Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton
Decryption of favourable haplotypes and potential candidate genes for five fibre quality properties using a relatively novel genome-wide association study procedure in upland cotton
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使用相对新颖的陆地棉全基因组关联研究程序解密五种纤维质量特性的有利单倍型和潜在候选基因
DOI：
10.1016/j.indcrop.2020.113004
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发表时间：
2020-12
影响因子：
5.9
通讯作者：
Xiongfeng Ma
中科院分区：
文献类型：
--
作者：
Junji Su;Caixiang Wang;Delong Yang;Chunhui Shi;Ai Zhang;Qi Ma;Juanjuan Liu;Xianliang Zhang;Long Huang;Xiongfeng Ma
通过全基因组关联分析（GWASs）确定育种资源中的全基因组数量性状位点（QTL）对于理解作物经济性状的遗传基础具有重要意义，但传统的GWASs方法主要集中在确定主要QTL的区域。本研究利用特异位点扩增片段测序技术，在315份高地棉材料的自然群体中检测了1，236，418个单核苷酸多态性（SNP）标记，以揭示控制棉花纤维品质性状的全基因组QTL（SLAF-seq）方法，并将13，391个高质量SNP组织成9244个SNP连锁不平衡块（SNPLDB），以开发具有多个单倍型/等位基因的分子标记。采用了一种相对新颖的限制性两阶段多位点多等位基因GWAS（RTM-GWAS）方法，包括两种方法，包括多环境和四种单环境。总共有75，77，66，66和60个显着的SNPLDB与上半平均长度（UHML），纤维强度（FS），纤维马克隆值（FM），纤维均匀度指数（FUI），和纤维伸长率（FE），分别通过多环境RTM-GWAS方法进行了鉴定。基于这些结果，单倍型/等位基因的显着SNPLDB基因座的影响进行了估计，QTL-等位基因矩阵的建立提供了简化的群体的遗传组成。最重要的是，9个稳定的SNPLDB位点同时检测到在多个环境和两个或更多个单一的测试环境与大的-lg（P）值和解释的表型变异的百分比。此外，有利的单倍型/等位基因的9个稳定的SNPLDB基因座被确定，和79个潜在的候选基因相关的UHML和FS性状预测从RNA-seq数据。研究陆地棉纤维品质性状的有利单倍型/等位基因、潜在候选基因和QTL-等位基因矩阵，有助于揭示陆地棉纤维品质性状的遗传基础，为选育优良纤维品质品种提供重要依据。
To understand the genetic basis of crop economic characteristics, identifying whole-genome quantitative trait loci (QTLs) in breeding resources via genome-wide association studies (GWASs) is important, but conventional GWAS procedures have mainly concentrated on identifying regions of major QTLs. In this study, to reveal whole-genome QTLs controlling cotton fibre quality traits, a total of 1,236,418 single-nucleotide polymorphism (SNP) markers were explored in a natural population of 315 upland cotton accessions using the specific-locus amplified fragment sequencing (SLAF-seq) method, and 13,391 high-quality SNPs were organized into 9244 SNP linkage disequilibrium blocks (SNPLDBs) to develop molecular markers with multiple haplotypes/alleles. A relatively novel procedure for restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS) involving two methods was applied, including multiple environments and four single environments. In total, 75, 77, 66, 66, and 60 significant SNPLDBs associated with the upper half mean length (UHML), fibre strength (FS), fibre micronaire (FM), fibre uniformity index (FUI), and fibre elongation (FE), respectively, were identified via the multiple-environment RTM-GWAS method. Based on these results, the haplotype/allele effects of the significant SNPLDB loci were estimated, and QTL-allele matrices were established to provide the abbreviated genetic composition of the population. Most importantly, nine stable SNPLDB loci were simultaneously detected in multiple environments and two or more single test environments with large –lg(P) values and percentages of explained phenotypic variation. Furthermore, favourable haplotypes/alleles of the nine stable SNPLDB loci were identified, and 79 potential candidate genes related to UHML and FS traits were predicted from RNA-seq data. Favourable haplotypes/alleles, potential candidate genes and QTL-allele matrices can offer important insights into the genetic basis of fibre quality traits in upland cotton and may facilitate the breeding of cotton varieties with excellent fibre quality properties.
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