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
Anhui Quanjiao Small Seed Cotton Hairy Seed 1Gossypium arboreumaccession
Anhui Liuan Big Flower Hairy SeedGossypium arboreumaccession
Anhui Taihe Shuangfuqu XingouxiangGossypium arboreumaccession
Anhui Dingyuan Purple FlowerGossypium arboreumaccession
Anhui Xuancheng Zhong Zi Mian White SeedGossypium arboreumaccession
Anhui Xuancheng Zhong Mian Clean SeedGossypium arboreumaccession
Anhui Huaining Black SeedGossypium arboreumaccession
Anhui Tongcheng Zhong Mian Clean SeedGossypium arboreumaccession
Anhui Chuxian Small Seed CottonGossypium arboreumaccession
Anhui Feixi Small Black SeedGossypium arboreumaccession
Anhui Shucheng Zhong MianGossypium arboreumaccession
Anhui Guichi Zhong MianGossypium arboreumaccession
Anhui Guichi Small Seed Cotton Grey SeedGossypium arboreumaccession
Anhui Guichi Small Seed Cotton White SeedGossypium arboreumaccession
Anhui Tongling Zhong MianGossypium arboreumaccession
Anhui Fuyang Er Yang HuaGossypium arboreumaccession
Anhui Fuyang Small Purple FlowerGossypium arboreumaccession
Anlong Small FlowerGossypium arboreumaccession
Wanxian Purple Stem Small White FlowerGossypium arboreumaccession
Wan Zi Zhong MianGossypium arboreumaccession
Dingtao Zhong MianGossypium arboreumaccession
Baoshan Purple FlowerGossypium arboreumaccession
Dui HuaGossypium arboreumaccession
CN-ZM-08004Gossypium arboreumaccession
Small White Flower (Haimen)Gossypium arboreumaccession

Pages

Features
This publication contains information about 25,394 features:
Feature NameUniquenameType
CRI-A2_INDEL_Ga09_18825011CRI-A2_INDEL_Ga09_18825011genetic_marker
CRI-A2_INDEL_Ga09_18825017CRI-A2_INDEL_Ga09_18825017genetic_marker
CRI-A2_SNP_Ga09_19542476CRI-A2_SNP_Ga09_19542476genetic_marker
CRI-A2_INDEL_Ga09_21350367CRI-A2_INDEL_Ga09_21350367genetic_marker
CRI-A2_INDEL_Ga09_21350369CRI-A2_INDEL_Ga09_21350369genetic_marker
CRI-A2_INDEL_Ga09_21350371CRI-A2_INDEL_Ga09_21350371genetic_marker
CRI-A2_INDEL_Ga09_21350372CRI-A2_INDEL_Ga09_21350372genetic_marker
CRI-A2_INDEL_Ga09_21351772CRI-A2_INDEL_Ga09_21351772genetic_marker
CRI-A2_SNP_Ga09_21629601CRI-A2_SNP_Ga09_21629601genetic_marker
CRI-A2_SNP_Ga09_21629896CRI-A2_SNP_Ga09_21629896genetic_marker
CRI-A2_SNP_Ga09_21733990CRI-A2_SNP_Ga09_21733990genetic_marker
CRI-A2_SNP_Ga09_21734206CRI-A2_SNP_Ga09_21734206genetic_marker
CRI-A2_SNP_Ga09_21734274CRI-A2_SNP_Ga09_21734274genetic_marker
CRI-A2_SNP_Ga09_21734325CRI-A2_SNP_Ga09_21734325genetic_marker
CRI-A2_SNP_Ga09_21755114CRI-A2_SNP_Ga09_21755114genetic_marker
CRI-A2_SNP_Ga09_21755255CRI-A2_SNP_Ga09_21755255genetic_marker
CRI-A2_SNP_Ga09_21938218CRI-A2_SNP_Ga09_21938218genetic_marker
CRI-A2_INDEL_Ga09_21996390CRI-A2_INDEL_Ga09_21996390genetic_marker
CRI-A2_SNP_Ga09_22025947CRI-A2_SNP_Ga09_22025947genetic_marker
CRI-A2_INDEL_Ga09_23029663CRI-A2_INDEL_Ga09_23029663genetic_marker
CRI-A2_INDEL_Ga09_23029664CRI-A2_INDEL_Ga09_23029664genetic_marker
CRI-A2_INDEL_Ga09_23030071CRI-A2_INDEL_Ga09_23030071genetic_marker
CRI-A2_SNP_Ga09_23395243CRI-A2_SNP_Ga09_23395243genetic_marker
CRI-A2_SNP_Ga09_23395568CRI-A2_SNP_Ga09_23395568genetic_marker
CRI-A2_INDEL_Ga09_23988822CRI-A2_INDEL_Ga09_23988822genetic_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