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.

The objective of this study was to investigate the genetic diversity of hexaploid wheat varieties of Uzbekistan breeding using simple sequence repeat (SSR) markers. These varieties are adapted to local conditions, and can be considered as the most important supplier of genetic resources for cultivation in Uzbekistan and other countries. Microsatellite markers are now most widely used and effective classes of DNA markers for genotyping, certification and classification of plant varieties. In this paper, genotyping results of 32 hexaploid wheat domestic varieties using 144 microsatellite primer pairs are presented. Microsatellite primer pairs were chosen from literature data and 36 primer pairs (from 144) gave polymorphic well-reproducible PCR-fragments. The individual SSR spectra differing in number of amplicons were obtained for each variety. A total number of 141 alleles for 36 microsatellite loci were detected. The number of alleles per locus ranged from 2 to 6, the mean number of alleles per locus (Na) was 3 alleles. For the studied genotypes group the effective number of alleles (ne) characterizing the loci by the allele frequency, varied from 1.7 to 4.8, the mean number of alleles per locus was 2.8. The expected heterozygosity (He) ranged from 0 to 0.792, averaging 0.626, in studied wheat population. The amplified fragment sizes ranged from 93 to 552 bp. The polymorphic index content (PIC) ranged from 0 to 0.758. A dendrogram was constructed using the alleles set of microsatellite loci, reflecting the phylogenetic differences of the studied hexaploid wheat varieties. It showed that Uzbekistan breeding varieties are divided into two main clusters, which may be evidence of their common origin.  A genetic formula has been developed for each Uzbek wheat variety. It can be used for identification, certification of these varieties, as well as for the selection of parental pairs in the wheat breeding programs.

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