Vasu Kuraparthy

Traditional breeding methods used to develop improved cotton varieties involve painstaking parental selection, developing breeding populations, extensive field evaluations all of which takes more than 8-12 years. However, given the expensive and time-consuming nature of the inbred line development and multi-environment trials, there is a clear need to integrate genomic technologies that can accelerate breeding for yield, fiber quality and other productivity traits in cotton. Specifically, genomic selection (GS), a genomics-based selection strategy in which the genomic-estimated breeding values obtained from genome-wide molecular markers are used for the selection of individuals has gained burgeoning interest in recent years and is advocated as an approach that can dramatically accelerate genetic gains and cultivar development. The objectives of this project are to: 1) Genotype the germplasm and cultivars from the major public cotton breeding program (Dr. Fred Bourland, University of Arkansas, AR). 2) Estimate the population structure, genetic diversity and linkage disequilibrium in this collection. 3) Estimate the genomic estimated breeding values (GEBVs) in this panel as a training set. 4) Genotype and phenotype the validation set comprised of current advanced breeding lines and biparental populations. 5) Develop genomic selection models and asses the accuracy of genomic prediction for fiber quality and yield in cotton.

Stand establishment and early vigor are critical for successful cotton production. In shorter season environments, cotton producers have to balance the risks associated with suboptimal temperatures for seedling growth and development when planting in a shorter window compared to other environments to meet crop insurance deadlines, and to avoid the increased likelihood of low temperatures during boll maturation in the fall. Planting cotton cultivars with ideal stand establishment and more vigorous early-season growth would alleviate some of the challenges associated with slow growth after planting. Further, rapid early growth could provide significant advantages to young plants relative to diseases, insects, weeds, herbicide injury, and abiotic stresses. Studies indicated seed vigor (determining germinability/stand establishment) and seedling vigor (early-season crop growth) are associated with seed quality. Although recent studies improved our understanding of seedling vigor, it is difficult and time-consuming to develop cotton cultivars with ideal seed and seedling vigor through conventional breeding. Identifying genomic regions controlling seed size, composition, and seed and seedling vigor would enable breeders to develop cultivars through marker-assisted selection, leading to increased breeding efficiency and accuracy for selection. The objectives of this project are: 1) Evaluate the elite Upland cotton diversity panel for genetic variation in seed traits (seed size and composition) and seed and seedling vigor traits. 2) Determine the relationship between seed traits, stand establishment and seedling vigor in broad diversity of cotton genotypes. 3) Identify DNA-based molecular markers for seed size, seed composition, and seed and seedling vigor through genome-wide association studies using diversity panel and single nucleotide polymorphism (SNP) makers. 4) Validate the SNP marker-trait associations for seed traits and seed vigor in bi-parental segregating mapping populations. 4) Convert and validate the associated SNP markers into easily assayable Kompetitive Allele Specific PCR (KASP) markers.

Objectives of Research are to: (1) Develop cotton germplasm with resistance to thrips; and (2) Develop cotton germplasm with resistance to bacterial leaf blight (BLB) disease.

Understanding the genetic basis of complex traits is vital for meeting the challenge of increased fiber quality and yield in this period of global climate change. Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for detection and fine mapping of Quantitative Trait Loci (QTL) underlying complex traits. Our research will support the construction of the largest immortal mapping population in cotton, which will ultimately help to bridge genomics and plant breeding through the dissection of complex traits and laying the foundation for genome-wide selection in breeding programs.

Before the general adoption of acid delinting of cotton planting seed, bacterial blight (BB) was one of the most common diseases of Upland cotton. But the disease had been largely absent for almost 20 years before an outbreak in the north Delta in 2011. Since that time, the occurrence of BB has been problematic each year. Host plant resistance would be the most economic means of managing this disease. The host differential panel originally used to develop resistance is not readily available; however a nested association marker (NAM) population representing the great majority of accessible diversity in Upland cotton in now available, and could be used for the purpose of identifying and developing markers for resistance to BB.

1. Develop linkage and association mapping populations that enable fine-mapping and cloning of photoperiod response and earliness per se genes. 2. Fine-mapping and cloning of a major photoperiod response locus in G. barbadense. Candidate gene validation of Gb_Ppd1 gene using mutagenesis and/or VIGS in pima cotton. 3. Association analysis of candidate genes of Gb_Ppd1 gene using SNP markers on a panel of photoperiod sensitive and insensitive G. barbadesnse accessions. 4. Develop isogenic lines of orthologous Gb-Ppd1 gene region in G. darwinii background using marker-assisted backcrossing.

1. Develop and screen the cotton germplasm for earliness. 2. Develop cotton germplasm with improved yield and fiber quality through conventional breeding.

Before the general adoption of acid delinting of cotton planting seed, Bacterial Blight (BB) was one of the most common diseases of Upland cotton. But the disease had been largely absent for almost 20 years before an outbreak in the north Delta in 2011. Since that time, the occurrence of BB has been worse each year. Host plant resistance would be the most economic means of managing this disease. The host differential panel originally used to develop resistance is not readily available; however a nested association marker (NAM) population representing the great majority of accessible diversity in Upland cotton in now available, and could be used for the purpose of identifying and developing markers for resistance to BB.

Construct a cotton NAM population of 6,000 F5 recombinant inbred lines 2) Survey the population structure and level of linkage disequilibrium (LD) in US Upland cotton, and 3) Conduct a Genome Wide Association Study (GWAS) for identifying QTLs associated with lint yield, fiber quality and other agronomic traits.

OBJECTIVES OF THIS RESEARCH ARE: 1. Screening and developing cotton germplasm for thrips tolerance 2. Mapping and developing linked molecular markers for thrips tolerance 3. Marker assisted transfer of thrips tolerance to adapted cotton germplasm lines