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

Pages

Features
This publication contains information about 25,394 features:
Feature NameUniquenameType
CRI-A2_INDEL_Ga13_22698292CRI-A2_INDEL_Ga13_22698292genetic_marker
CRI-A2_SNP_Ga13_22698372CRI-A2_SNP_Ga13_22698372genetic_marker
CRI-A2_SNP_Ga13_22763817CRI-A2_SNP_Ga13_22763817genetic_marker
CRI-A2_INDEL_Ga13_22843495CRI-A2_INDEL_Ga13_22843495genetic_marker
CRI-A2_INDEL_Ga13_22843496CRI-A2_INDEL_Ga13_22843496genetic_marker
CRI-A2_SNP_Ga13_22895732CRI-A2_SNP_Ga13_22895732genetic_marker
CRI-A2_SNP_Ga13_22958158CRI-A2_SNP_Ga13_22958158genetic_marker
CRI-A2_SNP_Ga13_23066033CRI-A2_SNP_Ga13_23066033genetic_marker
CRI-A2_SNP_Ga13_23247950CRI-A2_SNP_Ga13_23247950genetic_marker
CRI-A2_SNP_Ga13_23248146CRI-A2_SNP_Ga13_23248146genetic_marker
CRI-A2_SNP_Ga13_23648687CRI-A2_SNP_Ga13_23648687genetic_marker
CRI-A2_INDEL_Ga13_23648705CRI-A2_INDEL_Ga13_23648705genetic_marker
CRI-A2_SNP_Ga13_23649359CRI-A2_SNP_Ga13_23649359genetic_marker
CRI-A2_SNP_Ga13_23649910CRI-A2_SNP_Ga13_23649910genetic_marker
CRI-A2_SNP_Ga13_23992630CRI-A2_SNP_Ga13_23992630genetic_marker
CRI-A2_INDEL_Ga13_24198825CRI-A2_INDEL_Ga13_24198825genetic_marker
CRI-A2_INDEL_Ga13_24252526CRI-A2_INDEL_Ga13_24252526genetic_marker
CRI-A2_INDEL_Ga13_24252997CRI-A2_INDEL_Ga13_24252997genetic_marker
CRI-A2_INDEL_Ga13_24253039CRI-A2_INDEL_Ga13_24253039genetic_marker
CRI-A2_INDEL_Ga13_24253059CRI-A2_INDEL_Ga13_24253059genetic_marker
CRI-A2_SNP_Ga13_24253792CRI-A2_SNP_Ga13_24253792genetic_marker
CRI-A2_INDEL_Ga13_24253954CRI-A2_INDEL_Ga13_24253954genetic_marker
CRI-A2_INDEL_Ga13_24482403CRI-A2_INDEL_Ga13_24482403genetic_marker
CRI-A2_INDEL_Ga13_24482404CRI-A2_INDEL_Ga13_24482404genetic_marker
CRI-A2_INDEL_Ga13_24482410CRI-A2_INDEL_Ga13_24482410genetic_marker

Pages

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