Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China

Abstract

BackgroundSince upland cotton was introduced into China during the 1920s–1950s, hundreds of inbreed cultivars have been developed. To explore the molecular diversity, population structure and elite alleles, 503 inbred cultivars developed in China and some foreign cultivars from the United States and the Soviet Union were collected and analyzed by 494 genome-wide SSRs (Simple Sequence Repeats).MethodsFour hundred and ninety-four pairs of SSRs with high polymorphism and uniform distribution on 26 chromosomes were used to scan polymorphisms in 503 nation-wide upland cottons. The programming language R was used to make boxplots for the phenotypic traits in different environments. Molecular marker data and 6 fiber quality traits were analyzed by the method of MLM (mixed linear model) (P + G + Q + K) in the TASSEL software package on the basis of the population structure and linkage disequilibrium analysis. The loci of elite allelic variation and typical materials carrying elite alleles were identified based on phenotypic effect values.ResultsA total of 179 markers were polymorphic and generated 426 allele loci; the population based on molecular diversity was classified into seven subpopulations corresponding to pedigree origin, ecological and geographical distribution. The attenuation distance of linkage disequilibrium dropped significantly up to 0–5 cM. Association mapping for fiber quality showed that 216 marker loci were associated with fiber quality traits (P < 0.05) explaining 0.58 % ~ 5.12 % of the phenotypic variation, with an average of 2.70 %. Thirteen marker loci were coincident with other studies, and three were detected for the same trait. Seven quantitative trait loci were related to known genes in fiber development. Based on phenotypic effects, 48 typical materials that contained the elite allele loci related to fiber quality traits were identified and are widely used in practical breeding.ConclusionsThe molecular diversity and population structure of 503 nation-wide upland cottons in China were evaluated by 494 genome-wide SSRs, and association mapping for fiber quality revealed known and novel elite alleles. The molecular diversity provides a guide for parental mating in cotton breeding, and the association mapping results will aid in the fine-mapping genes related to fiber quality traits and facilitate further studies on candidate genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2662-x) contains supplementary material, which is available to authorized users.

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

“…In previous studies, a large number of association analyses of fiber quality traits and SSR markers in upland cotton have been reported13143637. However, these studies were limited by the number of the polymorphic SSR markers and the size of the natural populations.…”

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

“…In cotton, a few genetic studies using GWAS have been reported [2, 4, 23, 24]. Very recently another two GWAS papers in cotton have been published [25, 26]. All of those studies were based on using simple sequence repeat (SSR) markers.…”

“…Although scientists have successfully identified marker-trait associations using GBS-based SNPs in many plant species [14, 21, 28, 29], so far no GWAS study has been reported in Upland cotton using SNPs. There are a few GWAS studies that were reported using SSR markers in Upland cotton [2, 4, 23, 24, 26, 30] as mentioned earlier. Among those reports, our laboratory previously identified 131 fiber QTL and 37 QTL clusters using 1582 SSR markers and 275 RILs of the same MAGIC population [4].…”

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

“…The fast development of molecular maker technology has made it possible to map QTL for fiber quality and yield traits and to aggregate excellent genes controlling cotton yield and fiber quality using marker-assisted selection (MAS). The genome of upland cotton is complex and large [21], and the genetic background of upland cotton is narrow [22]. These reasons hinder the development of QTL mapping in upland cotton.…”