Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections.

Hongde Qin,Youlu Yuan,Xianda Yi,Cheng Zhang,Jiayang Lan,Youchang Zhang,Yanyan Meng,Min Chen,Chunhai Jiao,Shu Bie,David D Fang

doi:10.1371/journal.pone.0118073

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.

Highlights

Cotton is an important industrial crop in China
Zhao et al [22] carried out association mapping based on Verticillium Wilt Resistance using a collection of 329 cotton (G. hirsutum L.) accessions obtained from a Chinese cotton germplasm collection
All of the collections were derived from four sources: 1 elite varieties popularly cultivated in China; 2 germplasm resource lines with outstanding yield components or fiber qualities; 3 parental lines that are typically used in breeding programs; and 4 historical varieties and germplasm resources lines from abroad, including 20 collections from the US, 6 from the Uzbek, 6 from the Sudan, one from Australia and one from Cuba (S1 Table)

Summary

Introduction

Cotton is an important industrial crop in China. Many cotton breeders have focused on detecting and using marker-associated quantitative trait loci (QTLs) for marker-assisted selection. Most QTLs and linkage markers detected based on these interspecies populations are difficult to directly utilize for MAS because the Upland cotton varieties or lines are major material resources in breeding programs. Zhao et al [22] carried out association mapping based on Verticillium Wilt Resistance using a collection of 329 cotton (G. hirsutum L.) accessions obtained from a Chinese cotton germplasm collection The results of these studies indicated the feasibility of applying association analysis to explore complex traits in Upland cotton collections in China. To better understand the genetic foundation of the yield and fiber quality traits at the population level and identify associated SSR markers, we performed whole-genome association analyses using 359 SSR polymorphism markers well distributed in reference maps [23, 24] and a panel of 241 varieties and germplasm resource lines in the present study

Materials and Methods

Results

Discussion