Amerson, H.}, year={2006} }
 @article{mckeand_jokela_huber_byram_allen_li_mullin_2006, title={Performance of improved genotypes of loblolly pine across different soils, climates, and silvicultural inputs}, volume={227}, ISSN={["1872-7042"]}, DOI={10.1016/j.foreco.2006.02.016}, abstractNote={Deployment of improved loblolly pine (Pinus taeda L.) genotypes across the southern United States is a standard silvicultural practice. Most planting is conducted using open-pollinated (OP) families from first- or second-generation seed orchards, and these OP families typically display remarkable rank stability for productivity and quality traits across a range of site characteristics, climates, and silvicultural systems. With only a few exceptions, families are generally stable in performance across all sites within a climatic zone. As tree improvement and nursery programs progress towards deployment of more intensively selected genotypes and less genetically diverse full-sib families or clones, there may be a greater likelihood that genotype by environment (G × E) interactions will become important, particularly as the level of silvicultural treatment intensity increases. We present evidence from numerous trials with full-sib families and clones demonstrating that G × E for growth and other traits is no more significant than for OP families. At present and for the foreseeable future, G × E does not appear to be a major concern for the majority of deployed genetic sources under most silvicultural systems.}, number={1-2}, journal={FOREST ECOLOGY AND MANAGEMENT}, author={McKeand, Steven E. and Jokela, Eric J. and Huber, Dudley A. and Byram, Thomas D. and Allen, H. Lee and Li, Bailian and Mullin, Timothy J.}, year={2006}, month={May}, pages={178–184} }
 @inproceedings{aspinwall_li_mckeand_isik_gumpertz_2006, title={Predicting whole-stem wood properties in loblolly pine}, volume={40}, booktitle={Information Exchange Group 40 Conference, Incorporating Genetic Advances into Forest Productivity Systems: Value for All Landowners.
Exchange Group 40 Conference, Incorporating Genetic Advances into Forest
Productivity Systems: Value for All Landowners.}, author={Aspinwall, M. and Li, B. and McKeand, S. and Isik, F. and Gumpertz, M.}, year={2006} }
 @article{mckeand_abt_allen_li_catts_2006, title={What are the best loblolly pine genotypes worth to landowners?}, volume={104}, number={7}, journal={Journal of Forestry}, author={McKeand, S. E. and Abt, R. C. and Allen, H. L. and Li, B. L. and Catts, G. P.}, year={2006}, pages={352–358} }
 @article{li_mckeand_2005, title={Forest genetics and tree breeding in the age of genomics--IUFRO Conference}, volume={12}, number={2}, journal={Forest Genetics}, author={Li, B. and McKeand, S. E.}, year={2005}, pages={141–143} }
 @inproceedings{isik_li_goldfarb_2005, title={Genetic variation in MFA, MOE and wood density among clones of Pinus taeda L.}, volume={28}, booktitle={28th Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B. and Goldfarb, B.}, year={2005} }
 @article{lstiburek_mullin_mackay_huber_li_2005, title={Positive assortative mating with family size as a function of predicted parental breeding values}, volume={171}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.105.041723}, abstractNote={Abstract
               While other investigations have described benefits of positive assortative mating (PAM) for forest tree breeding, the allocation of resources among mates in these studies was either equal or varied, using schemes corresponding only to parental rank (i.e., more resources invested in higher-ranking parents). In this simulation study, family sizes were proportional to predicted midparent BLUP values. The distribution of midparent BLUP values was standardized by a constant, which was varied to study the range of distributions of family size. Redistributing progenies from lower- to higher-ranking families to a point where an equal number of progenies were still selected out of each family to the next generation caused minimal change in group coancestry and inbreeding in the breeding population (BP), while the additive genetic response and variance in the BP were both greatly enhanced. This generated additional genetic gains for forest plantations by selecting more superior genotypes from the BP (compared to PAM with equal family sizes) for production of improved regeneration materials. These conclusions were verified for a range of heritability under a polygenic model and under a mixed-inheritance model with a QTL contributing to the trait variation.}, number={3}, journal={GENETICS}, author={Lstiburek, M and Mullin, TJ and Mackay, TFC and Huber, D and Li, B}, year={2005}, month={Nov}, pages={1311–1320} }
 @article{isik_goldfarb_lebude_li_mckeand_2005, title={Predicted genetic gains and testing efficiency from two loblolly pine clonal trials}, volume={35}, ISSN={["1208-6037"]}, DOI={10.1139/X05-064}, abstractNote={Clonal field trials were established at two sites using rooted cuttings from 450 clones of eight full-sib families of loblolly pine (Pinus taeda L.). Height, survival, fusiform rust infection (caused by Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme), bole straightness, and diameter were measured after four growing seasons. There were significant differences among full-sib families and among clones within families for all traits studied. Moderately high within-family repeatabilities of clone means (0.50 to 0.75) for growth traits and a very high within-family repeatability of clone means (0.94) for fusiform rust infection were estimated. When the best eight clones were selected regardless of family structure, the volume yield was 52% greater than that of the unimproved seedlings at two sites. Selection of the best two clones from each of four families produced only slightly lower estimated genetic gains than the above scenario. The probability of fusiform rust infection ranged from 0.08 to 0.93 among clones at the South Carolina site. Predicted genetic gain for rust resistance was relatively insensitive to selection intensity, as there were numerous clones with high apparent resistance. The number of ramets per clone necessary to reliably characterize performance on one site was estimated to be between four and six. These results contribute to estimates of the gains available from clonal forestry and will help guide clonal testing and selection programs. Implementation of clonal forestry and cost issues are discussed.}, number={7}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Isik, F and Goldfarb, B and LeBude, A and Li, BL and McKeand, S}, year={2005}, month={Jul}, pages={1754–1766} }
 @article{sykes_li_hodge_goldfarb_kadla_chang_2005, title={Prediction of loblolly pine wood properties using transmittance near-infrared spectroscopy}, volume={35}, ISSN={["1208-6037"]}, DOI={10.1139/X05-161}, abstractNote={ Near-infrared (NIR) spectroscopy is a rapid nondestructive technique that has been used to characterize chemical and physical properties of a wide range of materials. In this study, transmittance NIR spectra from thin wood wafers cut from increment cores were used to develop calibration models for the estimation of α-cellulose content, average fiber length, fiber coarseness, and lignin content in the laboratory. Eleven-year-old trees from two sites were sampled using 12-mm increment cores. Earlywood and latewood of ring 3 and ring 8 from these samples were analyzed in the laboratory using microanalytical methods for α-cellulose content, average fiber length, fiber coarseness, and lignin content. NIR calibrations and laboratory measurements based on one site were generally reliable, with coefficients of determination (R2) ranging from 0.54 to 0.88 for average fiber length and α-cellulose content, respectively. Predicting ring 8 properties using ring 3 calibration equations showed potential for predicting α-cellulose content and fiber coarseness, with R2 values of approximately 0.60, indicating the potential for early selection. Predicting the wood properties using the calibration equations from one site to predict another showed moderate success for α-cellulose content (R2 = 0.64) and fiber coarseness (R2 = 0.63), but predictions for fiber length were relatively poor (R2 = 0.43). Prediction of lignin content using transmittance NIR spectroscopy was not as reliable in this study, partially because of low variation in lignin content in these wood samples and large errors in measuring lignin content in the laboratory. }, number={10}, journal={CANADIAN JOURNAL OF FOREST RESEARCH}, author={Sykes, R and Li, BL and Hodge, G and Goldfarb, B and Kadla, J and Chang, HM}, year={2005}, month={Oct}, pages={2423–2431} }
 @article{isik_boos_li_2005, title={The distribution of genetic parameter estimates and confidence intervals from small disconnected diallels}, volume={110}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-005-1957-0}, abstractNote={The distributions of genetic variance components and their ratios (heritability and type-B genetic correlation) from 105 pairs of six-parent disconnected half-diallels of a breeding population of loblolly pine (Pinus taeda L.) were examined. A series of simulations based on these estimates were carried out to study the coverage accuracy of confidence intervals based on the usual t-method and several other alternative methods. Genetic variance estimates fluctuated greatly from one experiment to another. Both general combining ability variance (sigma(2) (g)) and specific combining ability variance (sigma(2) (s)) had a large positive skewness. For sigma(2) (g) and sigma(2) (s), a skewness-adjusted t-method proposed by Boos and Hughes-Oliver (Am Stat 54:121-128, 2000) provided better upper endpoint confidence intervals than t-intervals, whereas they were similar for the lower endpoint. Bootstrap BCa-intervals (Efron and Tibshirani, An introduction to the bootstrap. Chapman & Hall, London 436 p, 1993) and Hall's transformation methods (Zhou and Gao, Am Stat 54:100-104, 2000) had poor coverages. Coverage accuracy of Fieller's interval endpoint(J R Stat Soc Ser B 16:175-185, 1954) and t-interval endpoint were similar for both h(2) and r(B) for sample sizes n</=10, but for n=30 the Fieller's method is much better.}, number={7}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Nature}, author={Isik, F and Boos, DD and Li, BL}, year={2005}, month={May}, pages={1236–1243} }
 @article{li_boyter_2005, title={Washfastness improvement for heavy shade microdenier nylon 6,6 fabric}, volume={5}, number={8}, journal={AATCC Review}, author={Li, S. Q. and Boyter, H.}, year={2005}, pages={36–40} }
 @article{zeng_ghosh_li_2004, title={A blocking Gibbs sampling method to detect major genes with phenotypic data from a diallel mating}, volume={83}, ISSN={["1469-5073"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-2942661466&partnerID=MN8TOARS}, DOI={10.1017/S0016672304006718}, abstractNote={Diallel mating is a frequently used design for estimating the additive and dominance genetic (polygenic) effects involved in quantitative traits observed in the half- and full-sib progenies generated in plant breeding programmes. Gibbs sampling has been used for making statistical inferences for a mixed-inheritance model (MIM) that includes both major genes and polygenes. However, using this approach it has not been possible to incorporate the genetic properties of major genes with the additive and dominance polygenic effects in a diallel mating population. A parent block Gibbs sampling method was developed in this study to make statistical inferences about the major gene and polygenic effects on quantitative traits for progenies derived from a half-diallel mating design. Using simulated data sets with different major and polygenic effects, the proposed method accurately estimated the major and polygenic effects of quantitative traits, and possible genotypes of parents and progenies. The impact of specifying different prior distributions was examined and was found to have little effect on inference on the posterior distribution. This approach was applied to an experimental data set of Loblolly pine (Pinus taeda L.) derived from a 6-parent half-diallel mating. The result indicated that there might be a recessive major gene affecting height growth in this diallel population.}, number={2}, journal={GENETICS RESEARCH}, author={Zeng, W and Ghosh, S and Li, BL}, year={2004}, month={Apr}, pages={143–154} }
 @article{lee_boerma_villagarcia_zhou_carter_li_gibbs_2004, title={A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars}, volume={109}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-004-1783-9}, abstractNote={Deployment of salt tolerant cultivars is an effective approach to minimize yield loss in a saline soil. In soybean, Glycine max (L.) Merr., substantial genetic variation exists for salt response. However, breeding for salt tolerance is hampered because no economically viable screening method has been developed for practical breeding. To facilitate the development of an effective screening method for salt tolerance in soybean, the present study was conducted to determine the heritability of salt tolerance and to identify associated quantitative trait loci (QTL). F2:5 lines from the cross of 'S-100' (salt tolerant) x 'Tokyo' (salt sensitive) were evaluated in a saline field in Hyde County, N.C., USA, in 1999 and in a greenhouse located in Raleigh, N.C., USA, in 2001. S-100 and Tokyo are ancestors of popular soybean cultivars released for the southern USA. The visual salt tolerance ratings of the F2:5 lines ranged from 0 (complete death) to 5 (normal healthy appearance). The entry-mean heritability for salt tolerance was 0.85, 0.48, and 0.57 in the field (four replications), greenhouse (two replications), and combined environments, respectively. The genotypic correlation between field and greenhouse ratings was 0.55, indicating reasonably good agreement between the two screening environments. To identify QTL associated with salt tolerance, each line was characterized with RFLP markers and an initial QTL single-factor analysis was completed. These results were used to identify genomic regions associated with the trait and to saturate the selected genomic regions with SSR markers to improve mapping precision. Subsequently, a major QTL for salt tolerance was discovered near the Sat_091 SSR marker on linkage group (LG) N, accounting for 41, 60, and 79% of the total genetic variation for salt tolerance in the field, greenhouse, and combined environments, respectively. The QTL allele associated with tolerance was derived from S-100. Pedigree tracking was used to examine the association between the salt tolerance QTL and flanking SSR marker alleles in U.S. cultivars descended from S-100 or Tokyo through 60 years of breeding. The presence of alleles from S-100 at the Sat_091 and Satt237 marker loci was always associated with salt tolerance in descendants. Alleles from Tokyo for these same markers were generally associated with salt sensitivity in descendent cultivars. The strong relationship between the SSR marker alleles and salt tolerance suggests that these markers could be used for marker-assisted selection in commercial breeding.}, number={8}, journal={THEORETICAL AND APPLIED GENETICS}, author={Lee, GJ and Boerma, HR and Villagarcia, MR and Zhou, X and Carter, TE and Li, Z and Gibbs, MO}, year={2004}, month={Nov}, pages={1610–1619} }
 @inproceedings{goldfarb_lebude_isik_mckeand_li_2004, title={Advance and Challenges in Clonal Forestry with Rooted Cuttings of Loblolly Pine}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Goldfarb, B. and LeBude, A. and Isik, F. and McKeand, S. and Li, B.}, editor={Li, B. and McKeand, S.Editors}, year={2004}, pages={41} }
 @inproceedings{li_jansson_isik_godlfarb_2004, title={Breeding and selection strategies for full-sib families and clones in Loblolly pine}, booktitle={IEG-40 Meeting}, author={Li, B. and Jansson, G. and Isik, F. and Godlfarb, B.}, year={2004} }
 @inproceedings{isik_li_goldfarb_frampton_mckeand_2004, title={Cloned genotypes are more efficient than seedlings for indirect selection}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Isik, F. and Li, B. and Goldfarb, B. and Frampton, J. and McKeand, S.}, editor={Li, B. and McKeand, S.Editors}, year={2004}, pages={465} }
 @article{isik_li_goldfarb_2004, title={Cloned progeny testing for within-family selection in forest tree improvement programs}, volume={2}, journal={IUFRO Joint Conference of Division 2: Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future}, author={Isik, F. and Li, B. and Goldfarb, B.}, year={2004} }
 @inproceedings{mullin_li_mckeand_2004, title={Delivering on the promise of tree improvement in the southeastern United States}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Mullin, T. and Li, B. and McKeand, S.}, editor={Li, B. and McKeand, S.Editors}, year={2004} }
 @inproceedings{goldfarb_mckeand_lebude_cumbie_isik_li_2004, title={Deployment issues: what kinds of research, development
and demonstration activities are needed to address critical topics, such as public concerns, performance monitoring, and technologies for merchandising harvested clones?}, booktitle={Conference Proceedings}, author={Goldfarb, B. and McKeand, S. E. and LeBude, A. V. and Cumbie, W. P. and Isik, F. and Li, B.}, year={2004} }
 @article{goldfarb_mckeand_lebude_cumbie_isik_li_2004, title={Deployment issues: what kinds of research, development and demonstration activities are needed to address critical topics, such as public concerns, performance monitoring, and technologies for merchandising harvested clones?}, journal={Agenda 2020 Technology Summit II: Meeting the Challenge of Deployment}, author={Goldfarb, B. and McKeand, S. E. and LeBude, A. V. and Cumbie, W. P. and Isik, F. and Li, B.}, year={2004} }
 @article{isik_li_goldfarb_frampton_mckeand_2004, title={Efficiency of clones versus seedlings for correlated response of wood density}, journal={IEG-40 Meeting}, author={Isik, F. and Li, B. and Goldfarb, B. and Frampton, J. and McKeand, S.}, year={2004} }
 @article{isik_li_frampton_goldfarb_2004, title={Efficiency of seedlings and rooted cuttings for testing and selection in Pinus taeda}, volume={50}, number={1}, journal={Forest Science}, author={Isik, F. and Li, B. L. and Frampton, J. and Goldfarb, B.}, year={2004}, pages={44–53} }
 @article{jansson_li_2004, title={Genetic gains of full-sib families from disconnected diallels in loblolly pine}, volume={53}, ISSN={["2509-8934"]}, DOI={10.1515/sg-2004-0011}, abstractNote={Abstract
                Breeding values for the 2nd-cycle of the loblolly pine (Pinus taeda L.) breeding program were analyzed with the NCSUIndustry Tree Improvement Cooperative database to estimate genetic gains and compare different strategies for full-sib deployment. In the disconnected half-diallel mating design used for loblolly pine, six parents within each diallel were crossed to generate 15 full-sib families for general combining ability (GCA) and specific combining ability (SCA) estimates. Parents among disconnected diallels were never crossed, and the SCA and full-sib family breeding values cannot be estimated directly. Using the GCA and SCA estimates from 60 diallels in the Atlantic Coastal region of loblolly pine, genetic gains were estimated in this study for full-sib families within the disconnected diallels and then compared with the potential gains that would be expected if we select parents for full-sib families based on GCA values for all parents within a geographic region. As the dominance variance was found to be much less than the additive variance, the SCA contribution to the full-sib genetic gain was relatively small. Higher full-sib genetic gains were obtained by crossing the best GCA parents from different diallels within a geographic region than selecting only those within diallels. The difference increased with increasing number of selected full-sibs. Results from different selection scenarios, with various selection intensities and relatedness managements, suggest that selection based on GCA from all parents within a geographic region would result in a higher genetic gain for full-sib families in loblolly pine. The deployment of full-sib families are very important for achieving higher genetic gains in a loblolly pine breeding program. But they were not due to the SCA contribution, but rather due to high GCA of best parents in creating these full-sib crosses. The strategies for family and clonal deployment are very attractive based on the data from this study.}, number={2}, journal={SILVAE GENETICA}, author={Jansson, G and Li, B}, year={2004}, pages={60–64} }
 @article{sykes_isik_li_kadla_chang_2004, title={Genetic variation in physiochemical wood properties in loblolly pine (Pinus taeda L.)}, volume={2}, number={12}, journal={TAPPI Journal}, author={Sykes, R. and Isik, F. and Li, B. and Kadla, J. and Chang, H.-M.}, year={2004}, pages={3–8} }
 @article{li_belonger_isik_2004, title={Hybrid heterosis of Larix decidua and L. leptolepis in US and implications on breeding strategies}, volume={2}, journal={Proceedings of International Symposium Larix}, author={Li, B. and Belonger, P. and Isik, F.}, year={2004} }
 @article{goldfarb_lebude_gocke_li_isik_mckeand_2004, title={Producing rooted cutting reforestation stock of Loblolly pine: progress and challenges}, journal={IEG-40 Meeting}, author={Goldfarb, B. and LeBude, A. and Gocke, M. and Li, B. and Isik, F. and McKeand, S.}, year={2004} }
 @article{kegley_mckeand_li_2004, title={Seedling evaluation of Atlantic coastal and piedmont sources of loblolly pine and their hybrids for height growth}, volume={28}, number={2}, journal={Southern Journal of Applied Forestry}, author={Kegley, A. J. and Mckeand, S. E. and Li, B. L.}, year={2004}, pages={83–90} }
 @article{xiang_li_isik_2004, title={Time trend of genetic parameters in growth traits of Pinus taeda L.}, volume={52}, number={3}, journal={Silvae Genetica}, author={Xiang, B. and Li, B. and Isik, F.}, year={2004}, pages={114–121} }
 @inproceedings{yu_capanema_batista_josserand_johnson_nelson_mckeand_mackay_kadla_li_et al._2004, title={Tracking down the effects of a rare mutant gene in loblolly pine: a first report}, booktitle={2004 Paper Summit, Spring Technical and International Environmental Conference}, publisher={CD-ROM published by TAPPI,  Norcross, GA}, author={Yu, Q. and Capanema, E. and Batista, V. B. and Josserand, S. and Johnson, G. and Nelson, C. D. and McKeand, S. E. and MacKay, J. J. and Kadla, J. F. and Li, B. and et al.}, year={2004} }
 @article{xiang_li_2003, title={Best linear unbiased prediction of clonal breeding values and genetic values from full-sib mating designs}, volume={33}, ISSN={["0045-5067"]}, DOI={10.1139/X03-118}, abstractNote={ Full-sib progeny tests with clonal replicates may provide better breeding value estimates and the greatest genetic gain in a tree improvement program. Clonal breeding values (CBV) that combine the family and within-family breeding values due to additive genetic effects can maximize the genetic gain for advanced generation breeding. Clonal genetic values (CGV) that further incorporate full-sib family specific combining ability due to nonadditive genetic effect can maximize gain for a deployment program with clonal propagation techniques. The best linear unbiased prediction (BLUP) is the best statistical method for estimating both CBV and CGV because of its desirable statistical properties compared with the heritability-based gain calculation. A BLUP method for determining both the CBV and CGV for full-sib clonal progeny tests was proposed in this paper. The formulas for CBV and CGV were derived using general BLUP methodology, and formulas were derived for the calculations of their standard errors. An analytical method by using a standard statistical package (SAS PROC MIXED) was presented for CBV and CGV calculations from any full-sib mating designs. }, number={10}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={Xiang, B and Li, BL}, year={2003}, month={Oct}, pages={2036–2043} }
 @article{isik_li_frampton_2003, title={Estimates of additive, dominance and epistatic genetic variances from a clonally replicated test of loblolly pine}, volume={49}, number={1}, journal={Forest Science}, author={Isik, F. and Li, B. L. and Frampton, J.}, year={2003}, pages={77–88} }
 @article{mckeand_amerson_li_mullin_2003, title={Families of loblolly pine that are the most stable for resistance to fusiform rust are the least predictable}, volume={33}, ISSN={["0045-5067"]}, DOI={10.1139/X03-050}, abstractNote={ In an extensive series of trials with open-pollinated families of loblolly pine (Pinus taeda L.), resistance to fusiform rust disease (caused by Cronartium quercuum (Berk.) Miyabe ex Shirai f. sp. fusiforme) at individual test sites was relatively unpredictable for the families deemed most resistant. The most resistant families were also the most stable for performance across test sites, with stability defined as the slope of the regression of family means for rust infection versus site means for rust infection. A family's R-50 value (its predicted rust infection level when the site mean infection is 50%) was correlated to its stability parameter or slope (r = 0.78). On average, any one family's level of infection (% galled) was reasonably predictable for any given infection level at a given site; the average coefficient of determination (r2) was 0.78 for the regression of family means for rust infection versus site means for rust infection. However, the six most stable families for resistance had the lowest r2 values (average r2 = 0.58). We speculated that the lower predictability for the most resistant families was due to interactions of specific resistance genes in these families and corresponding avirulence and (or) virulence levels in the pathogen populations that may differ among sites. Although the predictability of the individual resistant families was relatively low, if these families were bulked into a resistant seed lot, they performed in a more predictable manner with r2 = 0.74 for the regression of the bulk mean versus site means. Bulks of four to six highly resistant families appeared to be a good solution to obtain stable and predictable performance across a range of sites. }, number={7}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={McKeand, SE and Amerson, HV and Li, B and Mullin, TJ}, year={2003}, month={Jul}, pages={1335–1339} }
 @article{goldfarb_isik_lebude_mckeand_li_2003, title={Four-year results from a clonal test of loblolly pine}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Goldfarb, B. and Isik, F. and LeBude, A. and McKeand, S. and Li, B.}, year={2003}, pages={42} }
 @article{xiang_li_mckeand_2003, title={Genetic gain and selection efficiency of loblolly pine in three geographic regions}, volume={49}, number={2}, journal={Forest Science}, author={Xiang, B. and Li, B. L. and McKeand, S.}, year={2003}, pages={196–208} }
 @article{zhang_zhang_yang_li_2004, title={Genetic mapping in (Populus tomentosa x Populus bolleana) and P-tomentosa Carr. using AFLP markers}, volume={108}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-003-1478-7}, abstractNote={The AFLP genetic linkage maps for two poplar cultivars were constructed with the pseudo-test-cross mapping strategy. The hybrids were derived from an interspecific backcross between the female hybrid clone "TB01" (Populus tomentosa x Populus bolleana) and the male clone "LM50" ( P. tomentosa). A total of 782 polymorphic fragments were obtained with a PCR-based strategy using 49 enzyme-nested ( EcoRI/ MseI) primer combinations. Six hundred and thirty two of these fragments segregated in a 1:1 ratio ( P<0.01), indicating that these DNA polymorphisms are heterozygous in one parent and null in the other. The linkage analysis was performed using Mapmaker version 3.0 with LOD 5.0 and a maximum recombination fraction (theta) of 0.3. Map distances were estimated using the Kosambi mapping function. In the framework map for "LM50" (P. tomentosa), 218 markers were aligned in 19 major linkage groups. The linked loci spanned approximately 2,683 cM of the poplar genome, with an average distance of 12.3 cM between adjacent markers. For "TB01" (P. tomentosa x P. bolleana), the analysis revealed 144 loci, which were mapped to 19 major linkage groups and covered about 1,956 cM, with an average distance of 13.6 cM between adjacent markers. These maps covered about 87% and 77% of the estimated genome size of parents "LM50" and "TB01", respectively. The maps developed in this study lay an important foundation for future genomics research in poplar, providing a means for localizing genes controlling economically important traits in P. tomentosa.}, number={4}, journal={THEORETICAL AND APPLIED GENETICS}, author={Zhang, D and Zhang, Z and Yang, K and Li, B}, year={2004}, month={Feb}, pages={657–662} }
 @article{sykes_isik_li_kadla_chang_2003, title={Genetic variation of juvenile wood properties in a loblolly pine progeny test}, volume={2}, number={12}, journal={TAPPI Journal}, author={Sykes, R. and Isik, F. and Li, B. L. and Kadla, J. and Chang, H. M.}, year={2003}, pages={08-} }
 @article{sykes_isik_li_kadla_chang_2003, title={Genetic variation of juvenile wood properties in loblolly pine diallel test}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Sykes, R. and Isik, F. and Li, B. and Kadla, J. and Chang, H-M.}, year={2003}, pages={27} }
 @article{hu_zeng_li_2003, title={Impacts of one-way gene flow on genetic variance components in a natural population}, volume={52}, number={1}, journal={Silvae Genetica}, author={Hu, X. S. and Zeng, W. and Li, B. L.}, year={2003}, pages={18–24} }
 @article{hu_li_2003, title={On migration load of seeds and pollen grains in a local population}, volume={90}, ISSN={["1365-2540"]}, DOI={10.1038/sj.hdy.6800212}, abstractNote={We have extended Wright's model of migration load to hermaphrodite plants showing variation at a single locus with two alleles. The model incorporates independent migration of seeds and pollen grains, the selection at both the haploid gametophyte and the diploid sporophyte stages, and a mixed mating system. The analytical relations between migration load and migration rate of seeds and pollen grains are explicitly formulated. The results show that under certain conditions, seed flow can have a more effect on migration load than pollen flow. Pollen selection at the gametophyte stage cannot substantially affect the migration load at the sporophyte stage. Selection at the diploid sporophyte stage is critical in determining the migration load of pollen grains. The relative migration loads of pollen versus seeds can be approximately estimated in predominantly outcrossing populations by the ratio of pollen flow to twice the seed flow, when the selection coefficient (s(T)) is greater than, or approximately equal to, the migration rate (m).}, number={2}, journal={HEREDITY}, author={Hu, XS and Li, BL}, year={2003}, month={Feb}, pages={162–168} }
 @article{isik_li_2003, title={Rapid assessment of wood density of live trees using the Resistograph for selection in tree improvement programs}, volume={33}, ISSN={["0045-5067"]}, DOI={10.1139/X03-176}, abstractNote={ Wood density is traditionally determined by a volumetric method that is accurate but expensive for large-scale sampling. A new device called the Resistograph was investigated for rapid assessment of relative wood density of live trees in progeny trials. Fourteen full-sib families of loblolly pine (Pinus taeda L.) produced by a six-parent half-diallel mating design were tested at four sites. For each family, wood density was measured with the traditional volumetric method and then compared with the Resistograph readings (amplitude). Amplitude had weak (0.29) to moderate (0.65) phenotypic correlations with wood density on an individual-tree basis over the four sites. The family mean correlation between the two measurements, however, was much stronger (0.92). The additive genetic correlation between the two measures was also high (0.95). Individual-tree breeding values of amplitude yielded more accurate rankings than phenotypic values. The rankings of the parental, general-combining abilities were identical for the two measures. Both wood density and amplitude were under strong genetic control at the family level (full-sib family heritability (h2fs) = 0.95 for wood density and h2fs = 0.85 for amplitude). The efficiency of using the Resistograph as a means of indirect selection for improvement of wood density was 87% at the family level. Results from this study suggest that the Resistograph could be used reliably and efficiently to assess relative wood density of live trees for selection in tree improvement programs. The method is rapid, nondestructive, and much cheaper than the traditional volumetric method. }, number={12}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, publisher={Canadian Science Publishing}, author={Isik, F and Li, BL}, year={2003}, month={Dec}, pages={2426–2435} }
 @article{zeng_li_2003, title={Simple tests for detecting segregation of major genes with phenotypic data from a diallel mating}, volume={49}, number={2}, journal={Forest Science}, author={Zeng, W. and Li, B. L.}, year={2003}, pages={268–278} }
 @article{isik_li_2003, title={Time trend of genetic parameter estimates in growth traits of Pinus Taeda L}, volume={52}, journal={Silvae Genetica}, author={Isik, F. and Li, B.-L.}, year={2003}, pages={114–121} }
 @article{jansson_li_hannrup_2003, title={Time trends in genetic parameters for height and optimal age for parental selection in Scots pine}, volume={49}, number={5}, journal={Forest Science}, author={Jansson, G. and Li, B. L. and Hannrup, B.}, year={2003}, pages={696–705} }
 @article{isik_li_2003, title={Variation in estimation of genetic parameters from small disconnected diallel mating}, volume={27}, journal={Proc. 27th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B.}, year={2003}, pages={20} }
 @article{isik_isik_yildirim_li_2002, title={Annual shoot growth components related to growth of Pinus brutia}, volume={22}, ISSN={["0829-318X"]}, DOI={10.1093/treephys/22.1.51}, abstractNote={Shoot elongation patterns of Pinus brutia Ten. were studied in six natural populations and 10 open-pollinated families within each population. The data were collected from a provenance-progeny trial that was thinned at Ages 13 and 17 years. Annual height increment was partitioned into first flush (spring shoot) and subsequent flushes (summer shoots) and the contribution of each to annual height increment was measured from Ages 7 to 17. Spring shoot elongation patterns were similar in all populations and families for 9 out of 10 years. In contrast, at all ages, populations differed significantly in total summer shoot growth and number of summer flushes. Families within populations differed in number of summer flushes in 7 out of 10 years. Summer shoot growth was the major cause of the differences in annual height growth among the six populations. Significant and high correlations were observed between summer shoot growth at Ages 7 to 12 and height at Age 13. A population from near the middle of the species' altitudinal range had more summer flushes than populations from higher or lower elevations, indicating an opportunistic growth pattern. Compared with mid-elevation populations, low- and high-elevation populations had more conservative growth patterns that depended mainly on growth of spring shoots. We conclude that summer shoot growth can serve as an explanatory variable to predict height growth of populations. Differences in shoot elongation patterns among Pinus brutia populations may be useful for selecting seed sources and for gene conservation programs.}, number={1}, journal={TREE PHYSIOLOGY}, author={Isik, F and Isik, K and Yildirim, T and Li, BL}, year={2002}, month={Jan}, pages={51–58} }
 @article{hu_li_2002, title={Linking evolutionary quantitative genetics to the conservation of genetic resources in natural forest populations}, volume={51}, number={5-6}, journal={Silvae Genetica}, author={Hu, X. S. and Li, B.}, year={2002}, pages={177–183} }
 @article{hu_li_2002, title={Seed and pollen flow and cline discordance among genes with different modes of inheritance}, volume={88}, DOI={10.1038/sj/hdy/6800030}, abstractNote={The relationships between seed and pollen flow and cline discordance/concordance between cytoplasmic and nuclear genes, with the incorporation of the effects of natural selection, are formulated for one locus with two alleles, under assumptions of random mating, no drift and no mutation. Results show that under certain conditions, the relative roles of seed and pollen flow in shaping cline discordance/ concordance are very similar to their roles in influencing population differentiation for selectively neutral markers with different modes of inheritance. Where the disequilibria between cytoplasmic and nuclear genes are of the order similar to selection coefficient, cline discordance/concordance can be predicted from the relative values of the ratio of pollen to seed flow and the ratio of selection coefficients. Where the disequilibria attained by seed and pollen flow are significant, the integrated cytonuclear data are recommended for cline analysis. In both cases, the relative rates of selection coefficients between cytoplasmic and nuclear genes can be roughly estimated according to their characteristic length.}, number={2002 Mar}, journal={Heredity}, author={Hu, X. S. and Li, B.}, year={2002}, pages={212–217} }
 @article{isik_li_frampton_goldfarb_2002, title={Seedling vs clonal testing options for loblolly pine}, journal={Proc. of Silviculture and Genetic Impact on productivity of southern pine forests. IEG-40 Meeting}, author={Isik, F. and Li, B. and Frampton, J. and Goldfarb, G.}, year={2002} }
 @article{isik_li_2002, title={Using Resistograph to estimate genetic parameters from progeny trials and comparison with actual wood density}, volume={17}, journal={Proc. of Rocky Mountain Ecosystems: Diversity, complexity and interactions. Joint Meeting of 17th North American Forest Biology Workshop and Western Forest Genetics Association}, author={Isik, F. and Li, B.}, year={2002}, pages={59} }
 @article{xiang_li_2001, title={A new mixed analytical method for genetic analysis of diallel data}, volume={31}, DOI={10.1139/cjfr-31-12-2252}, abstractNote={Diallel is a popular mating design used for crop and tree breeding programs, but its unique feature of a single observation with two levels of the same main effect, general combining ability (GCA), makes it difficult to analyze with standard statistical programs. A new approach using the SAS PROC MIXED is developed in this study for analyzing genetic data from diallel mating. Dummy variables for GCA effects were first constructed with SAS PROC IML, then PROC MIXED procedure was used to estimate variance components and to obtain BLUE (best linear unbiased estimators) of fixed effects and BLUP (best linear unbiased predictors) of random genetic effects (GCA and specific combining ability (SCA) effects) simultaneously. The new method can also be used for predicting individual breeding values with BLUP methodology, applying SAS IML to the outputs provided by PROC MIXED to calculate breeding value for each individual in the progeny test, adjusted for the fixed effects such as test location. The accurate BLUP prediction, the ability to estimate individual breeding values, and the ease of use would make this new method especially attractive for analyzing tree breeding data.}, number={12}, journal={Canadian Journal of Forest Research}, author={Xiang, B. and Li, B. L.}, year={2001}, pages={2252–2259} }
 @article{hu_li_2001, title={Assessment of the ratio of pollen to seed flow in a cline for genetic variation in a quantitative trait}, volume={87}, ISSN={["1365-2540"]}, DOI={10.1046/j.1365-2540.2001.00876.x}, abstractNote={A dispersal–selection cline model is analysed to evaluate the role of the ratio of pollen to seed flow (r) in spatial genetic variation, with a focus on clines in additive and dominant variances of major genes affecting a quantitative trait, assuming one locus with two alleles, no genetic drift and no mutation. It is shown that under weak selection, steady-state departures from the value at Hardy–Weinberg equilibrium (HWE) for genotype frequency (D) and additive variance (ΔVa) generally display a small value on one side of the selection boundary point, a high value around the point, and a moderate value on the other side of the boundary point. A large value of r can enhance formation of this pattern. However, this is not the case for clines in the average effect of a gene substitution (Δα) or in dominance variance (ΔVd), where large values of r can eradicate the clines. Direct use of their values at HWE to approximate the real case is acceptable. There is an expected turning point that divides clines of either additive variance or dominance variance into two subclines, each with a shorter width than that of allele frequency. Integration of these properties can help to indicate the existence of major genes affecting a quantitative trait.}, journal={HEREDITY}, author={Hu, XS and Li, B}, year={2001}, month={Oct}, pages={400–409} }
 @article{olsson_lindgren_li_2001, title={Balancing genetic gain and relatedness in seed orchards}, volume={50}, number={5-6}, journal={Silvae Genetica}, author={Olsson, T. and Lindgren, D. and Li, B.}, year={2001}, pages={222–227} }
 @inproceedings{isik_li_frampton_2001, title={Comparison of genetic variances estimated from seedlings and rooted cuttings of the same families of Loblolly pine}, volume={26}, booktitle={Proceedings of the 26th Biennial Southern Forest Tree Improvement Conference}, publisher={Athens, GA : Georgia Center for Continuing Education, the University of Georgia}, author={Isik, F. and Li, B. and Frampton, J.}, year={2001}, pages={143–146} }
 @inproceedings{cumbie_li_goldfarb_mullin_mckeand_2001, title={Genetic parameters and uniformity of wood properties of full-sib families and clones of loblolly pine}, booktitle={Proceedings of the 26th Southern Forest Tree Improvement Conference}, author={Cumbie, W. P. and Li, B. and Goldfarb, B. and Mullin, T. and McKeand, S.}, year={2001}, pages={104–106} }
 @article{isik_li_2001, title={Genetic variation in wood density and its measurement using the Resistograph}, volume={26}, journal={Proc. 26th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B.}, year={2001}, pages={120} }
 @inproceedings{isik_li_2001, title={Genetic variation in wood density and its measurement using the Resistograph}, volume={26}, booktitle={Proc. 26th Biennial Southern Forest Tree Improvement Conference}, author={Isik, F. and Li, B.}, year={2001} }
 @article{wu_li_2000, title={A quantitative genetic model for analyzing species differences in outcrossing species}, volume={56}, ISSN={["0006-341X"]}, DOI={10.1111/j.0006-341X.2000.01098.x}, abstractNote={Summary.A genetic model based on a two‐level intra‐ and interspecific mating design is proposed to estimate the genetic architecture of species differences and heterosis for outcrossing species. The underlying genetic analyses make use of classical quantitative genetic theories and recent results from molecular genetic studies. Gene effects across different quantitative trait loci (QTL) can be approximated by a geometric series. Under natural selection, gene effects are often associated with allele frequencies in a particular way, which can be approximated by the gamma distribution. By incorporating these approximations into family structural analyses in the mating design, we are able to estimate a number of genetic parameters that contribute to quantitative genetic variation based on a nonlinear optimization approach. These parameters include the number of QTL, their gene effects, and their allele frequencies in the parental populations. We perform simulation studies and illustrate an example to demonstrate the statistical property and procedure of the method.}, number={4}, journal={BIOMETRICS}, author={Wu, RL and Li, BL}, year={2000}, month={Dec}, pages={1098–1104} }
 @article{frampton_li_goldfarb_2000, title={Early field growth of loblolly pine rooted cuttings and seedlings}, volume={24}, number={2}, journal={Southern Journal of Applied Forestry}, author={Frampton, J. and Li, B. and Goldfarb, B.}, year={2000}, pages={98–105} }
 @inbook{wu_li_zeng_2000, title={Molecular dissection of quantitative traits: new perspectives from populus}, volume={1}, booktitle={Molecular biology of woody plants}, publisher={Dordrecht; Boston: Kluwer Academic}, author={Wu, R. and Li, B. and Zeng, Z.-B.}, editor={Jain, S. M. and Minocha, S. C.Editors}, year={2000}, pages={475–490} }
 @article{isik_isik_yildirim_li_2000, title={Shoot growth patterns related to growth and adaptation of Pinus brutia}, volume={11}, journal={Bildiri, IUFRO XXI World Forestry Congress}, author={Isik, F. and Isik, K. and Yildirim, T. and Li, B.}, year={2000} }
 @article{wu_li_1999, title={A multiplicative-epistatic model for analyzing interspecific differences in outcrossing species}, volume={55}, DOI={10.1111/j.0006-341x.1999.00355.x}, abstractNote={Summary.Epistasis may play an important role in evolution and speciation. Under multiplicative interactions between different loci, an analytical model is proposed to estimate genetic parameters at the individual locus level that contribute to interspecific differences in outcrossing species. The multiplicative epistasis model, inferred from a number of animal and plant experiments, suggests that genotypes at a pair of loci have genotypic values equal to the product of genotypic values at the two different loci. By considering the genetic property of outcrossing species (i.e., high polymorphisms) in the multilevel family structure analysis for an intra‐ and interspecific factorial mating design, a method is developed to provide estimates for allele frequencies and additive and dominant effects at individual loci in each of the two parental populations, the genotypic values of newly formed heterozygotes through species combination each with one allele from a parental population and the second from the other parental population, and the numbers of genetic factors that lead to species differentiation. Use of clones offers a tremendous power to test the adequacy of the model. However, the utilization of the model with species that cannot be cloned is also discussed. An example with interspecific hybrids of two forest tree species is used to demonstrate the model.}, number={2}, journal={Biometrics}, author={Wu, R. L. and Li, B. L.}, year={1999}, pages={355–365} }
 @article{mckeand_li_amerson_1999, title={Genetic variation in fusiform rust resistance in loblolly pine across a wide geographic range}, volume={48}, number={5}, journal={Silvae Genetica}, author={McKeand, S. E. and Li, B. and Amerson, H. V.}, year={1999}, pages={255–260} }
 @article{li_mckeand_weir_2000, title={Impact of forest genetics on sustainable forestry: results from two cycles of loblolly pine breeding in the U.S.}, volume={10}, DOI={10.1300/j091v10n01_09}, number={1/2}, journal={Journal of Sustainable Forestry}, author={Li, B. and McKeand, Steven and Weir, R.}, year={2000}, pages={79–85} }
 @article{li_mckeand_weir_1999, title={Tree improvement and sustainable forestry- impact of two cycles of loblolly pine breeding in the U.S.A.}, volume={6}, number={4}, journal={Forest Genetics}, author={Li, B. and McKeand, S.E. and Weir, R.J.}, year={1999}, pages={229–234} }
 @article{robison_goldfarb_li_1998, title={Advancing hardwood production forestry}, volume={1998}, number={May}, journal={Paper Age}, author={Robison, D. J. and Goldfarb, B. and Li, B.}, year={1998}, pages={22–24} }
 @article{li_howe_wu_1998, title={Developmental factors responsible for heterosis in aspen hybrids (Populus tremuloides x P-tremula)}, volume={18}, DOI={10.1093/treephys/18.1.29}, abstractNote={Juvenile growth and bud set phenology were analyzed to study the biological basis of heterosis (hybrid vigor) in interspecific hybrids of Populus tremuloides Michx. (T) and P. tremula L. (Ta). Growth, measured as seedling volume index, was significantly higher for each of the two reciprocal interspecific crosses, T x Ta and Ta x T, than for the T x T intraspecific cross. Broad-sense heritabilities were 2-6 times larger than narrow-sense heritabilities for growth and shoot components in the T x T intraspecific cross, suggesting an important role for dominance or overdominance in aspen growth. Previous genetic analyses have indicated that hybrid vigor may be the result of overdominance at several key loci each with an allele inherited from each of parental species. Internode length and leaf number contributed substantially to the heterosis of stem volume, but their effects on heterosis differed between the T x Ta and Ta x T hybrids. In T x Ta seedlings, heterosis of stem volume was attributed to a high diameter growth rate, whereas in Ta x T seedlings heterosis of stem volume was probably the result of delayed bud set resulting in a longer duration of height growth. In addition to internode number and length and leaf number, other morphological or physiological components might affect heterosis, for example, extended leaf retention.}, number={1}, journal={Tree Physiology}, author={Li, B. L. and Howe, G. T. and Wu, R. L.}, year={1998}, pages={29–36} }
 @book{li_hatcher_sprauge_mckeand_weir_1998, title={Full-sib breeding values from 2nd-cycle diallel progeny tests}, number={2}, institution={N.C. State University-Industry Cooperative Tree Improvement Program}, author={Li, B. and Hatcher, A. V. and Sprauge, J. R. and McKeand, S. E. and Weir, R. J.}, year={1998} }
 @book{li_hatcher_sprauge_mckeand_weir_1998, title={Loblolly pine breeding values from 2nd-generation diallel progeny tests}, number={1}, institution={N.C. State University-Industry Cooperative Tree Improvement Program}, author={Li, B. and Hatcher, A. V. and Sprauge, J. R. and McKeand, S. E. and Weir, R. J.}, year={1998} }
 @book{mckeand_weir_hatcher_li_sprague_zanker_1997, title={Establishment of 2.5-generation seed orchards}, number={97-1}, institution={North Carolina State University-Industry Cooperative Tree Improvement Program}, author={McKeand, S. E. and Weir, B. and Hatcher, A. and Li, B. and Sprague, J. and Zanker, P.}, year={1997}, pages={11} }
 @inproceedings{li_mckeand_hatcher_weir_1997, title={Genetic gains of second generation selections from the NCSU-Industry Cooperative Tree Improvement Program}, booktitle={Proceedings of the 24th Southern Forest Tree Improvement Conference}, author={Li, B. and McKeand, S. E. and Hatcher, A. V. and Weir, R. J.}, year={1997}, pages={234–238} }
 @article{li_mckeand_weir_1997, title={Genetically improved seedlings can benefit small forest landowners}, volume={55}, number={5}, journal={Forest Landowner}, author={Li, B. and McKeand, S. E. and Weir, R. J.}, year={1997}, pages={20–23} }
 @article{li_wu_1997, title={Heterosis and genotype x environment interactions of juvenile aspens in two contrasting sites}, volume={27}, DOI={10.1139/97-110}, number={10}, journal={Canadian Journal of Forest Research}, author={Li, B.-L. and Wu, R.-L.}, year={1997}, pages={1525–1537} }
 @article{enebak_bucciarelli_ostry_li_1997, title={Histological analyses of the host response of two aspen genotypes to wounding and inoculation with Hypoxylon mammatum}, volume={27}, DOI={10.1111/j.1439-0329.1997.tb01448.x}, abstractNote={SummaryRamets derived from root sprouts of two quaking aspen (Populus tremuloides) parents were either mechanically wounded or wounded and inoculated with mycelium of Hypoxylon mammatum. Female aspen parents were considered either resistant or susceptible based on a 30‐year field trial of their open‐pollinated progenies that had 21% and 93% mortality, respectively, caused by H. mammatum. Each stem was wounded twice at the base and in the nonlignified zone. Samples were taken 5 mm above the site of wounding at 7 and 14 days. Histochemicals used were phloroglucinol‐HCl and Sudan Black B to detect lignin and suberin, respectively. Thin sections of the resistant aspen ramets showed intensive staining phloroglucinol‐HCl, which was localized along both sides of the wound margin. Collenchyma callus was well developed by day 7 and was derived from the phloem tissue internal to the cell walls staining positive for phloroglucinol‐HCl, near the vascular cambium. In contrast, the tissues of susceptible aspen ramets were less stained, the stained cells were less scattered and less collenchyma callus had formed than on the resistant ramets. The presence of the fungus increased the amount of staining observed with phloroglucinol‐HCl and delayed wound closure in both aspen genotypes. No distinguishing pattern could be identified between the two aspen genotypes with respect to suberin formation. When comparing stem response to phloroglucinol‐HCl with respect to the tissue type on the same stem (succulent versus woody), the inoculation of older woody tissue resulted in a more defined host response and thus were better in separating the two aspen genotypes.}, number={6}, journal={European Journal of Forest Pathology}, author={Enebak, S. A. and Bucciarelli, B. and Ostry, M. E. and Li, B.}, year={1997}, pages={337–345} }
 @inproceedings{mckeand_li_1997, title={Stability of fusiform rust resistance in loblolly pine}, booktitle={Proceedings of the 24th Southern Forest Tree Improvement Conference}, author={McKeand, S. E. and Li, B.}, year={1997}, pages={261–266} }
 @inproceedings{mckeand_li_1997, title={Two generations of genetic gains with loblolly pine in the southeastern United States}, booktitle={Proceedings of the 26th Meeting of the Canadian Tree Improvement Association, Part 2 Symposium}, author={McKeand, S. E. and Li, B.}, editor={Beaulieu, J. and Simpson, J. D.Editors}, year={1997}, pages={16–20} }
 @book{li_mckeand_hatcher_sprauge_weir_1996, title={Breeding value predictions and genetic gains from second generation loblolly pine open-pollinated progeny tests}, journal={Special Technical Report}, institution={N.C. State University-Industry Cooperative Tree Improvement Program}, author={Li, B. and McKeand, S. E. and Hatcher, A. V. and Sprauge, J. R. and Weir, R. J.}, year={1996}, pages={78p.} }
 @inproceedings{li_mckeand_weir_1996, title={Genetic parameter estimates and selection efficiency for the loblolly pine breeding the south-eastern U.S}, booktitle={Tree Improvement for Sustainable Tropical Forestry: Proceedings of the QFRI-IUFRO Conference}, author={Li, B. and McKeand, S. E. and Weir, R. J.}, editor={M. J. Dieters, A. C. Matheson and D. G. Nikles, C. E. Harwood and Walker, S. M.Editors}, year={1996}, pages={164–168} }
 @article{li_mckeand_allen_1991, title={Genetic variation in nitrogen use efficiency of loblolly pine seedlings}, volume={37}, number={2}, journal={Forest Science}, author={Li, B. and McKeand, S. E. and Allen, H. L.}, year={1991}, pages={613–626} }
 @article{li_allen_mckeand_1991, title={Nitrogen and family effects on biomass allocation of loblolly pine seedlings}, volume={37}, number={1}, journal={Forest Science}, author={Li, B. and Allen, H. L. and McKeand, S. E.}, year={1991}, pages={271–283} }
 @article{li_mckeand_allen_1991, title={SEEDLING SHOOT GROWTH OF LOBLOLLY-PINE FAMILIES UNDER 2 NITROGEN LEVELS AS RELATED TO 12-YEAR HEIGHT}, volume={21}, ISSN={["0045-5067"]}, DOI={10.1139/x91-118}, abstractNote={ Seedling shoot elongation and biomass were examined for 23 open-pollinated loblolly pine (Pinustaeda L.) families grown in a greenhouse under two nitrogen regimes. Significant genetic variation was detected among families for the number of growth cycles, total seedling height, cyclic-growth elongation, the number of stem units, and biomass of stem free growth, cyclic growth, total stem, needles, and total shoot. Heritability estimates were generally high for shoot characteristics except for mean stem-unit length. Shoot biomass measures were weakly or negatively correlated with 12-year-height performance. Elongation of cyclic growth, number of growth cycles, and number of stem units showed stronger correlations with field performance than did seedling height. Juvenile–mature correlations were higher for the low nitrogen treatment, suggesting that 12-year height of loblolly pine families can be more accurately predicted when the seedlings are grown under greenhouse conditions that mimic field nitrogen levels. }, number={6}, journal={CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE}, author={LI, BL and MCKEAND, SE and ALLEN, HL}, year={1991}, month={Jun}, pages={842–847} }
 @inproceedings{li_mckeand_allen_1989, title={Early selection of loblolly pine families based on seedling shoot elongation characters}, booktitle={Proceedings of the 20th Southern Forest Tree Improvement Conference}, author={Li, B. and McKeand, S. E. and Allen, H. L.}, year={1989}, pages={228–234} }
 @article{li_mckeand_1989, title={Stability of loblolly pine families in the Southeastern U.S}, volume={38}, number={3-4}, journal={Silvae Genetica}, author={Li, B. and McKeand, S. E.}, year={1989}, pages={96–101} }
 @article{li_jett_weir_1988, title={A preliminary study of geographic variation in Fraser fir seedlings}, volume={12}, number={2}, journal={Southern Journal of Applied Forestry}, author={Li, B. and Jett, J. B. and Weir, R. J.}, year={1988}, pages={128} }