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Title:   Author  item
                                            Fang, Daviditem
                                            Jenkins, Johnieitem
                                            Deng, Dewayneitem
                                            McCarty, Jackitem
                                            Li, Pingitem
                                            WU, JIXIANG - South Dakota State University
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 5/8/2014
                                    Publication  Date: 5/24/2014
                                    Citation: Fang, D.D., Jenkins, J.N., Deng, D.D., McCarty Jr, J.C., Li, P., Wu, J. 2014. Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Genomics. 15:397.Interpretive Summary: Upland cotton accounts for about 95 % of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy. 
In this research, we developed a random-mated recombinant inbred (RI) population consisting of 550 RI lines using 11 diverse Upland cotton cultivars as parents after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for three years in Mississippi State, MS, USA to obtain fiber quality data.  We selected 1582 molecular markers covering 83 % of cotton genome to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3 % for short fiber content to 82.8 % for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel. Since the 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars,  the fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy.
                                Technical Abstract: Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for three years in Mississippi State, MS, USA to obtain fiber quality data.  After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83 % of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3 % for short fiber content to 82.8 % for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel. Since the 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars, the fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.


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