Summary
Fine mapping QTLs and identifying candidate genes for cotton fibre‐quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high‐density genetic map by specific‐locus amplified fragment sequencing (SLAF‐seq) to identify QTLs associated with fibre‐quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high‐yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre‐quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF‐based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co‐located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre‐related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre‐length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint‐percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre‐related traits and would be helpful for cloning fibre‐development‐related genes as well as for marker‐assisted genetic improvement in cotton.
The improvement of fiber quality is an essential goal in cotton breeding. In our previous studies, several quantitative trait loci (QTLs) contributing to improved fiber quality were identified in different introgressed chromosomal regions from Sea Island cotton (Gossypium barbadense L.) in a primary introgression population (Pop. A) of upland cotton (G. hirsutum L.). In the present study, to finely map introgressed major QTLs and accurately dissect the genetic contribution of the target introgressed chromosomal segments, we backcrossed two selected recombinant inbred lines (RILs) that presented desirable high fiber quality with their high lint-yielding recurrent parent to ultimately develop two secondary mapping populations (Pop. B and Pop. C). Totals of 20 and 27 QTLs for fiber quality were detected in Pop. B and Pop. C, respectively, including four and five for fiber length, four and eight for fiber micronaire, two and four for fiber uniformity, five and four for fiber elongation, and six and four for fiber strength, respectively. Two QTLs for lint percentage were detected only in Pop. C. In addition, seven stable QTLs were identified, including two for both fiber length and fiber strength and three for fiber elongation. Five QTL clusters for fiber quality were identified in the introgressed chromosomal regions, and negative effects of these chromosomal regions on lint percentage (a major lint yield parameter) were not observed. Candidate genes with a QTL-cluster associated with fiber strength and fiber length in the introgressed region of Chr.7 were further identified. The results may be helpful for revealing the genetic basis of superior fiber quality contributed by introgressed alleles from G. barbadense. Possible strategies involving marker-assisted selection (MAS) for simultaneously improving upland cotton fiber quality and lint yield in breeding programs was also discussed.
Cotton (Gossypium spp.) is an important natural textile ber and oilseed crop widely cultivated in the world. Lint percentage (LP, %) is one of the important yield factor, thus increasing lint percentage is a core goal of cotton breeding improvement. However, the underlying genetic and molecular mechanisms that control lint percentage in upland cotton remain largely unknown. Here, we performed a Genome-wide association study (GWAS) for LP based on phenotypic tests of 254 upland cotton accessions in four environments and BLUPs using the high-density CottonSNP80K array. A total of 41,413 high-quality singlenucleotide polymorphisms (SNPs) were screened and 34 SNPs within 22 QTLs were identi ed as signi cantly associated with lint percentage trait in different environments. In total, 175 candidate genes were identi ed from two major genomic loci (GR1 and GR2) of upland cotton and 50 hub genes were identi ed through GO enrichment and WGCNA analysis. Furthermore, two candidate/causal genes, Gh_D01G0162 and Gh_D07G0463, which pleiotropically increased lint percentage were identi ed and further veri ed its function through LD blocks, haplotypes and qRT-PCR analysis. Co-expression network analysis showed that the candidate/causal and hub gene, Gh_D07G0463, was signi cantly related to another candidate gene, Gh_D01G0162, and the simultaneous pyramid of the two genes lays the foundation for a more e cient increase in cotton production. Our study provides crucial insights into the genetic and molecular mechanisms underlying variations of yield traits and serves as an important foundation for lint percentage improvement via marker-assisted breeding.
Key MessageA total of 34 SNPs within 22 QTLs associated with lint percentage were identi ed by a GWAS. Two candidate genes underlying this trait were detected based on signi cant SNPs as well.
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