@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={Summary}, 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{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}, 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{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}, 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_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{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{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{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{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{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}, 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{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{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}, 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{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{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{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={Abstract}, 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{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{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_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}, 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 Pinus taeda 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}, 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