Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.)
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Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China. Three subpopulations were found after the estimation of population structure. The pair-wise kinship values varied from 0 to 0.867. Only 1.59% of the total marker locus pairs showed significant linkage disequilibrium (LD, p < 0.001). The genome-wide LD decayed within the genetic distance of ~30 to 32 cM at r 2 = 0.1, and decreased to ~1 to 2 cM at r 2 = 0.2, indicating the potential for association mapping. Analysis based on a mixed linear model detected 57 significant (p < 0.01) marker–trait associations, including seven associations for fiber length, ten for fiber micronaire, nine for fiber strength, eight for fiber elongation, five for fiber uniformity index, five for fiber uniformity ratio, six for boll weight and seven for lint percent, for a total of 35 SSR markers, of which 11 markers were associated with more than one trait. Among marker–trait associations, 24 associations coincided with the previously reported quantitative trait loci (QTLs), the remainder were newly identified QTLs/genes. The QTLs identified in this study will potentially facilitate improvement of fiber yield and quality in the future cotton molecular breeding programs.
KeywordsUpland cotton SSRs Linkage disequilibrium Association mapping Fiber quality QTLs
This project was financially supported by the National Natural Science Foundation of China (31301365), the Crop Germplasm Conservation Program of Ministry of Agriculture China (2014NWB034) and the National Science and Technology Support Program of China (2013BAD01B03). We thank the national mid-term cotton gene bank of ICR-CAAS for providing the cotton genotypes.
Compliance with ethical standards
This study was funded by the National Natural Science Foundation of China (31301365), the Crop Germplasm Conservation Program of Ministry of Agriculture China (2014NWB034) and the National Science and Technology Support Program of China (2013BAD01B03).
Conflict of interest
All the authors declare that they have no any conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors. There is additional documentation related to this study. You may login to the system and click the ‘View Attachments’ link in the Action column.
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