ZHAO Hai-Hong, HE Xin-Yu, LI Wei-Xin, LI Xue-Mei, ZHANG Yu-Qi, DU Lei, DONG Cheng-Guang, LI Cheng-Qi
Fiber quality is an important economic trait of cotton and one of the major breeding targets. In this study, 408 upland cotton accessions were genotyped using the CottonSNP80K chip, yielding 12 874 high-quality SNP linkage disequilibrium block (SNPLDB) markers. A total of 128 SNPLDBs significantly associated with fiber length, 163 with fiber strength, 149 with fiber fineness, 94 with fiber uniformity, and 92 with fiber elongation were detected across six environments (five single environments and one multi-environment) using restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS). Among these, 10, 13, 9, 4 and 4 SNPLDBs associated with the five traits, respectively, were detected in at least two environments. Further single-marker/haplotype analysis revealed significant phenotypic differences among alleles of 6, 12, 9, 3 and 3 SNPLDBs associated with these five traits, respectively. A total of 11 loci associated with fiber length, 15 with fiber strength, 8 with fiber fineness, 6 with fiber uniformity, and 4 with fiber elongation identified in this study were found to overlap with QTLs/markers reported in previous studies. Among them, the loci Block_A13_74977977_75077975 (associated with fiber strength), Block_A05_24309961_24322003 and Block_D03_2459185_2528302 (associated with fiber fineness), and Block_D04_47711028_47718399 (associated with fiber elongation) were detected in multiple environments in this study as well as in previous studies. Combining GO enrichment and RNA-seq analysis indicated that 8 genes related to fiber length, 5 genes related to fiber strength, 8 genes related to fiber fineness, 4 genes related to fiber uniformity, and 3 genes related to fiber elongation may be potential candidate genes for fiber quality. This study provides a new perspective for elucidating the genetic basis of fiber quality in upland cotton and lays an important foundation for molecular breeding of fiber quality.