Abstract
Fiber quality is an important economic index and a major breeding goal in cotton, but direct phenotypic selection is often hindered due to environmental influences and linkage with yield traits. A genome-wide association study (GWAS) is a powerful tool to identify genes associated with phenotypic traits. In this study, we identified fiber quality genes in upland cotton (Gossypium hirsutum L.) using GWAS based on a high-density CottonSNP80K array and multiple environment tests. A total of 30 and 23 significant single nucleotide polymorphisms (SNPs) associated with five fiber quality traits were identified across the 408 cotton accessions in six environments and the best linear unbiased predictions, respectively. Among these SNPs, seven loci were the same, and 128 candidate genes were predicted in a 1-Mb region (±500 kb of the peak SNP). Furthermore, two major genome regions (GR1 and GR2) associated with multiple fiber qualities in multiple environments on chromosomes A07 and A13 were identified, and within them, 22 candidate genes were annotated. Of these, 11 genes were expressed [log2(1 + FPKM)>1] in the fiber development stages (5, 10, 20, and 25 dpa) using RNA-Seq. This study provides fundamental insight relevant to identification of genes associated with fiber quality and will accelerate future efforts toward improving fiber quality of upland cotton.
Highlights
Cotton (Gossypium spp.) is the most important natural textile fiber source globally
A total of 408 upland cotton accessions were selected, comprising 201 accessions that originated from the Northwestern Inland Region (NIR), 88 that originated from the Yellow River region (YRR), 63 from the Yangtze River Region (YtRR), 29 from the northern specific early maturation region (NSEMR) and 27 introduced from abroad (Supplementary Table S1)
The correlations between the five fiber quality traits using the best linear unbiased prediction (BLUP) results showed that FL was significantly positively correlated with FS, FU, and FE, and a positive correlation was found for FS with FU and FE
Summary
Cotton (Gossypium spp.) is the most important natural textile fiber source globally. The genus Gossypium includes approximately 50 species, 45 diploid (2n = 2x = 26) and 5 tetraploid (2n = 4x = 52). The cultivated types of cotton include two diploids, G. arboreum L. and G. herbaceum L., and two tetraploids, G. hirsutum L. and G. barbadense L. Upland cotton (G. hirsutum L.) is the most widely cultivated tetraploid cotton species and accounts for 95% of the world’s cotton production because of its high yield and preferable fiber quality, the chromosomes are often numbered in two sets of 13, A1 through A13 and D1 through D13, the genome sizes is approximately 2,500 Mb in the upland cotton (Wendel and Cronn, 2003; Zhang T. et al, 2015). In recent years, reform of the supply side structure of cotton has Identification of Fiber Qualities in Gossypium hirsutum L
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