Genome-wide association study reveals novel quantitative trait loci and candidate genes of lint percentage in upland cotton based on the CottonSNP80K array

Abstract

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.

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

“…4 , and 5 ; Tables S 8 , S 9 , S 10 ). This result is consistent with the findings of previous studies [ 48 , 50 , 55 , 66 , 67 ]. The difference is that a greater number of candidate genes in QTLs for LP were involved in gene expression processes, and a greater number of candidate genes in QTLs for BW were involved in metabolic pathways.…”

“…The numbers of these QTLs are increasing continually. Recently, 34 SNPs corresponding to 22 QTLs for LP, including 13 novel QTLs, were detected from 254 upland cotton accessions via GWAS [ 55 ]. Two stable LP QTLs and three BW QTLs were identified in the RIL mapping population derived from the inter-specific cross between G. hirsutum cv DS-28 and G. barbadense cv SBYF-425 [ 56 ].…”

“…Understanding the molecular mechanisms of LP and BW developments is essential for the molecular breeding of cotton plants with high yield, especially via genetic engineering. Many candidate genes of the QTLs for LP and BW have been studied [ 48 – 50 , 55 ]. The TIP41-like family protein ( TIP41L ) gene ( GH_A12G0194 ) is thought to be the candidate gene of a stable major QTL ( q ( BW + SI ) -A12-1 ) for BW [ 49 ].…”

“…Two candidate genes ( Gh_D01G0162 and Gh_D07G0463 ) of QTLs for LP were identified. Gh_D01G0162 is a homolog of the auxin-responsive GH3 family protein gene, and Gh_D07G0463 is a homolog of the NADPH/respiratory burst oxidase protein D gene ( RBOHD ) in Arabidopsis [ 55 ]. A molecular regulatory network for LP has been proposed based on the functions of the candidate genes of QTLs for LP [ 50 ].…”

Inter-Specific Hybridization in Cotton (Gossypium hirsutum) for Crop Improvement

“…In every commercial cotton breeding program, lint output remains the top objective [39][40][41]. Lint percent, which is a component of lint output, was probably one of the first qualities to be chosen throughout the domestication process and in early breeding, and is still the most desired character [23,[42][43][44][45][46]. Environmental stability [47,48] and early maturity [49][50][51] are two more agronomic features that have risen in relevance [37].…”