Identification of Associated SSR Markers for Yield Component and Fiber Quality Traits Based on Frame Map and Upland Cotton Collections

Abstract

Detecting QTLs (quantitative trait loci) that enhance cotton yield and fiber quality traits and accelerate breeding has been the focus of many cotton breeders. In the present study, 359 SSR (simple sequence repeat) markers were used for the association mapping of 241 Upland cotton collections. A total of 333 markers, representing 733 polymorphic loci, were detected. The average linkage disequilibrium (LD) decay distances were 8.58 cM (r2 > 0.1) and 5.76 cM (r2 > 0.2). 241 collections were arranged into two subgroups using STRUCTURE software. Mixed linear modeling (MLM) methods (with population structure (Q) and relative kinship matrix (K)) were applied to analyze four phenotypic datasets obtained from four environments (two different locations and two years). Forty-six markers associated with the number of bolls per plant (NB), boll weight (BW), lint percentage (LP), fiber length (FL), fiber strength (FS) and fiber micornaire value (FM) were repeatedly detected in at least two environments. Of 46 associated markers, 32 were identified as new association markers, and 14 had been previously reported in the literature. Nine association markers were near QTLs (at a distance of less than 1–2 LD decay on the reference map) that had been previously described. These results provide new useful markers for marker-assisted selection in breeding programs and new insights for understanding the genetic basis of Upland cotton yields and fiber quality traits at the whole-genome level.

Linkage disequilibrium and association mapping of fibre quality traits in elite Asiatic cotton (Gossypium arboreum) germplasm populations

“…Similar observations were also made by Qin et al (2015). In the present study, except 3 associations (BNL-1440 with micronaire, BNL 3992 with micronaire and NAU-2363 with uniformity ratio), the remaining 29 associations of MLM were also detected by GLM.…”

Identification of QTL for Fiber Quality and Yield Traits Using Two Immortalized Backcross Populations in Upland Cotton

“…Additionally, qFS-c7 was also verified in F 2 and RIL populations [46]. qFS-c13-1 and qFS-c13-2 were detected in an RIL population [44] and a natural population [47], respectively. The stable QTL qFE-c22 was also confirmed as qELO-c22 in the previous study [45].…”

Assessment of Genetic Diversity, Population Structure, and Evolutionary Relationship of Uncharacterized Genes in a Novel Germplasm Collection of Diploid and Allotetraploid Gossypium Accessions Using EST and Genomic SSR Markers

“…However, other studies showed a variable allele number per locus. For example, 2.13, 2.20, 5.46, and 7.64 alleles per marker have been found in several genetic diversity assessments for the cotton germplasm [26,59,60,61]. The semi-wild accessions retaining a diverse germplasm showed high allele numbers in the majority of studies consistent with a recent study because these accessions have not yet been exposed to extensive human selection pressure for accumulating a particular type of alleles [26,62,63].…”