Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield

First author: Zhiying Ma; Affiliations: Hebei Agricultural University (河北农业大学): Baoding, China

Corresponding author: Zhiying Ma (马峙英)

Upland cotton is the most important natural-fiber crop. The genomic variation of diverse germplasms and alleles underpinning fiber quality and yield should be extensively explored. Here, we resequenced a core collection comprising 419 accessions with 6.55-fold coverage depth and identified approximately 3.66 million SNPs for evaluating the genomic variation. We performed phenotyping across 12 environments and conducted genome-wide association study of 13 fiber-related traits. 7,383 unique SNPs were significantly associated with these traits and were located within or near 4,820 genes; more associated loci were detected for fiber quality than fiber yield, and more fiber genes were detected in the D than the A subgenome. Several previously undescribed causal genes for days to flowering, fiber length, and fiber strength were identified. Phenotypic selection for these traits increased the frequency of elite alleles during domestication and breeding. These results provide targets for molecular selection and genetic manipulation in cotton improvement.

陆地棉是最重要产自然纤维作物，控制其纤维质量和产量的种质和等位基因的基因组变异值得我们深入研究和探索。本文对419个陆地棉品种进行了平均深度为6.55×的重测序，鉴定了大约3.66百万个SNP用于评估基因组变异。作者对12个不同环境下的陆地棉进行了表型鉴定，并对13个纤维相关的性状进行了全基因组关联分析。作者发现有7383个SNP与这些性状显著相关，这些SNP坐落在4820个基因内或附近，相比于纤维产量，作者鉴定到了更多的与纤维质量相关的SNP，并且在D套染色体上的纤维相关基因要比A套染色体上多。一些之前报道过的与开花时间、纤维长度以及纤维强度相关的基因在本研究均被鉴定出来。研究显示在驯化和育种过程中，人们对于这些性状的表型选择增加了优良等位基因的频率。本文的结果为棉花的遗传改良提供了分子选择和基因操作的分子靶标。

通讯：马峙英 (http://nongxue.hebau.edu.cn/szjj/ycyz/1440.html)

研究方向：抗病虫高产优质棉花新品种选育、强优势棉花杂交种创制及应用、棉花种质资源研究与利用、棉花重要性状分子标记与基因克隆、棉花转基因育种技术及应用等。

doi: 10.1038/s41588-018-0119-7

Journal: Nature Genetics

Published online: 07 May, 2018

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

First author: Xiongming Du; Affiliations: State Key Laboratory of Cotton Biology (棉花生物学国家重点实验室): Anyang, China

Corresponding author: Fuguang Li (李付广)

The ancestors of Gossypium arboreum (木本棉) and Gossypium herbaceum (草本棉) provided the A subgenome for the modern cultivated allotetraploid (异源四倍体) cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243  G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii (雷蒙德氏棉). Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid (脂肪酸) composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease (枯萎病) is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.

木本棉和草本棉的祖先为现代栽培种异源四倍体棉花提供了A套染色体。本文通过最新的几种技术更新了木本棉的基因组组装。作者对243个木本棉和草本棉进行了重测序分析，构建了一张基因组变异图谱，发现这两个棉花与二倍体雷蒙德氏棉的遗传分化一致。进一步分析显示中国的木本棉源自于中国南方，而后被引种到长江和黄河流域。大多数的品种驯化性状都经历了地理隔离。全基因组关联分析鉴定了98个峰值与11个木本棉重要农艺性状相关。GaKASIII基因上一个半胱氨酸向精氨酸的非同义突变可能导致了棉花种子中大量脂肪酸的产生。而对于枯萎病的抗性与GaGSTF9基因表达的激活相关。本文的研究对于进一步理解和探索棉花的A套染色体具有非常重要的意义。

通讯：李付广 (http://www.sklcb.cn/sh.asp?s=22)

研究方向：棉花组织培养及外源基因功能验证、高效广适双价转基因抗虫棉、高产优质多抗新品种棉花选育等。

doi: 10.1038/s41588-018-0116-x

Journal: Nature Genetics

Published online: 07 May, 2018

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