@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{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{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{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{sanchez g_cruz l_vidal m_ron p_taba_santacruz-ruvalcaba_sood_holland_ruiz c_carvajal_et al._2011, title={THREE NEW TEOSINTES (ZEA SPP., POACEAE) FROM MEXICO}, volume={98}, ISSN={["1537-2197"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84857141107&partnerID=MN8TOARS}, DOI={10.3732/ajb.1100193}, abstractNote={•Premise of the study:Teosinte species are the closest relatives of maize and represent an important but increasingly rare genetic resource for maize improvement and the study of evolution by domestication. Three morphologically and ecologically distinct teosinte populations were recently discovered in México. The taxonomic status of these rare and endangered populations was investigated by detailed comparisons to previously characterized wildZeaspecies.•Methods:Three new teosinte populations were compared to known teosinte taxa on the basis of morphological, ecogeographic, cytological, and molecular characteristics. Phenetic and phylogenetic analyses were performed using morphological and molecular data, respectively.•Key results:The newly discovered populations are distinct from each other and from otherZeaspecies to represent three new entities based on their unique combinations of morphological, ecological, ploidy, and DNA markers. A perennial diploid population from Nayarit is distinguished by early maturing plants, and having male inflorescences with few tassel branches and long spikelets. A perennial tetraploid population from Michoacán is characterized by tall and late maturing plants, and having male inflorescences with many branches. An annual diploid population from Oaxaca is characterized by having male inflorescences with fewer branches and longer spikelets than those found in the sister taxaZ. luxuriansandZ. nicaraguensis, plants with high thermal requirements, and very long seed dormancy.•Conclusions:Evidence from multiple independent sources suggests placement of the three new populations of teosinte as distinct entities within sectionLuxuriantesof the genusZea. However, more extensive DNA marker or sequence data are required to resolve the taxonomy of this genus.}, number={9}, journal={AMERICAN JOURNAL OF BOTANY}, author={Sanchez G, J. J. and Cruz L, L. De and Vidal M, V. A. and Ron P, J. and Taba, S. and Santacruz-Ruvalcaba, F. and Sood, S. and Holland, J. B. and Ruiz C, J. A. and Carvajal, S. and et al.}, year={2011}, month={Sep}, pages={1537–1548} }