Detection of favorable alleles for yield and yield components by association mapping in upland cotton

Abstract

Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(- lgP > 1.30, P < 0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci's alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.

Genetic structure, gene flow pattern, and association analysis of superior germplasm resources in domesticated upland cotton (Gossypium hirsutum L.)

“…In addition, SSR markers NAU4951, NAU5013, NAU5195, NAU5148, NAU5260, NAU5088, and NAU5017 were mainly associated with yield quality traits, including HF, NB, SB, PH, LP. These identified associations for different fiber and yield quality traits in domesticated upland cotton, along with those reported in previous studies, add toa rich cluster of yield and fiber quality QTLs ( Cai et al., 2014 , Adhikari et al., 2017 , Ademe et al., 2017 , Dong et al., 2018a , Dong et al., 2018b ).…”

“…The major target traits of cotton during the breeding process are quantitative; thus, phenotypic variation of each trait is directly or indirectly affected by that of other traits ( Huang et al., 2018 , Keerio et al., 2018 , Wen et al., 2018 ). Numerous QTL mapping studies aimed at improving cotton fiber quality and yield traits have been previously reported ( Mei et al., 2013 , Adhikari et al., 2017 , Wang et al., 2017a , Wang et al., 2017b , Dong et al., 2018a , Dong et al., 2018b ). In this study, a total of 16 SSR markers for yield and fiber quality traits were detected.…”

Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

“…These genes are all located in chromosomal regions, which show a strong association with important agronomic traits and they can thus be considered as suitable target genes for future breeding programs. We calculated the phenotypic effect of favorable alleles, as described by Dong et al [59] to show that they affected grain yield only slightly but had much larger effect on thousand kernel weight, spike length and leaf greenness. On the other hand, alleles that contribute to an improvement in thousand kernel weight and leaf greenness also have pleiotropic effects thereby decreasing plant height, peduncle length and canopy temperature under stressful conditions.…”

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

“…Recent years, association mapping as an important method for the identi cation of complex quantitative traits has been widely used in cotton for various traits including salt tolerance [35][36][37][38][39][40]. Jia et al [21] identi ed 3 simple sequence repeats (SSR) markers signi cantly associated with the relative survival rate under salt stress through association mapping methods using 323 G. hirsutum germplasms.…”