@article{gowda_fang_tyagi_bourland_dever_campbell_zhang_abdelraheem_sood_jones_et al._2024, title={Genome-wide association study of fiber quality traits in US upland cotton (<i>Gossypium hirsutum</i> L.)}, volume={137}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-024-04717-7}, number={9}, journal={THEORETICAL AND APPLIED GENETICS}, author={Gowda, S. Anjan and Fang, Hui and Tyagi, Priyanka and Bourland, Fred and Dever, Jane and Campbell, Benjamin Todd and Zhang, Jinfa and Abdelraheem, Abdelraheem and Sood, Shilpa and Jones, Don C. and et al.}, year={2024}, month={Sep} }
 @article{caton_fang_pallipparambil_manoukis_2023, title={Transect-based trapping for area-wide delimitation of insects}, volume={4}, ISSN={["1938-291X"]}, DOI={10.1093/jee/toad059}, abstractNote={AbstractTypical delimitation trapping survey designs for area-wide (nonlocalized) insect populations are regularly spaced grids, and alternative shapes have not been evaluated. We hypothesized that transect-based designs could give similar detection rates with significantly shorter servicing distances. We used the TrapGrid model to investigate novel “trap-sect” designs incorporating crossed, spoked, and parallel lines of traps, comparing them to a regular grid, in single survey and multiple-site scenarios. We calculated minimum servicing distances and simulated mean probabilities of detecting a pest population, judging overall performance of trap network designs using both metrics. For single sites, trap-sect designs reduced service distances by 65–89%, and most had similar detection probabilities as the regular grid. Kernel-smoothed intensity plots indicated that the best performing trap-sect designs distributed traps more fully across the area. With multiple sites (3 side by side), results depended on insect dispersal ability. All designs performed similarly in terms of detection for highly mobile insects, suggesting that designs minimizing service distances would be best for such pests. For less mobile pests the best trap-sect designs had 4–6 parallel lines, or 8 spokes, which reduced servicing distances by 33–50%. Comparisons of hypothetical trap-sect arrays to real program trap locations for 2 pests demonstrated that the novel designs reduced both trap numbers and service distances, with little differences in mean nearest trap distance to random pest locations. Trap-sect designs in delimitation surveys could reduce costs and increase program flexibility without harming the ability to detect populations.}, journal={JOURNAL OF ECONOMIC ENTOMOLOGY}, author={Caton, Barney P. and Fang, Hui and Pallipparambil, Godshen R. and Manoukis, Nicholas C.}, year={2023}, month={Apr} }
 @article{gowda_shrestha_harris_phillips_fang_sood_zhang_bourland_bart_kuraparthy_2022, title={Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.)}, volume={10}, ISSN={["1432-2242"]}, url={https://publons.com/wos-op/publon/54751063/}, DOI={10.1007/s00122-022-04229-2}, abstractNote={Identification and genomic characterization of major resistance locus against cotton bacterial blight (CBB) using GWAS and linkage mapping to enable genomics-based development of durable CBB resistance and gene discovery in cotton. Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm), has periodically been a damaging disease in the USA. Identification and deployment of genetic resistance in cotton cultivars is the most economical and efficient means of reducing crop losses due to CBB. In the current study, genome-wide association study (GWAS) of CBB resistance using an elite diversity panel of 380 accessions, genotyped with the cotton single nucleotide polymorphism (SNP) 63 K array, and phenotyped with race-18 of CBB, localized the CBB resistance to a 2.01-Mb region in the long arm of chromosome D02. Molecular genetic mapping using an F 6  recombinant inbred line (RIL) population showed the CBB resistance in cultivar Arkot 8102 was controlled by a single locus (BB-13). The BB-13 locus was mapped within the 0.95-cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i04890Gh and i04907Gh of the BB-13 locus, identified from the combined linkage analysis and GWAS, targeted it to a 371-Kb genomic region. Candidate gene analysis identified thirty putative gene sequences in the targeted genomic region. Nine of these putative genes and two NBS-LRR genes adjacent to the targeted region were putatively involved in plant disease resistance and are possible candidate genes for BB-13 locus. Genetic mapping and genomic targeting of the BB13 locus in the current study will help in cloning the CBB-resistant gene and establishing the molecular genetic architecture of the BB-13 locus towards developing durable resistance to CBB in cotton.}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Science and Business Media LLC}, author={Gowda, S. Anjan and Shrestha, Navin and Harris, Taylor M. and Phillips, Anne Z. and Fang, Hui and Sood, Shilpa and Zhang, Kuang and Bourland, Fred and Bart, Rebecca and Kuraparthy, Vasu}, year={2022}, month={Oct} }
 @article{fang_caton_manoukis_pallipparambil_2022, title={Simulation-based evaluation of two insect trapping grids for delimitation surveys}, volume={12}, url={http://dx.doi.org/10.1038/s41598-022-14958-5}, DOI={10.1038/s41598-022-14958-5}, abstractNote={AbstractIn the United States of America, delimitation trapping surveys with square grids have been used for decades for exotic insects without rigorous evaluation. We used simulations to investigate the effectiveness of two representative designs: an 8-km grid for Acrolepiopsis assectella (leek moth) and a 14.5-km grid for Ceratitis capitata (Mediterranean fruit fly, “Medfly”). We investigated grid compositions and design factors, measuring performance as the mean probability of pest capture over all traps, p(capture), and designed improved grids for both species. For the standard designs, p(capture) was 0.86 for leek moth and 0.71 for Medfly, with the latter performing better due to greater lure and trap attractiveness. For both designs, 86 percent or more of mean p(capture) came from core area captures. Egress testing indicated that both grids were oversized. An improved grid for leek moths would use 177 traps in a 4.8-km diameter circle, which had mean p(capture) = 0.73 and reduced the cost by 80 percent. The best Medfly grid was a 4.8-km diameter circle with 232 traps, which gave mean p(capture) of 0.66 and reduced the cost by 86 percent. Simulation may be used to improve trapping survey plans, often saving significantly on costs while maintaining survey performance.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Fang, Hui and Caton, Barney and Manoukis, Nicholas C. and Pallipparambil, Godshen}, year={2022}, month={Dec} }
 @article{caton_fang_manoukis_pallipparambil_2021, title={Quantifying insect dispersal distances from trapping detections data to predict delimiting survey radii}, volume={146}, ISSN={["1439-0418"]}, url={https://publons.com/wos-op/publon/47440398/}, DOI={10.1111/JEN.12940}, abstractNote={AbstractThe spread potential of invasive pests is a major concern for delimitation, quarantine and eradication efforts. We analysed trapping survey detections data for five insects and one low‐dispersing mollusc to quantify 30‐day dispersal kernels (mean total distance [MTD], m). We hypothesized that MTD would increase with species’ reported diffusion coefficients (D, m2 per day), and that D could be used to predict containment radius lengths for delimiting surveys for exotic pests. We collected trapping data for the following six invasive pest species: European grapevine moth (EGVM; Lobesia botrana [Denis & Schiffermüller]), Giant African land snail (GALS; Lissachatina fulica [Bowdich]), Japanese beetle (JB; Popillia japonica [Newman]), Mediterranean fruit fly (Medfly; Ceratitis capitata [Wiedemann]), Mexican fruit fly (Mexfly; Anastrepha ludens [Loew]) and Oriental fruit fly (OFF; Bactrocera dorsalis [Hendel]). We used K‐means clustering to group detections that were proximate in space and time, then finalized them manually. We calculated MTD from the cluster centroid for each detection. Probability histograms for MTD were fit to a two‐parameter exponential function, and from those functions we estimated species’ dispersal limits for four percentiles (99th to 99.99th). The least vagile species, GALS and EGVM, had the greatest decay rates, and smallest MTD and percentile distances. OFF, with the greatest reported D, had the smallest decay rates and greatest MTD and percentile distances. Medfly, Mexfly and JB had intermediate MTD and percentile distances. Each regression of percentile distance as a logarithmic function of D fit the data well. The best regression used adjusted 99.9th percentile distances. These empirical results indicated that many delimiting surveys currently in use are oversized; adopting the new recommendations could yield significant cost savings. These results could be a general solution for estimating delimiting survey radii (for durations of ca. 30 days) across a wide range of insect dispersal abilities.}, number={1-2}, journal={JOURNAL OF APPLIED ENTOMOLOGY}, publisher={Wiley}, author={Caton, Barney P. and Fang, Hui and Manoukis, Nicholas C. and Pallipparambil, Godshen R.}, year={2021}, month={Oct} }
 @article{fang_zhang_bowman_jones_kuraparthy_2021, title={Registration of two germplasm lines with improved lint yield and fiber elongation in upland cotton}, volume={15}, ISSN={["1940-3496"]}, url={https://publons.com/wos-op/publon/54751099/}, DOI={10.1002/plr2.20121}, abstractNote={AbstractTwo conventional upland cotton (Gossypium hirsutum L.) germplasm lines, NC18‐05 (Reg. no. GP‐1082, PI 697272) and NC18‐06 (Reg. no. GP‐1083, PI 697273), were developed by the Department of Crop and Soil Sciences at North Carolina State University. The lines were bred for fiber elongation within yield‐competitive phenotypes. The two lines were derived from a randomly mated population using multiple parental lines. Both NC18‐05 and NC18‐06 produced equivalent or higher lint than commercial cultivars ‘DP393’, ‘SG747’, and ‘UA48’ during 2 yr in Clayton, NC. Germplasm line NC18‐05 produced 1507.2 kg ha–1 of lint, which was 36.2% higher than DP393 and 29.4% higher than UA48 (p < .05). Germplasm line NC18‐06 produced 1428.6 kg ha–1 of lint, which was 29.1% higher than DP393 and 22.6% higher than UA48 (p < .05). However, neither line yielded more lint per hectare than SG747 or the average of the parental lines (p > .05). Both NC18‐05 and NC18‐06 exhibited equal or higher fiber elongation values (6.0–49.2%) than the commercial cultivar controls. These two lines had higher lint percentages than UA48 (p < .05). NC18‐06 also demonstrated stronger fiber than DP393 and SG747 (p < .05). These two germplasm lines offer breeders a new source of exceptional fiber elongation before break within a high‐yielding background.}, number={2}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Fang, Hui and Zhang, Kuang and Bowman, Daryl T. and Jones, Don C. and Kuraparthy, Vasu}, year={2021}, month={May}, pages={359–365} }
 @article{caton_fang_manoukis_pallipparambil_2021, title={Simulation-Based Investigation of the Performance of Delimiting Trapping Surveys for Insect Pests}, volume={114}, ISSN={["1938-291X"]}, url={https://publons.com/wos-op/publon/41676571/}, DOI={10.1093/jee/toab184}, abstractNote={AbstractFully trapped survey designs are widely used to delimit adventive pests populations that can be detected using traps and lures. Delimitation includes verifying the presence of the pest and determining its spatial extent. The size and shape of the survey design and the density of traps can vary; however, resulting variation in detecting efficiency is often unknown. We used a trapping network simulation model with diffusion-based insect movement to investigate delimiting survey trapping design performance for fully trapped and some modified designs. Simulations included randomized outbreak locations in a core area and a duration of 30 d. We assessed impacts of insect dispersal ability, grid size and shape, and trap attractiveness and density on survey performance, measured as mean probability of capturing individual pests [p(capture)]. Most published grids are square, but circles performed equally well and are more efficient. Over different grid sizes, p(capture) increased for insects with greater dispersal ability but was generally unresponsive to size because most captures occurred in central areas. For low dispersing insects, the likelihood of egress was approximately zero with a 3.2-km square grid, whereas an 11.3-km grid was needed to contain highly vagile insects. Trap attractiveness affected p(capture) more strongly than density: lower densities of poorly attractive traps may underperform expectations. Variable density designs demonstrated potential for cost savings but highlighted that resource-intensive outer bands are critical to boundary determination. Results suggesting that many grids are oversized need empirical verification, whereas other principles, such as using circular shapes, are readily adoptable now.}, number={6}, journal={JOURNAL OF ECONOMIC ENTOMOLOGY}, author={Caton, Barney P. and Fang, Hui and Manoukis, Nicholas C. and Pallipparambil, Godshen R.}, year={2021}, month={Dec}, pages={2581–2590} }
 @article{zhang_kuraparthy_fang_zhu_sood_jones_2019, title={High-density linkage map construction and QTL analyses for fiber quality, yield and morphological traits using CottonSNP63K array in upland cotton (Gossypium hirsutum L.)}, volume={20}, ISSN={["1471-2164"]}, url={https://publons.com/wos-op/publon/36765240/}, DOI={10.1186/s12864-019-6214-z}, abstractNote={AbstractBackgroundImproving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits.ResultsMolecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41 cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development.ConclusionWe constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.}, number={1}, journal={BMC GENOMICS}, publisher={Springer Science and Business Media LLC}, author={Zhang, Kuang and Kuraparthy, Vasu and Fang, Hui and Zhu, Linglong and Sood, Shilpa and Jones, Don C.}, year={2019}, month={Nov} }
 @article{fang_bowman_zhang_zhu_jones_kuraparthy_2019, title={Registration of Four Germplasm Lines of Upland Cotton with High Fiber Quality}, volume={13}, ISSN={["1940-3496"]}, url={https://publons.com/wos-op/publon/31419926/}, DOI={10.3198/jpr2019.02.0005crg}, abstractNote={Four upland cotton (Gossypium hirsutum L.) germplasm lines, NC18‐11 (Reg. no. GP‐1056, PI 690771), NC18‐12 (Reg. no. GP‐1057, PI 690772), NC18‐13 (Reg. no. GP‐1058, PI 690773), and NC18‐14 (Reg. no. GP‐1059, PI 690774), were developed by the Department of Crop and Soil Sciences at North Carolina State University. These four cotton lines had improved fiber quality traits and exhibited 915.5 to 1180.9 kg ha−1 lint yield. All four lines were derived from a random mated population using multiple parental lines. The four lines were compared with commercial cultivars ‘DP393’, ‘Sure‐Grow 747’, and ‘UA48’ over 2 yr using a replicated randomized complete block design in Clayton, NC. Lines NC18‐11, NC18‐12, and NC18‐13 had significantly (p = 0.05) better micronaire values than the checks and significantly higher strength values (8.3–25.3%) than DP393, Sure‐Grow 747, and the parental lines. These three lines also had significantly (p = 0.05) greater upper half mean length values (4.9–11.6%) than DP393 and Sure‐Grow 747. Germplasm line NC18‐14 had a 15.4 to 62.5% significantly (p = 0.05) higher fiber elongation value than all checks and parental lines and showed 5.0 to 12.8% more lint fraction than the checks. These lines could be additional sources of genetic variability for cotton breeding programs focusing on improving fiber quality traits while still producing more than 900 kg ha−1 of lint.}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Fang, Hui and Bowman, Daryl T. and Zhang, Kuang and Zhu, Linglong and Jones, Don C. and Kuraparthy, Vasu}, year={2019}, month={Sep}, pages={401–405} }
 @article{fang_zhang_bowman_jones_kuraparthy_2019, title={Registration of Four Germplasm Lines of Upland Cotton with High Lint Yield}, volume={13}, ISSN={["1940-3496"]}, url={https://publons.com/wos-op/publon/31419922/}, DOI={10.3198/jpr2018.12.0079crg}, abstractNote={Four upland cotton (Gossypium hirsutum L.) lines, NC18‐07 (Reg. no. GP‐1052, PI 690767), NC18‐08 (Reg. no. GP‐1053, PI 690768), NC18‐09 (Reg. no. GP‐1054, PI 690769), and NC18‐10 (Reg. no. GP‐1055, PI 690770), were developed by the Department of Crop and Soil Sciences at North Carolina State University. The four upland cotton lines have improved yield production and some good fiber quality traits. All four lines were derived from a random mated population using multiple parental lines. These four lines were compared with commercial check cultivars ‘DP393’, ‘Sure‐Grow 747’, and ‘UA48’ over 2 yr in Clayton, NC. NC18‐07 produced 7.6 to 34.2% greater lint yields than that of the checks and had 15.2% greater elongation value than that of UA48. NC18‐08 produced 5.9 to 32.1% greater lint yield than the checks. NC18‐09 yielded 2.2 to 27.5% greater lint than checks and showed 44.7 and 22.3% greater elongation values than that of UA48 and parental lines, respectively. Germplasm line NC18‐10 produced 1.0 to 26.0% greater lint yield than the commercial checks and also displayed 26.5 and 7.0% greater elongation values than that of UA48 and parental lines, respectively. These lines could be valuable sources for cotton breeding and programs focusing on improving yield as well as fiber elongation.}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Fang, Hui and Zhang, Kuang and Bowman, Daryl T. and Jones, Don C. and Kuraparthy, Vasu}, year={2019}, month={Sep}, pages={396–400} }
 @article{kaur_kuraparthy_bacheler_fang_bowman_2018, title={Screening Germplasm and Quantification of Components Contributing to Thrips Resistance in Cotton}, volume={111}, ISSN={["1938-291X"]}, url={https://publons.com/wos-op/publon/31419923/}, DOI={10.1093/jee/toy201}, abstractNote={Abstract Three hundred and ninety-one Gossypium hirsutum and 34 Gossypium barbadense accessions were screened for thrips resistance under field conditions at the Upper Coastal Plain Research Station in Rocky Mount, North Carolina in years 2014 and 2015. Visual damage ratings, thrips counts, and seedling dry weights were recorded at 2.5, 3.5, and 4.5 wk after planting, respectively. Population density and thrips arrival times varied between years. Data from the three separate damage scoring dates provided a better estimate of resistance or susceptibility to thrips than ratings from the individual dates over the season. Tobacco thrips [Frankliniella fusca (Hinds) (Thysanoptera: Thripidae)], followed by western flower thrips [Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)], were the dominant thrips species observed in the study. Five resistant G. barbadense accessions and five moderately resistant upland cotton accessions were identified from field evaluations. Greenhouse experiments were conducted in Fall 2015 and Spring 2016 to determine if plant height, growth rate, leaf pubescence, and leaf area were significantly different in resistant and susceptible groups of G. hirsutum and G. barbadense accessions identified from the field screenings. Leaf pubescence and relative growth rate were significantly higher in resistant accessions compared with susceptible accessions in absence of thrips. There was no difference for plant height and leaf area between resistant and susceptible groups. Results suggest thrips-resistant plants have a possible competitive advantage through faster growth and higher trichome density, which limits thrips movement.}, number={5}, journal={JOURNAL OF ECONOMIC ENTOMOLOGY}, publisher={Oxford University Press (OUP)}, author={Kaur, Baljinder and Kuraparthy, Vasu and Bacheler, Jack and Fang, Hui and Bowman, Daryl T.}, year={2018}, month={Oct}, pages={2426–2434} }
 @article{li_an_angelovici_bagaza_batushansky_clark_coneva_donoghue_edwards_fajardo_et al._2018, title={Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace}, volume={9}, ISSN={["1664-462X"]}, url={https://publons.com/wos-op/publon/12063358/}, DOI={10.3389/fpls.2018.00553}, abstractNote={Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.}, journal={FRONTIERS IN PLANT SCIENCE}, publisher={Frontiers Media SA}, author={Li, Mao and An, Hong and Angelovici, Ruthie and Bagaza, Clement and Batushansky, Albert and Clark, Lynn and Coneva, Viktoriya and Donoghue, Michael J. and Edwards, Erika and Fajardo, Diego and et al.}, year={2018}, month={Apr} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2017, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, DOI={10.1101/062612}, abstractNote={AbstractLeaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus,okra(L-D1). Theokralocus is not only of agricultural importance in cotton (Gossypium hirsutumL.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at theL-D1locus are controlled by a HD-Zip transcription factor most similar toLate Meristem Identity1 (LMI1)gene. The classicalokraleaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-typenormalleaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of thisLMI1-likegene in anokravariety was sufficient to induce normal leaf formation. An intermediate leaf shape allele,sub-okra, lacks both the promoter duplication and the exonic deletion. Our results indicate thatsub-okrais the ancestral leaf shape of tetraploid cotton andnormalis a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton.}, number={1}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Andres, R. J. and Coneva, V. and Frank, M. H. and Tuttle, J. R. and Samayoa, L. F. and Han, S. W. and Kaur, B. and Zhu, L. L. and Fang, Hui and Bowman, D. T. and et al.}, year={2017}, pages={E57–66} }
 @article{fang_zhou_sanogo_zhang_2014, title={Development of STS markers for Verticillium wilt resistance in cotton based on RGA–AFLP analysis}, volume={34}, url={http://dx.doi.org/10.1007/s11032-014-0085-4}, DOI={10.1007/s11032-014-0085-4}, number={3}, journal={Molecular Breeding}, publisher={Springer Science and Business Media LLC}, author={Fang, Hui and Zhou, Huiping and Sanogo, Soum and Zhang, Jinfa}, year={2014}, month={Oct}, pages={917–926} }
 @article{zhang_fang_zhou_sanogo_ma_2014, title={Genetics, Breeding, and Marker‐Assisted Selection for Verticillium Wilt Resistance in Cotton}, volume={54}, url={http://dx.doi.org/10.2135/cropsci2013.08.0550}, DOI={10.2135/cropsci2013.08.0550}, abstractNote={ABSTRACTVerticillium wilt (VW), caused by the soil‐borne fungus Verticillium dahliae Kleb., is one of the most destructive diseases in Upland cotton (Gossypium hirsutum L.) production in the U.S. and worldwide. Development of VW‐resistant cultivars remains the only economic option for controlling the disease. The objective of this review was to summarize the progress in screening methods, resistance sources, and genetics, quantitative trait locus (QTL) mapping, marker‐assisted selection (MAS) and breeding for VW resistance in cotton. Even though Gossypium barbadense L. carries high levels of resistance, its resistance has not been transferred into commercial Upland cultivars. Many Acala cotton cultivars developed in New Mexico and California between the 1940s and the 1990s, and some commercial transgenic cultivars are tolerant or moderately resistant to VW. However, due to difficulties in achieving consistent and uniform inoculation and infection with V. dahliae, both qualitative and quantitative inheritance of VW resistance have been reported in numerous studies for resistant G. barbadense and Upland genotypes. Several QTL analyses have shown the existence of VW resistance QTLs on almost all the tetraploid cotton chromosomes; however, QTLs have most frequently been detected on c5, c7, c8, c11, c16, c17, c19, c21, c23, c24, and c26. This has led to MAS for progeny with favorable QTL alleles for VW resistance in several experiments. Phenotypic selection for VW resistance has been inefficient, while the effectiveness and efficiency of MAS remain to be validated. There is an urgent need for the development of better plant inoculation and screening methods, and for more molecular mapping studies to discern the genetic basis of VW resistance in cotton.}, number={4}, journal={Crop Science}, publisher={Wiley}, author={Zhang, Jinfa and Fang, Hui and Zhou, Huiping and Sanogo, Soum and Ma, Zhiying}, year={2014}, month={Jul}, pages={1289–1303} }
 @article{zhou_fang_sanogo_hughs_jones_zhang_2014, title={Evaluation of Verticillium wilt resistance in commercial cultivars and advanced breeding lines of cotton}, volume={196}, url={http://dx.doi.org/10.1007/s10681-013-1045-5}, DOI={10.1007/s10681-013-1045-5}, number={3}, journal={Euphytica}, publisher={Springer Science and Business Media LLC}, author={Zhou, Huiping and Fang, Hui and Sanogo, Soum and Hughs, Sidney E. and Jones, Don C. and Zhang, Jinfa}, year={2014}, month={Apr}, pages={437–448} }
 @article{inheritance and transfer of thrips resistance from pima cotton to upland cotton_2013, url={https://www.cotton.org/journal/2013-17/3/}, journal={Journal of Cotton Science}, year={2013}, month={Feb} }
 @article{fang_zhou_sanogo_lipka_fang_percy_hughs_jones_gore_zhang_2014, title={Quantitative trait locus analysis of Verticillium wilt resistance in an introgressed recombinant inbred population of Upland cotton}, volume={33}, url={http://dx.doi.org/10.1007/s11032-013-9987-9}, DOI={10.1007/s11032-013-9987-9}, number={3}, journal={Molecular Breeding}, publisher={Springer Science and Business Media LLC}, author={Fang, Hui and Zhou, Huiping and Sanogo, Soum and Lipka, Alexander E. and Fang, David D. and Percy, Richard G. and Hughs, Sidney E. and Jones, Don C. and Gore, Michael A. and Zhang, Jinfa}, year={2014}, month={Mar}, pages={709–720} }
 @article{fang_zhou_sanogo_flynn_percy_hughs_ulloa_jones_zhang_2013, title={Quantitative trait locus mapping for Verticillium wilt resistance in a backcross inbred line population of cotton (Gossypium hirsutum × Gossypium barbadense) based on RGA-AFLP analysis}, volume={194}, url={http://dx.doi.org/10.1007/s10681-013-0965-4}, DOI={10.1007/s10681-013-0965-4}, number={1}, journal={Euphytica}, publisher={Springer Science and Business Media LLC}, author={Fang, Hui and Zhou, Huiping and Sanogo, Soum and Flynn, Robert and Percy, Richard G. and Hughs, Sidney E. and Ulloa, Mauricio and Jones, Don C. and Zhang, Jinfa}, year={2013}, month={Nov}, pages={79–91} }
 @article{revilla-molina_bastiaans_keulen_kropff_hui_castilla_mew_zhu_leung_2009, title={Does resource complementarity or prevention of lodging contribute to the increased productivity of rice varietal mixtures in Yunnan, China?}, volume={111}, url={http://dx.doi.org/10.1016/j.fcr.2009.01.003}, DOI={10.1016/j.fcr.2009.01.003}, abstractNote={We conducted an experiment in Gejiu, Yunnan Province of China during the wet season of 2002 to examine the importance of resource complementarity and prevention of lodging in the fast-spreading practice of growing rice varietal mixtures in China to suppress rice blast disease and its associated damage. The hybrid rice variety Shanyou 63 and the glutinous or sticky rice variety Huangkenuo were used to study intra- and inter-varietal competition in the rice intercropping system. The experiment was laid out as a randomized complete block design in four replications with pure stands and mixtures of both varieties at different total planting densities and mixing ratios. In half of the pure stand treatments of glutinous rice a metal frame was installed to prevent lodging. The results showed that resource complementarity between the two rice varieties, resulting from niche differentiation, was marginal and did not greatly enhance the productivity of the rice varietal mixtures. In contrast, prevention of lodging of glutinous rice was identified as an important additional advantage of growing these rice varieties in mixture.}, number={3}, journal={Field Crops Research}, publisher={Elsevier BV}, author={Revilla-Molina, I.M. and Bastiaans, L. and Keulen, H. Van and Kropff, M.J. and Hui, F. and Castilla, N.P. and Mew, T.W. and Zhu, Y.Y. and Leung, H.}, year={2009}, month={Apr}, pages={303–307} }
 @article{zhu_fang_wang_fan_yang_mew_mundt_2005, title={Panicle Blast and Canopy Moisture in Rice Cultivar Mixtures}, volume={95}, url={http://dx.doi.org/10.1094/phyto-95-0433}, DOI={10.1094/phyto-95-0433}, abstractNote={ Glutinous rice cultivars were sown after every fourth row of a nonglutinous, hybrid cultivar in an additive design. The glutinous cultivars were 35 to 40 cm taller and substantially more susceptible to blast than was the nonglutinous cultivar. Interplanting of glutinous and nonglutinous rice reduced the incidence and severity of panicle blast on the glutinous cultivars by >90%, and on the nonglutinous cultivar by 30 to 40%. Mixing increased the per unit area yield of glutinous rice by 80 to 90% relative to pure stand, whereas yield of the nonglutinous cultivar was essentially unaffected by mixing. To determine whether the different plant heights and canopy structures may contribute to a microclimate that is less favorable to blast infection, we monitored the moisture status of the glutinous cultivars in pure stand and mixture at 0800 h by measuring relative humidity at the height of the glutinous panicles using a swing psychrometer and by visually estimating the percentage of leaf area covered by dew. Averaged over the two seasons, the number of days of 100% humidity at 0800 h was 20.0 and 2.2 for pure stands and mixtures, respectively. The mean percentage of glutinous leaf area covered by dewwas 84 and 36% for the pure stands and mixtures, respectively. Although other mechanisms also were operative, reduced leaf wetness was likely a substantial contributor to panicle blast control in the mixtures. }, number={4}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Zhu, You-Yong and Fang, Hui and Wang, Yun-Yue and Fan, Jin Xiang and Yang, Shi-Sheng and Mew, Twng Wah and Mundt, Christopher C.}, year={2005}, month={Apr}, pages={433–438} }