Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton
Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton
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全基因组关联研究确定了中国陆地棉株型组成性状的遗传变异和候选基因
DOI：
10.1007/s00122-018-3079-5
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发表时间：
2018-03
影响因子：
5.4
通讯作者：
Shuxun Yu
中科院分区：
文献类型：
--
作者：
Junji Su;Libei Li;Chi Zhang;Caixiang Wang;Lijiao Gu;Hantao Wang;Hengling Wei;Qibao Liu;Long Huang;Shuxun Yu
关键信息通过 GWAS 确定了中国陆地棉 22 个 SNP 与 5 个植物结构组成性状之间的 30 个显着关联。位于染色体 D03 上的四个峰值 SNP 位点同时与更多的植物结构组成性状相关。候选基因Gh_D03G0922可能与陆地棉的株高有关。 摘要中国机械化收获过程越来越需要紧凑的植物结构。因此，棉花株型是一个重要性状，其株高、果枝长度、果枝角度等组成因素影响着品种机械化采收的适宜性。为了确定棉花株型的遗传基础，使用由 355 个种质和 93,250 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)，这些单核苷酸多态性 (SNP) 是通过特定位点扩增片段测序方法鉴定的。通过 GWAS 确定了 22 个 SNP 和 5 个植物结构组成性状之间的 30 个显着关联。最重要的是，位于D03染色体上的四个峰值SNP位点同时与更多的植物结构组成性状相关，并且这些SNP隐藏在一个连锁不平衡块中。此外，在 0.95 Mb 区域中预测了 21 个植物结构候选基因，包括四个峰值 SNP。其中一个基因 (Gh_D03G0922) 靠近重要的 SNP D03_31584163 (8.40 kb)，其拟南芥同源物包含可能参与植物生长和发育的 MADS-box 结构域。 qRT-PCR显示，矮小紧凑型棉花品种的顶芽和幼叶中Gh_D03G0922的表达上调，病毒诱导的基因沉默（VIGS）证明沉默的植株表现出PH升高。这些结果表明Gh_D03G0922可能是棉花PH的候选基因。本研究确定的遗传变异和候选基因为未来中国棉花育种计划培育中短紧凑品种奠定了基础。
Key messageThirty 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.AbstractA 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 itsArabidopsishomologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression ofGh_D03G0922was 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 thatGh_D03G0922is 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.
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