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

Publication Overview
TitleResequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits
AuthorsDu X, Huang G, He S, Yang Z, Sun G, Ma X, Li N, Zhang X, Sun J, Liu M, Jia Y, Pan Z, Gong W, Liu Z, Zhu H, Ma L, Liu F, Yang D, Wang F, Fan W, Gong Q, Peng Z, Wang L, Wang X, Xu S, Shang H, Lu C, Zheng H, Huang S, Lin T, Zhu Y, Li F
TypeJournal Article
Journal NameNature genetics
Year2018
CitationDu X, Huang G, He S, Yang Z, Sun G, Ma X, Li N, Zhang X, Sun J, Liu M, Jia Y, Pan Z, Gong W, Liu Z, Zhu H, Ma L, Liu F, Yang D, Wang F, Fan W, Gong Q, Peng Z, Wang L, Wang X, Xu S, Shang H, Lu C, Zheng H, Huang S, Lin T, Zhu Y, Li F. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature genetics. 2018 May 07.

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.

Germplasm
This publication contains information about 244 stocks:
Stock NameGRIN IDSpeciesType
Jiangsu Changshu Yang Mao WhiteGossypium arboreumaccession
Jiangsu Changshu OkraGossypium arboreumaccession
Jiangsu Changshu Black SeedGossypium arboreumaccession
Jiangsu Changshu Long Zhong 1Gossypium arboreumaccession
Jiangsu Xuzhou Zhong MianGossypium arboreumaccession
Jiangsu Red Stem OkraGossypium arboreumaccession
Jiangxi Xiushui Zhong Mian Hairy SeedGossypium arboreumaccession
Jiangyin White Seed 102Gossypium arboreumaccession
Jiangyin White Seed 111Gossypium arboreumaccession
Jiangyin Okra Clean SeedGossypium arboreumaccession
Tangshan White Seed Zhong MianGossypium arboreumaccession
Henan Shangcai Zhong MianGossypium arboreumaccession
Henan Shangqiu Grey SeedGossypium arboreumaccession
Henan Huaiyang Tu Mian Clean SeedGossypium arboreumaccession
Henan Huaiyang Tu Mian White SeedGossypium arboreumaccession
Faku White SeedGossypium arboreumaccession
Siyang Cangji Green Stem Zhong MianGossypium arboreumaccession
Zhejiang Shangyu Green Big PlantGossypium arboreumaccession
Zhejiang Shangyu Qingshan Red StemGossypium arboreumaccession
Zhejiang Yuyao Purple SnowGossypium arboreumaccession
Zhejiang Yuyao Huang Di Da BuGossypium arboreumaccession
Zhejiang Haiyan Red StemGossypium arboreumaccession
Zhejiang Haiyan Green PlantGossypium arboreumaccession
Zhejiang Xiaoshan Darkred Stem Big Plant Naked SeedGossypium arboreumaccession
Zhejiang Xiaoshan Darkred Stem Big Plant White SeedGossypium arboreumaccession

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Features
This publication contains information about 25,394 features:
Feature NameUniquenameType
seed cotton weight per bollGWAS0000092GWAS
seed cotton weight per bollGWAS0000093GWAS
seed cotton weight per bollGWAS0000094GWAS
seed cotton weight per bollGWAS0000095GWAS
seed cotton weight per bollGWAS0000096GWAS
lint percentGWAS0000097GWAS
lint percentGWAS0000098GWAS
EVM_prediction_Ga11G1047evm.TU.Ga11G1047_CRI-A2_v1.0.a1gene
EVM_prediction_Ga11G2352evm.TU.Ga11G2352_CRI-A2_v1.0.a1gene
EVM_prediction_Ga11G2353evm.TU.Ga11G2353_CRI-A2_v1.0.a1gene
EVM_prediction_Ga07G2114evm.TU.Ga07G2114_CRI-A2_v1.0.a1gene
EVM_prediction_Ga07G2116evm.TU.Ga07G2116_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G2687evm.TU.Ga08G2687_CRI-A2_v1.0.a1gene
EVM_prediction_Ga02G0376evm.TU.Ga02G0376_CRI-A2_v1.0.a1gene
EVM_prediction_Ga04G1780evm.TU.Ga04G1780_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0466evm.TU.Ga08G0466_CRI-A2_v1.0.a1gene
EVM_prediction_Ga13G2269evm.TU.Ga13G2269_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0087evm.TU.Ga08G0087_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0092evm.TU.Ga08G0092_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0109evm.TU.Ga08G0109_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0111evm.TU.Ga08G0111_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0113evm.TU.Ga08G0113_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0114evm.TU.Ga08G0114_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0116evm.TU.Ga08G0116_CRI-A2_v1.0.a1gene
EVM_prediction_Ga08G0117evm.TU.Ga08G0117_CRI-A2_v1.0.a1gene

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Projects
This publication contains information about 2 projects:
Project NameDescription
A2-CRI_key-agronomics_CRI-Li-2018_GWAS
A2-CRI_key-agronomics_CRI-Li-2018_PHENO
Properties
Additional details for this publication include:
Property NameValue
DOI10.1038/s41588-018-0116-x
eISSN1546-1718
Elocation10.1038/s41588-018-0116-x
ISSN1546-1718
Journal AbbreviationNat. Genet.
Journal CountryUnited States
LanguageEnglish
Language Abbreng
Publication Date2018 May 07
Publication ModelPrint-Electronic
Publication TypeJournal Article
Published Location