一种 RTM-GWAS 程序揭示了陆地棉三个产量相关性状的 QTL 等位基因和候选基因。

An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton.

机构信息

Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.

Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China.

出版信息

BMC Plant Biol. 2020 Sep 7;20(1):416. doi: 10.1186/s12870-020-02613-y.

BACKGROUND

Cotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutum L.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions.

RESULTS

A total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region.

CONCLUSION

This study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.

背景

棉花（Gossypium spp.）纤维产量是关键目标性状之一，提高纤维产量一直被认为是棉花育种计划和生产的重要目标。尽管已经有一些研究旨在了解与棉花产量相关性状的遗传基础，但检测到的与这些性状相关的数量性状位点（QTL）仍然非常有限。为了揭示控制陆地棉（Gossypium hirsutum L.）三个产量相关性状的全基因组 QTL，在一个由 315 个品系组成的关联群体中，利用 9244 个单核苷酸多态性连锁不平衡块（SNPLDB）标记，在四个种植环境下对表型性状进行了研究。

结果

通过在多个环境下进行的受限两阶段多基因多等位基因全基因组关联研究（RTM-GWAS）程序，共检测到与铃数（BN）、铃重（BW）和衣分（LP）分别显著相关的 53、70 和 68 个 SNPLDB 位点。对显著 SNPLDB 位点的单倍型/等位基因效应进行了估计，并组织了 QTL-等位基因矩阵，为群体提供了简化的遗传组成。在显著的 SNPLDB 位点中，有 6 个在两个或两个以上的单一种植环境中同时被鉴定出来，被认为是稳定的 SNPLDB 位点。此外，在这六个稳定的 SNPLDB 位点附近区域共注释了 115 个基因，通过两个 RNA-seq 数据预测到其中 16 个共同的潜在候选基因控制目标性状。其中一个基因（GH_D06G2161）主要在早期胚珠发育阶段表达，而稳定的 SNPLDB 位点（LDB_19_62926589）则位于其启动子区域。