State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China.
Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Ministry of Agriculture, Shihezi, China.
Theor Appl Genet. 2018 Jun;131(6):1299-1314. doi: 10.1007/s00122-018-3079-5. Epub 2018 Mar 1.
Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.
通过 GWAS，在中国陆地棉中鉴定到 22 个 SNP 与 5 个植物结构组成性状之间的 30 个显著关联。四个位于染色体 D03 上的峰 SNP 位点同时与更多的植物结构组成性状相关。一个候选基因 Gh_D03G0922 可能与陆地棉的株高有关。在中国，机械化收获过程越来越需要紧凑的植物结构。因此，棉花的植物结构是一个重要的特征，其组成部分，如株高、果枝长度和果枝角度，影响品种对机械化收获的适应性。为了确定棉花植物结构的遗传基础，使用由 355 个系谱和通过特异基因座扩增片段测序方法鉴定的 93250 个单核苷酸多态性（SNP）组成的小组进行了全基因组关联研究（GWAS）。通过 GWAS 鉴定到 22 个 SNP 与 5 个植物结构组成性状之间的 30 个显著关联。最重要的是，位于染色体 D03 上的四个峰 SNP 位点同时与更多的植物结构组成性状相关，这些 SNP 位于一个连锁不平衡块中。此外，在包括四个峰 SNP 的 0.95-Mb 区域中预测到 21 个与植物结构相关的候选基因。其中一个基因（Gh_D03G0922）位于显著 SNP D03_31584163（8.40 kb）附近，其拟南芥同源物包含 MADS 框结构域，可能参与植物的生长和发育。qRT-PCR 显示，Gh_D03G0922 在短而紧凑的棉花品种的顶芽和幼叶中表达上调，病毒诱导基因沉默（VIGS）证明沉默的植物表现出增加的 PH。这些结果表明，Gh_D03G0922 可能是棉花 PH 的候选基因。本研究中鉴定的遗传变异和候选基因为未来中国棉花育种计划中培育中度短而紧凑的品种奠定了基础。
