|Abdullaev, Alisher - UZBEKISTAN ACADEMY OF SCIENCES|
|Salakhutdinov, Ilkhom - UZBEKISTAN ACADEMY OF SCIENCES|
|Egamberdiev, Sharof - UZBEKISTAN ACADEMY OF SCIENCES|
|Khurshut, Ernest - UZBEKISTAN ACADEMY OF SCIENCES|
|Rizaeva, Sofiya - UZBEKISTAN ACADEMY OF SCIENCES|
|Abdurakhmonov, Ibrokhim - UZBEKISTAN ACADEMY OF SCIENCES|
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2017
Publication Date: 11/14/2017
Citation: Abdullaev, A.A., Salakhutdinov, I.B., Egamberdiev, S.S., Khurshut, E.E., Rizaeva, S.M., Ulloa, M., Abdurakhmonov, I.Y. 2017. Genetic diversity, linkage disequilibrium, and association mapping analyses of gossypium barbadense l. germplasm and cultivars. PLoS One. 12(11):1-30. doi:10.1371/pone.0188125.
Interpretive Summary: Cultivated cotton is the most important natural fiber worldwide. Fiber quality is a key factor for determining price and quality of cotton textile products. Genetic improvement of fiber quality is a challenge due to the narrow genetic base of modern cotton cultivars and the effect of the environment on fiber quality. The narrow genetic base is due to the use of a few elite cotton lines to develop progeny also known as a genetic bottleneck through historic domestication. This narrow genetic base and the breeding challenges of cotton highlight a great need to study genetic resources preserved and maintained in world cotton germplasm collections, and the use of these resources in breeding of superior cotton cultivars. In this study, 288 worldwide Gossypium barbadense L. also known as Sea Island, Egyptian, or extra-long staple (ELS) cotton germplasm and cultivars were evaluated in two diverse environments, Uzbekistan and the USA. Molecular and fiber trait (strength, length, etc.) analyses in the two diverse environments provide insights into the breeding history and genetic relationship of G. barbadense germplasm and cultivars. Molecular markers were associated with fiber quality traits and these markers were found to be consistent with previous fiber trait-associations. Results from this study should also be helpful for improvement of cotton cultivars using a molecular breeding approach.
Technical Abstract: Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 = 0.1 and r2 = 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 = 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 = 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.