Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.)

Abstract

Background: Upland cotton (Gossypium hirsutum L.) 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.

Results: 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 two 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.

Conclusions: 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.

Figure 1

A heat map showing the relatedness between RILs. Relationship matrix was estimated for the relationships among the lines using marker data, which the output serves as the matrix for representing familial relatedness. The heat map displays the relationships among the 275 RILs of Set 1. The red diagonal represents perfect relationship of each line with itself, and the symmetric off-diagonal elements represent relationship measures [in this case identity by descent (IBD)] for pairs of lines. There is not an obviously block of warmer color on the diagonal which shows a cluster of closely related lines. The dendrogram (tree diagram) on the right shows the results of a cluster analysis on the IBD matrix.

Figure 2

The effect of marker selection on fiber bundle strength (STR). Based on the genotypes of seven markers (QTLs), the 275 RILs of Set 2 (panel A) and all 550 RILs (panel B) were divided into two groups: 1) RILs containing 3 or more favorable alleles (Selected in red) and 2) the remaining RILs (Non-selected in black). The mean STR values of the selected and non-selected RILs were shown in red and black circle, respectively. The STR difference between the two groups was significant at p < 0.001. Y axis in g/tex.

Figure 3

The effect of two marker loci selection on short fiber content (SFC) (panel A), fiber bundle strength (STR) (panel B), upper half mean fiber length (UHM) (panel C) and length uniformity (UI) (panel D). Based on the genotypes of two marker loci, i.e., C2-0114a on Chr.07 and CM0066a on Chr.16, the 275 RILs of Set 2 were divided into two groups: 1) RILs with favorable alleles at both loci (Favor in red) and 2) RILs with unfavorable alleles at both loci (Unfavor in black). The mean trait values of the two groups were shown in red and black circle, respectively. The trait value difference between the two groups was significant at p < 0.001. Y axis for SFC: %, STR: g/tex, UHM: mm, and UI: %.