@article{ghimire_spivey_kuraparthy_campbell_jones_thomas_bridges jr_narayanan_2024, title={Phenotypic variability in the US upland cotton core set for root traits and water use efficiency at the late reproductive stage}, volume={3}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.21229}, abstractNote={Abstract To incorporate root traits that improve water use efficiency (WUE) in cotton ( Gossypium hirsutum L.) variety development, harnessing the genetic variability for root traits is essential. The objectives of this study were to characterize the US upland cotton core set for root traits and WUE and determine the traits associated with WUE. The core set includes 23 of the 381 accessions of the cotton diversity panel and represents 74% of the allelic diversity in US upland cotton. Plants were grown in polyvinyl chloride columns (125‐cm height, 15‐cm diameter) in a greenhouse in 2021–2022 and 2022–2023. Half of the columns contained a synthetic hardpan (1 cm thickness, 300 PSI penetration resistance) at a depth of 25 cm. Plants were harvested when >50% of the population opened bolls. Based on 16 root‐ and shoot‐traits, water use, and WUE, Deltapine 14, Station Miller, and Southland M1 were the best performers, and Toole, Paymaster HS200, Western Stormproof, CD3HCABCUH‐1‐89, and PD 2164 were the poor performers irrespective of the presence or absence of hardpan stress to root growth. The WUE of the core set genotypes was positively correlated with very fine root (diameter <0.25 mm) length, surface area, and volume and total root weight (correlation coefficient ≥0.45). These traits serve as beneficial root traits for developing new varieties with enhanced WUE. The identified genotypes and traits will be valuable for developing the next generation of water‐use‐efficient cotton varieties with a broad genetic base through advanced breeding techniques involving genomic tools and genetic diversity.}, journal={CROP SCIENCE}, author={Ghimire, Om Prakash and Spivey, W. Walker and Kuraparthy, Vasu and Campbell, B. Todd and Jones, Michael and Thomas, Joe and Bridges Jr, William C. and Narayanan, Sruthi}, year={2024}, month={Mar} }
 @article{pettit_gowda_shrestha_harris_bart_bourland_brown-guedira_jones_kuraparthy_2023, title={Development and validation of Kompetitive allele-specific PCR (KASP) markers for bacterial blight resistant locus BB-13 in Upland cotton (Gossypium hirsutum L.)}, volume={8}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.21072}, abstractNote={Cotton bacterial blight (CBB), caused by the pathogen Xanthomonas citri subsp. malvacearum (Xcm), can inflict significant damage to cotton (Gossypium hirsutum L.) production. Previously we identified and mapped the broad‐spectrum CBB resistant locus BB‐13 on the long arm of chromosome D02 using array‐based single nucleotide polymorphisms (SNPs). In the current study, linked SNPs were converted into easily assayable Kompetitive Allele‐Specific PCR (KASP) markers to enable efficient detection and marker assisted selection (MAS) of alleles at the BB‐13 locus. The KASP marker's efficiency in detecting the BB‐13 resistant gene was validated using an Upland cotton diversity panel of 72 accessions phenotyped with Xanthomonas citri subsp. malvacearum (Xcm) race 18. The KASP marker NCBB‐KASP4, derived from the CottonSNP63K array‐based marker i25755Gh that is closely associated with BB‐13, predicted the CBB response phenotypes with an error rate of 4.17% in the diversity panel. Additionally, two independent biparental recombinant inbred line (RIL) populations segregating for resistance to Xcm race 18 were used for KASP marker validation and to test their utility in detecting the presence of the BB‐13 locus in the resistant accession CABD3CABCH‐1‐89. NCBB‐KASP4, validated across breeding populations and broad germplasm, is a reliable KASP marker for detection and testing of BB‐13 locus in cotton. Further, diagnostic array‐based SNP marker i25755Gh's allele pattern and the potential CBB response is described for 875 Gossypium accessions. These SNP based phenotypic predictions for 875 accessions along with disease response phenotypes to Xcm race 18 for 253 accessions provide a reference for CBB resistance in diverse cotton germplasm in the U.S.This article is protected by copyright. All rights reserved}, journal={CROP SCIENCE}, author={Pettit, Nicole and Gowda, Satyanarayna Anjan and Shrestha, Navin and Harris, Taylor and Bart, Rebecca and Bourland, Fred and Brown-Guedira, Gina and Jones, Don C. and Kuraparthy, Vasu}, year={2023}, month={Aug} }
 @article{gowda_bourland_kaur_jones_kuraparthy_2023, title={Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (<i>Gossypium hirsutum</i> L.)}, volume={136}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-023-04477-w}, number={11}, journal={THEORETICAL AND APPLIED GENETICS}, author={Gowda, S. Anjan and Bourland, Fred M. and Kaur, Baljinder and Jones, Don C. and Kuraparthy, Vasu}, year={2023}, month={Nov} }
 @article{shrestha_zhang_gowda_abdelraheem_jones_kuraparthy_2023, title={Identification of quantitative trait loci for fiber quality, yield, and plant height traits in Upland cotton}, volume={3}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20937}, abstractNote={Abstract In cotton, most agronomic traits are controlled by polygenes. In this study, 110 F 6 recombinant inbred lines (RILs), derived from Upland cotton cross NC05AZ06 x NC11‐2100, were used to develop a linkage map and to identify quantitative trait loci (QTL) for six fiber quality traits, three yield traits, and plant height. These RILs were genotyped using the CottonSNP63K array and phenotyped for fiber quality, yield traits, and plant height in 2‐year field trials. Analysis of variance revealed significant ( p < 0.05) differences among RILs for all traits studied, and the heritability estimates were moderate (30%–60%) to high (> 60%). Both positive and negative correlations were observed for fiber quality and yield traits. A total of 3,774 polymorphic SNP markers were used to develop a genetic map with an average marker density of 1.54 SNP/cM. Thirty QTL for fiber quality traits, yield traits, and plant height were detected on 15 different chromosomes, explaining 6.80%–20.02% of the phenotypic variance (PVE). Of these, 14 were major QTL (PVE > 10%), and three major QTL were detected in both years. Candidate gene analysis in the major QTL detected in both years and plant height QTL with PVE of 20.02% revealed five putative genes for fiber quality traits and one putative gene for plant height. The linkage map and identified QTL along with the candidate genes in the study could serve as additional breeding resources for Upland cotton genetic improvement.}, journal={CROP SCIENCE}, author={Shrestha, Navin and Zhang, Kuang and Gowda, S. Anjan and Abdelraheem, Abdelraheem and Jones, Don C. and Kuraparthy, Vasu}, year={2023}, month={Mar} }
 @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 F6 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{elassbli_abdelraheem_zhu_teng_wheeler_kuraparthy_hinze_stelly_wedegaertner_zhang_2021, title={Evaluation and genome-wide association study of resistance to bacterial blight race 18 in US Upland cotton germplasm}, volume={296}, ISSN={["1617-4623"]}, DOI={10.1007/s00438-021-01779-w}, abstractNote={Bacterial blight (BB), caused by Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease to cotton production in many countries. In the U.S., Xcm race 18 is the most virulent and widespread race and can cause serious yield losses. Planting BB-resistant cotton cultivars is the most effective method of controlling this disease. In this study, 335 U.S. Upland cotton accessions were evaluated for resistance to race 18 using artificial inoculations by scratching cotyledons on an individual plant basis in a greenhouse. The analysis of variance detected significant genotypic variation in disease incidence, and 50 accessions were resistant including 38 lines with no symptoms on either cotyledons or true leaves. Many of the resistant lines were developed in the MAR (multi-adversity resistance) breeding program at Texas A&M University, whereas others were developed before race 18 was first reported in the U.S. in 1973, suggesting a broad base of resistance to race 18. A genome-wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative trait loci (QTL) anchored by 79 SNPs, including three QTL on each of the three chromosomes A01, A05 and D02, and one QTL on each of D08 and D10. This study has identified a set of obsolete Upland germplasm with resistance to race 18 and specific chromosomal regions delineated by SNPs for resistance. The results will assist in breeding cotton for BB resistance and facilitate further genomic studies in fine mapping resistance genes to enhance the understanding of the genetic basis of BB resistance in cotton.}, number={3}, journal={MOLECULAR GENETICS AND GENOMICS}, author={Elassbli, Hanan and Abdelraheem, Abdelraheem and Zhu, Yi and Teng, Zonghua and Wheeler, Terry A. and Kuraparthy, Vasu and Hinze, Lori and Stelly, David M. and Wedegaertner, Tom and Zhang, Jinfa}, year={2021}, month={May}, pages={719–729} }
 @article{abdelraheem_kuraparthy_hinze_stelly_wedegaertner_zhang_2021, title={Genome-wide association study for tolerance to drought and salt tolerance and resistance to thrips at the seedling growth stage in US Upland cotton}, volume={169}, ISSN={["1872-633X"]}, DOI={10.1016/j.indcrop.2021.113645}, abstractNote={Upland cotton (Gossypium hirsutum L.) is the most important fiber-producing crop, and its seedlings are sensitive to abiotic and biotic stresses including drought, salt and thrips [Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)]. In this study, an association mapping panel of 376 Upland cotton accessions was evaluated to identify quantitative trait loci (QTL) for thrips resistance in two replicated tests and drought (DT) and salt tolerance (ST) each in three replicated tests. Significant genotypic differences were detected for severity rating-based thrips resistance and morphological traits (including plant height, fresh shoot weight, fresh root weight, dry shoot weight and dry root weight (except for ST), and physiological traits (including chlorophyll content reading, stomatal conductance, photosynthesis rate, transpiration, and leaf temperature) under DT and ST conditions. Heritability estimates were low for physiological traits, moderate for morphological traits measured for both DT and ST and moderate to high for thrips resistance. Based on a genome-wide association study (GWAS) using 26,301 polymorphic SNPs, 53 and 78 QTL were detected for DT and ST, respectively, on all 26 chromosomes except for A02, A04, A06, A12 and D07. Eleven and 15 QTL were common between tests for DT and ST, respectively. Twenty-three of 131 QTL were common between DT and ST. Eight QTL were identified for thrips resistance on five chromosomes (A09, D01, D02, D03 and D11). Thirteen QTL clusters were detected on 11 chromosomes (i.e., A01, A08, D01, D02, D03, D05, D06, D10, D11, D12, and D13). Among the 13 QTL clusters, the one on D03 contained a QTL for thrips resistance and four QTL for abiotic resistance. This study represented the first attempt to map thrips resistance QTL in cotton, providing important information for biotic and abiotic stress resistance to select QTL that will be useful for marker-assisted selection (MAS) in cotton.}, journal={INDUSTRIAL CROPS AND PRODUCTS}, author={Abdelraheem, Abdelraheem and Kuraparthy, Vasu and Hinze, Lori and Stelly, David and Wedegaertner, Tom and Zhang, Jinfa}, year={2021}, month={Oct} }
 @article{zhu_andres_zhang_kuraparthy_2021, title={High-density linkage map construction and QTL analysis of fiber quality and lint percentage in tetraploid cotton}, volume={7}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.20519}, abstractNote={Abstract Improving fiber quality and yield are major research objectives for cotton breeders in the United States. Identifying broadly existing and stable quantitative trait loci (QTLs) related to fiber quality is critical to properly utilizing genomic resources in cotton improvement programs. An F 6 recombinant inbred line (RIL) population derived from the cross of NC05AZ21 × TX‐2324 was used to develop linkage maps and for QTL analysis of six fiber quality traits and lint percentage. The Illumina 63K single nucleotide polymorphism (SNP) array was used to genotype the RIL population. Analysis of variance of phenotypic trait data showed significant differences among lines and years for all traits tested. The heritability for tested traits ranged from 0.56 to 0.91. Genetic mapping was performed using 3,009 polymorphic SNP markers on the RILs. We constructed a genetic map with a total length of 4,983.73 cM and an average distance of 1.66 cM between markers. The linkage map corresponded well with the Upland cotton ( Gossypium hirsutum L.) sequence‐based physical map. Thirty‐two QTLs with additive effects for lint percentage and fiber quality traits were identified on 15 chromosomes, explaining 7.9–22.2% of the phenotypic variance. The majority of these QTLs were mapped in the D subgenome, indicating that functional mutations in the D subgenome are responsible for the major fiber quality improvements in Upland cotton. Furthermore, five QTL clusters were located on four chromosomes (Chr.05, Chr.18, Chr.19, and Chr.26), which may explain the strong correlation between fiber quality traits measured. The QTLs identified in the current study could be targeted for marker‐assisted selection and map‐based cloning of fiber quality traits in Upland cotton.}, journal={CROP SCIENCE}, author={Zhu, Linglong and Andres, Ryan J. and Zhang, Kuang and Kuraparthy, Vasu}, year={2021}, month={Jul} }
 @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={Abstract Two 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{abdelraheem_elassbli_zhu_kuraparthy_hinze_stelly_wedegaertner_zhang_2020, title={A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton}, volume={133}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-019-03487-x}, abstractNote={A high-resolution GWAS detected consistent QTL for resistance to Verticillium wilt and Fusarium wilt race 4 in 376 U.S. Upland cotton accessions based on six independent replicated greenhouse tests. Verticillium wilt (VW, caused by Verticillium dahliae Kleb.) and Fusarium wilt (FOV, caused by Fusarium oxysporum f.sp. vasinfectum Atk. Sny & Hans) are the most important soil-borne fungal diseases in cotton. To augment and refine resistance quantitative trait loci (QTL), we conducted a genome-wide association study (GWAS) using high-density genotyping with the CottonSNP63K array. Resistance of 376 US Upland cotton accessions to a defoliating VW and virulent FOV4 was evaluated in four and two independent replicated greenhouse tests, respectively. A total of 15 and 13 QTL for VW and FOV4 resistances were anchored by 30 (on five chromosomes) and 56 (on six chromosomes) significant single nucleotide polymorphic (SNPs) markers, respectively. QTL on c8, c10, c16, and c21 were consistent in two or more tests for VW resistance, while two QTL on c8 and c14 were consistent for FOV4 resistance in two tests. Two QTL clusters on c16 and c19 were observed for both VW and FOV4 resistance, suggesting that these genomic regions may harbor genes in response to both diseases. Using BLAST search against the sequenced TM-1 genome, 30 and 35 candidate genes were identified on four QTL for VW resistance and on three QTL for FOV4 resistance, respectively. These genomic regions were rich in NBS-LRR genes presented in clusters. The results create opportunities for further studies to determine the correlations of field resistance with these QTL, molecular examinations of VW and FOV4 resistances, marker-assisted selection (MAS) and eventual cloning of QTL for disease resistance in cotton.}, number={2}, journal={THEORETICAL AND APPLIED GENETICS}, author={Abdelraheem, Abdelraheem and Elassbli, Hanan and Zhu, Yi and Kuraparthy, Vasu and Hinze, Lori and Stelly, David and Wedegaertner, Tom and Zhang, Jinfa}, year={2020}, month={Feb}, pages={563–577} }
 @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={Abstract Background Improving 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. Results Molecular 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. Conclusion We 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{zhu_kuraparthy_2019, title={Rapid Isolation of Loss-of-Function Mutations for Dominant Traits: A Case Study Using Photoperiod Sensitivity Trait in Pima Cotton}, volume={59}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2019.02.0133}, abstractNote={In its natural state, cotton (Gossypium spp.) is a perennial that flowers only under short-day conditions. Early selection efforts eliminated this photoperiod requirement, allowing cotton cultivation to shift predominantly to annual growth under long summer daylengths throughout the world. Photoperiod sensitivity persists in many wild cottons and remains a major barrier to the introgression of beneficial alleles into elite breeding material. Identification of the variation and genetic factors underlying photoperiod response in cotton is needed to fully harness the genetic diversity of wild cotton and broaden the cultivated germplasm pool. Genetic variants, especially loss-of-function mutations in dominant genes conferring photoperiod sensitivity, would be highly valuable in this regard. After mutagenizing pima cotton (G. barbadense L.) seeds heterozygous for the major photoperiod response gene Gb_Ppd1 with γ rays, we identified plants no longer sensitive to photoperiod. Genetic analysis of BC₁F₁ plants derived from backcrossing the mutants with their photoperiod-insensitive parent confirmed the loss-of-function mutations were allelic with Gb_Ppd1. Characterization of the mutants with molecular markers confirmed that all but one were deletions of Gb_Ppd1. Further, genotyping localized Gb_Ppd1 to a 12-Mb region on chromosome D10. The newly identified genomic region and loss-of-function mutants may help assist with the identification and functional validation of candidate genes for photoperiod response in cotton, facilitating the valuable introgression of genetic diversity into cotton breeding programs.}, number={5}, journal={CROP SCIENCE}, author={Zhu, Linglong and Kuraparthy, Vasu}, year={2019}, pages={2028–2035} }
 @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{kaur_tyagi_kuraparthy_2017, title={Genetic Diversity and Population Structure in the Landrace Accessions of Gossypium hirsutum}, volume={57}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2016.12.0999}, abstractNote={In this study, genetic diversity and population structure was assessed in a set of 185 Gossypium hirsutum L. landrace accessions, collected mainly from Central America during the mid‐1900s using genomewide simple sequence repeat (SSR) markers. Genotyping the diversity panel using 122 SSRs detected 143 marker loci. A total of 819 alleles were identified across 143 markers loci, and out of these, 23.3% were unique alleles, observed only in one accession. Average genetic distance between accessions was 0.36, suggesting higher levels of genetic variation present in the cotton tropical landrace germplasm. Using Bayesian model‐based structure analysis, five major subgroups were identified that roughly corresponded to the geographical origins of accessions. Substantial admixture was observed as accessions from different geographical locations were grouped together. Results from phylogenetic analysis, principal component analysis, and analysis of molecular variance supported clustering based on STRUCTURE analysis. Pairwise kinship estimates suggested that most of the accessions were unrelated. Finally, core sets representing various levels of allelic richness were identified using POWERMARKER. Assessing genetic diversity, population structure, and identifying the core sets in the landraces will facilitate the utilization of unexploited tropical genetic diversity towards developing improved cotton cultivars.}, number={5}, journal={CROP SCIENCE}, author={Kaur, Baljinder and Tyagi, Priyanka and Kuraparthy, Vasu}, year={2017}, pages={2457–2470} }
 @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={Leaf 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). The okra locus is not only of agricultural importance in cotton (Gossypium hirsutum L.), 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 the L-D1 locus are controlled by a HD-Zip transcription factor most similar to Late Meristem Identity1 (LMI1) gene. The classical okra leaf 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-type normal leaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of this LMI1-like gene in an okra variety 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 that sub-okra is the ancestral leaf shape of tetraploid cotton and normal is 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{kaur_andres_kuraparthy_2016, title={Major Leaf Shape Genes, Laciniate in Diploid Cotton and Okra in Polyploid Upland Cotton, Map to an Orthologous Genomic Region}, volume={56}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2015.10.0627}, abstractNote={Gossypium arboreum L, which produces spinnable cotton fibers, is an A‐genome diploid progenitor species of tetraploid cotton. With its diploid genome, publicly available genome sequence, adapted growth, and developmental and agronomic attributes, G. arboreum could make an ideal cotton species to study the genetic basis of biological traits that are controlled by orthologous loci in diploid and polyploid species. Leaf shape is an important agronomic trait in cotton. Normal, subokra, okra, and laciniate are the predominant leaf shapes in cotton cultivars. Laciniate in diploids is phenotypically similar to okra leaf shape in tetraploid. In the present study, a population of 135 F 2 plants derived from accessions NC 501 and NC 505 was used for genetic and molecular mapping of laciniate leaf shape in diploid cotton ( G. arboreum ). An inheritance study showed that laciniate leaf shape was controlled by a single incompletely dominant gene ( L L –A 2 ). Molecular genetic mapping using simple‐sequence repeat (SSR) markers placed the leaf shape locus L‐A 2 on chromosome 2. Targeted mapping using putative genes from the delineated region established that laciniate leaf shape in G. arboreum and okra leaf shape in Gossypium hirsutum L. were controlled by genes at orthologous loci. Collinearity was well conserved between the diploid A‐ ( G. arboreum ) and D‐ ( G. raimondii Ulbr.) genomes in the targeted genomic region narrowing the candidate region for the leaf shape locus ( L‐A 2 ) to nine putative genes. Establishing the orthologous genomic region for the L loci could help use the diploid cotton resources toward map‐based cloning of leaf shape genes in Gossypium .}, number={3}, journal={CROP SCIENCE}, author={Kaur, Baljinder and Andres, Ryan and Kuraparthy, Vasu}, year={2016}, pages={1095–1105} }
 @article{bowman_bourland_kuraparthy_2016, title={Measuring maturity in cotton cultivar trials}, volume={20}, number={1}, journal={Journal of Cotton Science}, author={Bowman, D. T. and Bourland, F. and Kuraparthy, V.}, year={2016}, pages={40–45} }
 @article{andres_coneva_frank_tuttle_samayoa_han_kaur_zhu_fang_bowman_et al._2016, title={Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)}, volume={114}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1613593114}, DOI={10.1073/PNAS.1613593114}, abstractNote={Significance Leaves are the primary source of photoassimilate in crop plants. A precise understanding of the genetic architecture underlying leaf morphology is critical to engineering climate-resilient crop varieties. An ideal cotton cultivar would produce a lower canopy of broad, normal leaves before transitioning to an upper canopy of highly lobed, okra leaves. Here we show that the major leaf shapes of cotton are controlled by the okra locus, which encodes an HD-Zip transcription factor Gossypium hirsutum LATE MERISTEM IDENTITY1-D1b (GhLMI1-D1b). Using gene silencing, we temporarily induced normal leaf formation in okra, thus validating the candidate gene and creating the leaf shape ideotype in cotton. This study, identifying a single locus responsible for cotton leaf shape, expands the genetic toolbox for breeders to produce superior cotton varieties. Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.}, number={1}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Andres, Ryan J. and Coneva, Viktoriya and Frank, Margaret H. and Tuttle, John R. and Samayoa, Luis Fernando and Han, Sang-Won and Kaur, Baljinder and Zhu, Linglong and Fang, Hui and Bowman, Daryl T. and et al.}, year={2016}, month={Dec}, pages={E57–E66} }
 @article{hancock_kuraparthy_kernodle_lewis_2015, title={Identification of maternal haploids of Nicotiana tabacum aided by transgenic expression of green fluorescent protein: evidence for chromosome elimination in the N-tabacum x N-africana interspecific cross}, volume={35}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-015-0372-8}, number={9}, journal={MOLECULAR BREEDING}, author={Hancock, Wesley G. and Kuraparthy, Vasu and Kernodle, Sheri P. and Lewis, Ramsey S.}, year={2015}, month={Sep} }
 @misc{bowman_kuraparthy_2015, title={Vertical blocking in cotton cultivar performance trials in North Carolina}, volume={19}, number={2}, journal={Journal of Cotton Science}, author={Bowman, D. T. and Kuraparthy, V.}, year={2015}, pages={250–257} }
 @article{tyagi_bowman_bourland_edmisten_campbell_fraser_wallace_kuraparthy_2014, title={Components of hybrid vigor in upland cotton (Gossypium hirsutum L.) and their relationship with environment}, volume={195}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-013-0987-y}, number={1}, journal={EUPHYTICA}, author={Tyagi, Priyanka and Bowman, Daryl T. and Bourland, Fred M. and Edmisten, Keith and Campbell, B. Todd and Fraser, Dawn E. and Wallace, Ted and Kuraparthy, Vasu}, year={2014}, month={Jan}, pages={117–127} }
 @article{tyagi_gore_bowman_campbell_udall_kuraparthy_2014, title={Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)}, volume={127}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-013-2217-3}, abstractNote={Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.}, number={2}, journal={THEORETICAL AND APPLIED GENETICS}, author={Tyagi, Priyanka and Gore, Michael A. and Bowman, Daryl T. and Campbell, B. Todd and Udall, Joshua A. and Kuraparthy, Vasu}, year={2014}, month={Feb}, pages={283–295} }
 @article{andres_bowman_kaur_kuraparthy_2014, title={Mapping and genomic targeting of the major leaf shape gene (L) in Upland cotton (Gossypium hirsutum L.)}, volume={127}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-013-2208-4}, abstractNote={A major leaf shape locus (L) was mapped with molecular markers and genomically targeted to a small region in the D-genome of cotton. By using expression analysis and candidate gene mapping, two LMI1 -like genes are identified as possible candidates for leaf shape trait in cotton. Leaf shape in cotton is an important trait that influences yield, flowering rates, disease resistance, lint trash, and the efficacy of foliar chemical application. The leaves of okra leaf cotton display a significantly enhanced lobing pattern, as well as ectopic outgrowths along the lobe margins when compared with normal leaf cotton. These phenotypes are the hallmark characteristics of mutations in various known modifiers of leaf shape that culminate in the mis/over-expression of Class I KNOX genes. To better understand the molecular and genetic processes underlying leaf shape in cotton, a normal leaf accession (PI607650) was crossed to an okra leaf breeding line (NC05AZ21). An F2 population of 236 individuals confirmed the incompletely dominant single gene nature of the okra leaf shape trait in Gossypium hirsutum L. Molecular mapping with simple sequence repeat markers localized the leaf shape gene to 5.4 cM interval in the distal region of the short arm of chromosome 15. Orthologous mapping of the closely linked markers with the sequenced diploid D-genome (Gossypium raimondii) tentatively resolved the leaf shape locus to a small genomic region. RT-PCR-based expression analysis and candidate gene mapping indicated that the okra leaf shape gene (L (o) ) in cotton might be an upstream regulator of Class I KNOX genes. The linked molecular markers and delineated genomic region in the sequenced diploid D-genome will assist in the future high-resolution mapping and map-based cloning of the leaf shape gene in cotton.}, number={1}, journal={THEORETICAL AND APPLIED GENETICS}, author={Andres, Ryan J. and Bowman, Daryl T. and Kaur, Baljinder and Kuraparthy, Vasu}, year={2014}, month={Jan}, pages={167–177} }
 @article{zhu_kuraparthy_2014, title={Molecular genetic mapping of the major effect photoperiod response locus in Pima cotton (Gossypium barbadense L.)}, volume={54}, number={6}, journal={Crop Science}, author={Zhu, L. L. and Kuraparthy, V.}, year={2014}, pages={2492–2498} }
 @article{hutmacher_ulloa_wright_campbell_percy_wallace_myers_bourland_weaver_chee_et al._2013, title={Elite Upland Cotton Germplasm-Pool Assessment of Fusarium Wilt Resistance in California}, volume={105}, ISSN={["1435-0645"]}, DOI={10.2134/agronj2013.0264}, abstractNote={During the past 9 yr, a new race of Fusarium (Fusarium oxysporum f. sp. vasinfectum [FOV Race 4]) has increasingly impacted cotton (Gossypium spp.) in the San Joaquin Valley of California. To assess the vulnerability of upland cotton (G. hirsutum L.) in California to FOV disease, elite upland germplasm lines from 13 U.S. public breeding programs across the Cotton Belt and commercial cultivars were evaluated for disease resistance to FOV Races 1 and 4. Ten independent replicated field trials were conducted: three in 2008, four in 2010, and three in 2011. Significant differences (P ≤ 0.05) were observed for disease severity index of leaves, vascular root staining, and plant survival values among the elite germplasm lines in all 3 yr for the levels of resistance–response to FOV Races 1 and 4. Also, significant interactions among germplasm lines, FOV races (1 and 4), and evaluation sites indicated that germplasm lines differed in mechanisms of plant‐defense response for the two FOV races. Selected lines from programs in the states of Alabama, Arkansas, Louisiana, and Mississippi showed at least a moderate level of tolerance to both FOV races; however, several of these lines produced weak and coarse fibers. Based on these evaluations, many of the entries in public breeders’ current elite upland germplasm pools may be more susceptible than expected to some FOV races, and sources of acceptable levels of resistance may be limited when tested under infestation levels that resulted in only 5 to 35% plant survival in susceptible check cultivars.}, number={6}, journal={AGRONOMY JOURNAL}, author={Hutmacher, Robert B. and Ulloa, Mauricio and Wright, Steven D. and Campbell, B. Todd and Percy, Richard and Wallace, Ted and Myers, Gerald and Bourland, Fred and Weaver, David and Chee, Peng and et al.}, year={2013}, pages={1635–1644} }
 @article{kuraparthy_bowman_jones_2013, title={Registration of NC05AZ21 Okra-Leaf and NC05-11 Normal-Leaf Upland Cotton Germplasms}, volume={7}, ISSN={["1936-5209"]}, DOI={10.3198/jpr2013.03.0011crg}, abstractNote={NC05AZ21 (Reg. No. GP‐966, PI 667659) is an okra‐leaf line and NC05‐11 (Reg. No., GP‐965, PI 667658) is a normal‐leaf line of Upland cotton (Gossypium hirsutum L.). NC05AZ21 was developed from a cross of NC 72 and an unknown okra leaf, red stem line from Louisiana while NC05‐11 was developed from a cross of NC 72 and Fiber Max 989 (FM 989). NC 72 is a normal and smooth leaf line. FM 989 is a commercial, normal‐leaf cultivar. A pedigree breeding method was followed in developing these lines. Both lines were compared with two commercial cultivars across multiple environments for agronomic traits. Line NC05AZ21 was also compared with a commercial okra‐leaf cultivar FM 832 for agronomic performance. NC05AZ21 showed superior lint yield and lint percentage to and comparable fiber length as FM 832. It had a lower lint yield but longer fibers than Deltapine 455BG/RR (DP 455BG/RR) and Stoneville 5327B2RF (ST 5327B2RF) and comparable fiber strength. It has good resistance to Fusarium wilt [caused by Fusarium oxysporum Schlet.f.sp. vasinfectum (Atk.) Snyd. &Hans.] as well. It could be a good source of earliness and Fusarium wilt resistance and perhaps tolerance to boll rot (caused by numerous organisms)—the latter because of its okra‐leaf shape. NC05‐11 had comparable lint yields as DP 451BG/RR and DP 455BG/RR with superior fiber length and strength. It also had good resistance to Fusarium wilt. Both NC05AZ21 and NC05‐11 could prove to be valuable sources of additional genetic variability for cotton breeding programs having an emphasis on improving Fusarium wilt resistance and fiber quality.}, number={3}, journal={JOURNAL OF PLANT REGISTRATIONS}, author={Kuraparthy, Vasu and Bowman, Daryl T. and Jones, Don C.}, year={2013}, month={Sep}, pages={334–338} }
 @article{kuraparthy_sood_guedira_gill_2011, title={Development of a PCR assay and marker-assisted transfer of leaf rust resistance gene Lr58 into adapted winter wheats}, volume={180}, ISSN={["1573-5060"]}, DOI={10.1007/s10681-011-0383-4}, abstractNote={Leaf rust resistance gene Lr58 derived from Aegilops triuncialis L. was transferred to the hard red winter wheat (HRWW) cultivars Jagger and Overley by standard backcrossing and marker-assisted selection (MAS). A co-dominant PCR-based sequence tagged site (STS) marker was developed based on the sequence information of the RFLP marker (XksuH16) diagnostically detecting the alien segment in T2BS·2BL-2tL(0.95). STS marker Xncw-Lr58-1 was used to select backcross F1 plants with rust resistance. The co-dominant marker polymorphism detected by primer pair NCW-Lr58-1 efficiently identified the homozygous BC3F2 plants with rust resistance gene Lr58. The STS marker Xncw-Lr58-1 showed consistent diagnostic polymorphism between the resistant source and the wheat cultivars selected by the US Wheat Coordinated Agricultural Project. The utility and compatibility of the STS marker in MAS programs involving robust genotyping platforms was demonstrated in both agarose-based and capillary-based platforms. Screening backcross derivatives carrying Lr58 with various rust races at seedling stage suggested the transferred rust resistance in adapted winter wheats is stable in both cultivar backgrounds. Lr58 in adapted winter wheat backgrounds could be used in combination with other resistance genes in wheat rust resistance breeding.}, number={2}, journal={EUPHYTICA}, author={Kuraparthy, Vasu and Sood, Shilpa and Guedira, Gina-Brown and Gill, Bikram S.}, year={2011}, month={Jul}, pages={227–234} }
 @article{kuraparthy_sood_gill_2009, title={Molecular genetic description of the cryptic wheat-Aegilops geniculata introgression carrying rust resistance genes Lr57 and Yr40 using wheat ESTs and synteny with rice}, volume={52}, ISSN={["1480-3321"]}, DOI={10.1139/G09-076}, abstractNote={The cryptic wheat–alien translocation T5DL·5DS-5MgS(0.95), with leaf rust and stripe rust resistance genes Lr57 and Yr40 transferred from Aegilops geniculata (UgMg) into common wheat, was further analyzed. Molecular genetic analysis using physically mapped ESTs showed that the alien segment in T5DL·5DS-5MgS(0.95) represented only a fraction of the wheat deletion bin 5DS2-0.78-1.00 and was less than 3.3 cM in length in the diploid wheat genetic map. Comparative genomic analysis indicated a high level of colinearity between the distal region of the long arm of chromosome 12 of rice and the genomic region spanning the Lr57 and Yr40 genes in wheat. The alien segment with genes Lr57 and Yr40 corresponds to fewer than four overlapping BAC or PAC clones of the syntenic rice chromosome arm 12L. The wheat–alien translocation breakpoint in T5DL·5DS-5MgS(0.95) was further localized to a single BAC clone of the syntenic rice genomic sequence. The small size of the terminal wheat–alien translocation, as established precisely with respect to Chinese Spring deletion bins and the syntenic rice genomic sequence, further confirmed the escaping nature of cryptic wheat–alien translocations in introgressive breeding. The molecular genetic resources and information developed in the present study will facilitate further fine-scale physical mapping and map-based cloning of the Lr57 and Yr40 genes.}, number={12}, journal={GENOME}, author={Kuraparthy, Vasu and Sood, Shilpa and Gill, Bikram S.}, year={2009}, month={Dec}, pages={1025–1036} }
 @article{sood_kuraparthy_bai_gill_2009, title={The major threshability genes soft glume (sog) and tenacious glume (Tg), of diploid and polyploid wheat, trace their origin to independent mutations at non-orthologous loci}, volume={119}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-009-1043-0}, abstractNote={Threshability is an important crop domestication trait. The wild wheat progenitors have tough glumes enveloping the floret that make spikes difficult to thresh, whereas cultivated wheats have soft glumes and are free-threshing. In hexaploid wheat, the glume tenacity gene Tg along with the major domestication locus Q control threshability. The Q gene was isolated recently and found to be a member of the AP2 class of transcription factors. However, only a few studies have reported on the tough glume trait. Here, we report comparative mapping of the soft glume (sog) gene of diploid Triticum monococcum L. and tenacious glume (Tg) gene of hexaploid T. aestivum L. using chromosome-specific SSR and RFLP markers. The sog gene was flanked by Xgwm71 and Xbcd120 in a 6.8 cM interval on chromosome 2A(m)S of T. monococcum whereas Tg was targeted to a 8.1 cM interval flanked by Xwmc503 and Xfba88 on chromosome 2DS of T. aestivum. Deletion bin mapping of the flanking markers assigned sog close to the centromere on 2AS, whereas Tg was mapped to the most distal region on 2DS. Both 2AS and 2DS maps were colinear ruling out the role of chromosome rearrangements for their non-syntenic positions. Therefore, sog and Tg are not true orthologues suggesting the possibility of a diverse origin.}, number={2}, journal={THEORETICAL AND APPLIED GENETICS}, author={Sood, Shilpa and Kuraparthy, Vasu and Bai, Guihua and Gill, Bikram S.}, year={2009}, month={Jul}, pages={341–351} }
 @article{gill_huang_kuraparthy_raupp_wilson_friebe_2008, title={Alien genetic resources for wheat leaf rust resistance, cytogenetic transfer, and molecular analysis}, volume={59}, ISSN={0004-9409}, url={http://dx.doi.org/10.1071/AR07315}, DOI={10.1071/AR07315}, abstractNote={Wild relatives of wheat are useful sources of alien resistance genes for wheat breeding. The objective of this review is to document research on the evaluation, transfer, and molecular analysis of alien resistance to wheat leaf rust especially in Aegilops tauschii, the diploid D-genome donor of common wheat. Nine named resistance genes (Lr1, Lr2, Lr15, Lr21, Lr22, Lr32, Lr34, Lr39, and Lr42) occur in the D genome. Twelve new leaf rust resistance genes have been documented in Ae. tauschii. The south-west Caspian Sea region is the centre of genetic diversity for seedling resistance. Adult-plant resistance is widespread in all geographic regions and should be exploited more in the future. Lr1 and Lr21 have been cloned and are typical NBS-LRR genes. The recent documentation of cryptic introgressions of Lr57/Yr40 from Ae. geniculata and Lr58 from Ae. triuncialis offers exciting possibilities for transferring alien genes without linkage drag. Both Lr21 and Lr34 presumably arose during or following the origin of common wheat ~8000 years ago. Leaf rust resistance genes often are located towards the physical ends of wheat chromosomes. These regions are known to be high in recombination, and this may explain their rapid rate of evolution.}, number={3}, journal={Australian Journal of Agricultural Research}, publisher={CSIRO Publishing}, author={Gill, B. S. and Huang, L. and Kuraparthy, V. and Raupp, W. J. and Wilson, D. L. and Friebe, B.}, year={2008}, pages={197} }
 @article{kuraparthy_sood_gill_2008, title={Genomic targeting and mapping of tiller inhibition gene (tin3) of wheat using ESTs and synteny with rice}, volume={8}, ISSN={1438-793X 1438-7948}, url={http://dx.doi.org/10.1007/S10142-007-0057-4}, DOI={10.1007/S10142-007-0057-4}, abstractNote={Changes in plant architecture have been central to the domestication of wild species. Tillering or the degree of branching determines shoot architecture and is a key component of grain yield and/or biomass. Previously, a tiller inhibition mutant with monoculm phenotype was isolated and the mutant gene (tin3) was mapped in the distal region of chromosome arm 3AmL of Triticum monococcum. As a first step towards isolating a candidate gene for tin3, the gene was mapped in relation to physically mapped expressed sequence tags (ESTs) and sequence tag site (STS) markers developed based on synteny with rice. In addition, we investigated the relationship of the wheat region containing tin3 with the corresponding region in rice by comparative genomic analysis. Wheat ESTs that had been previously mapped to deletion bins provided a useful framework to identify closely related rice sequences and to establish the most likely syntenous region in rice for the wheat tin3 region. The tin3 gene was mapped to a 324-kb region spanned by two overlapping bacterial artificial chromosomes (BACs) of rice chromosome arm 1L. Wheat-rice synteny was exceptionally high at the tin3 region despite being located in the high-recombination, gene-rich region of wheat. Identification of tightly linked flanking EST and STS markers to the tin3 gene and its localization to highly syntenic rice BACs will assist in the future development of a high-resolution map and map-based cloning of the tin3 gene.}, number={1}, journal={Functional & Integrative Genomics}, publisher={Springer Science and Business Media LLC}, author={Kuraparthy, Vasu and Sood, Shilpa and Gill, Bikram S.}, year={2008}, month={Feb}, pages={33–42} }
 @article{kuraparthy_chhuneja_dhaliwal_kaur_bowden_gill_2007, title={Characterization and mapping of cryptic alien introgression from Aegilops geniculata with new leaf rust and stripe rust resistance genes Lr57 and Yr40 in wheat}, volume={114}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/S00122-007-0524-2}, DOI={10.1007/S00122-007-0524-2}, abstractNote={Leaf rust and stripe rust are important foliar diseases of wheat worldwide. Leaf rust and stripe rust resistant introgression lines were developed by induced homoeologous chromosome pairing between wheat chromosome 5D and 5M(g) of Aegilops geniculata (U(g)M(g)). Characterization of rust resistant BC(2)F(5) and BC(3)F(6) homozygous progenies using genomic in situ hybridization with Aegilops comosa (M) DNA as probe identified three different types of introgressions; two cytologically visible and one invisible (termed cryptic alien introgression). All three types of introgression lines showed similar and complete resistance to the most prevalent pathotypes of leaf rust and stripe rust in Kansas (USA) and Punjab (India). Diagnostic polymorphisms between the alien segment and recipient parent were identified using physically mapped RFLP probes. Molecular mapping revealed that cryptic alien introgression conferring resistance to leaf rust and stripe rust comprised less than 5% of the 5DS arm and was designated T5DL.5DS-5M(g)S(0.95). Genetic mapping with an F(2)population of Wichita x T5DL.5DS-5M(g)S(0.95) demonstrated the monogenic and dominant inheritance of resistance to both diseases. Two diagnostic RFLP markers, previously mapped on chromosome arm 5DS, co-segregated with the rust resistance in the F(2) population. The unique map location of the resistant introgression on chromosome T5DL.5DS-5M(g)S(0.95) suggested that the leaf rust and stripe rust resistance genes were new and were designated Lr57 and Yr40. This is the first documentation of a successful transfer and characterization of cryptic alien introgression from Ae. geniculata conferring resistance to both leaf rust and stripe rust in wheat.}, number={8}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Kuraparthy, Vasu and Chhuneja, Parveen and Dhaliwal, Harcharan S. and Kaur, Satinder and Bowden, Robert L. and Gill, Bikram S.}, year={2007}, month={Mar}, pages={1379–1389} }
 @article{kuraparthy_sood_dhaliwal_chhuneja_gill_2006, title={Identification and mapping of a tiller inhibition gene (tin3) in wheat}, volume={114}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/S00122-006-0431-Y}, DOI={10.1007/S00122-006-0431-Y}, abstractNote={Tillering is one of the most important agronomic traits in cereal crops because tiller number per plant determines the number of spikes or panicles per plant, a key component of grain yield and/or biomass. In order to characterize the underlying genetic variation for tillering, we have isolated mutants that are compromised in tillering ability using ethyl methanesulphonate (EMS)-based mutagenesis in diploid wheat (Triticum monococcum subsp. monococcum). The tillering mutant, tiller inhibition (tin3) produces only one main culm compared to the wild type with many tillers. The monoculm phenotype of tin3 is due to a single recessive mutation. Genetic and molecular mapping in an F(2) population of diploid wheat located the tin3 gene on the long arm of chromosome 3A(m). One codominant RFLP marker Xpsr1205 cosegregated with tin3 in the F(2) population. Physical mapping of PSR1205 in a set of Chinese Spring deletion lines of group-3 chromosomes placed the tin3 gene in the distal 10% of the long arm of chromosome 3A, which is a recombination-rich region in wheat. The implications of the mapping of tin3 on chromosome arm 3A(m)L are discussed with respect to putative orthologs of tin3 in the 3L colinear regions across various cereal genomes and other tillering traits in grasses.}, number={2}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Kuraparthy, Vasu and Sood, Shilpa and Dhaliwal, H. S. and Chhuneja, Parveen and Gill, Bikram S.}, year={2006}, month={Nov}, pages={285–294} }