Abstract
Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.
Highlights
Cotton is cultivated in many countries globally because it provides the most important natural textile fiber (Chen et al, 2007)
The Best Linear Unbiased Prediction (BLUP) showed that fiber length (FL), fiber strength (FS), and Mic ranged from 26.19 to 31.31 mm, 25.76 to 32.47 cN·tex−1, and 3.80 to 5.56, respectively (Figure 1 and Table 1)
We found three genes with different haplotypes to be significantly related to the corresponding fiber quality trait
Summary
Cotton is cultivated in many countries globally because it provides the most important natural textile fiber (Chen et al, 2007). With the advancement of textile technology, low-quality cotton fiber has difficulty meeting the machining requirements; improving fiber quality has become an essential goal for modern cotton breeding. Several quantitative trait loci (QTLs) for fiber quality traits have been identified by using bi-parental linkage mapping analysis (Said et al, 2013, 2015), which provided the candidate loci for the improvement of fiber quality traits. Based on the high-density single nucleotide polymorphisms (SNPs), genome-wide association study (GWAS) has been identified as an effective tool for discovering QTLs and genes associated with target traits in various crops such as wheat (Juliana et al, 2019), rice (Chen et al, 2014), soybean (Lu et al, 2020), and maize (Wang et al, 2020)
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