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Nat Genet. 2018 Jun;50(6):796-802. doi: 10.1038/s41588-018-0116-x. Epub 2018 May 7.

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

Author information

1
Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, China.
2
Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
3
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China.
4
Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China.
5
Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
6
Biomarker Technologies Corporation, Beijing, China.
7
Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. lintao_solab@126.com.
8
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China. zhuyx@whu.edu.cn.
9
Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China. zhuyx@whu.edu.cn.
10
Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, China. aylifug@163.com.
11
Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. aylifug@163.com.

Abstract

The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid 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. 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 composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.

PMID:
29736014
DOI:
10.1038/s41588-018-0116-x

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