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
Nantong Green Stem Tong MianGossypium arboreumaccession
Nantong Green Stem Okra Ya Ling Guo Yellow FlowerGossypium arboreumaccession
Shangqiu Small White FlowerGossypium arboreumaccession
Jiading Zhong MianGossypium arboreumaccession
Jiading White SeedGossypium arboreumaccession
Sichuan Shuangliu Zhong MianGossypium arboreumaccession
Sichuan Fushun Zhong MianGossypium arboreumaccession
Sichuan Mianyang Zhong MianGossypium arboreumaccession
Sichuan Zizhong Zhong MianGossypium arboreumaccession
Sichuan Suining Zhong Mian Naked SeedGossypium arboreumaccession
Sichuan Suining Zhong Mian Grey SeedGossypium arboreumaccession
Sichuan Suining Zhong Mian White SeedGossypium arboreumaccession
HuangzhouGossypium arboreumaccession
Daye Da RongGossypium arboreumaccession
Daye Thin StapleGossypium arboreumaccession
Big Purple StemGossypium arboreumaccession
Taicang White Seed (Liu)Gossypium arboreumaccession
Rudong Okra Ya GuoGossypium arboreumaccession
Xiaogan Tie Zi Da Yi HuaGossypium arboreumaccession
Xiaogan Tie Zi Xiao Yi HuaGossypium arboreumaccession
Xiaogan Qing Pi Su Zhong Mian Bai Zi (Da Yi Fen)Gossypium arboreumaccession
Anguo Liu Shuang Shu Big Green StemGossypium arboreumaccession
Anguo White Stem White FlowerGossypium arboreumaccession
Anhui Quanjiao Zhong MianGossypium arboreumaccession
Anhui Quanjiao Small Seed Cotton Clean SeedGossypium arboreumaccession

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Features
This publication contains information about 25,394 features:
Feature NameUniquenameType
CRI-A2_INDEL_Ga01_6055297CRI-A2_INDEL_Ga01_6055297genetic_marker
CRI-A2_SNP_Ga01_6181099CRI-A2_SNP_Ga01_6181099genetic_marker
CRI-A2_SNP_Ga01_6182214CRI-A2_SNP_Ga01_6182214genetic_marker
CRI-A2_INDEL_Ga01_6182303CRI-A2_INDEL_Ga01_6182303genetic_marker
CRI-A2_INDEL_Ga01_6182305CRI-A2_INDEL_Ga01_6182305genetic_marker
CRI-A2_SNP_Ga01_6182445CRI-A2_SNP_Ga01_6182445genetic_marker
CRI-A2_SNP_Ga01_6182507CRI-A2_SNP_Ga01_6182507genetic_marker
CRI-A2_INDEL_Ga01_6183583CRI-A2_INDEL_Ga01_6183583genetic_marker
CRI-A2_INDEL_Ga01_6183585CRI-A2_INDEL_Ga01_6183585genetic_marker
CRI-A2_INDEL_Ga01_6184571CRI-A2_INDEL_Ga01_6184571genetic_marker
CRI-A2_INDEL_Ga01_6184575CRI-A2_INDEL_Ga01_6184575genetic_marker
CRI-A2_INDEL_Ga01_6184720CRI-A2_INDEL_Ga01_6184720genetic_marker
CRI-A2_INDEL_Ga01_6184723CRI-A2_INDEL_Ga01_6184723genetic_marker
CRI-A2_SNP_Ga01_6270522CRI-A2_SNP_Ga01_6270522genetic_marker
CRI-A2_SNP_Ga01_6271466CRI-A2_SNP_Ga01_6271466genetic_marker
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CRI-A2_SNP_Ga01_6272561CRI-A2_SNP_Ga01_6272561genetic_marker
CRI-A2_SNP_Ga01_6377144CRI-A2_SNP_Ga01_6377144genetic_marker
CRI-A2_INDEL_Ga01_6432625CRI-A2_INDEL_Ga01_6432625genetic_marker
CRI-A2_INDEL_Ga01_6454468CRI-A2_INDEL_Ga01_6454468genetic_marker
CRI-A2_INDEL_Ga01_6458231CRI-A2_INDEL_Ga01_6458231genetic_marker
CRI-A2_INDEL_Ga01_6482091CRI-A2_INDEL_Ga01_6482091genetic_marker
CRI-A2_SNP_Ga01_6490270CRI-A2_SNP_Ga01_6490270genetic_marker
CRI-A2_SNP_Ga01_6490830CRI-A2_SNP_Ga01_6490830genetic_marker
CRI-A2_SNP_Ga01_6490951CRI-A2_SNP_Ga01_6490951genetic_marker

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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