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_Ga01_40028331CRI-A2_INDEL_Ga01_40028331genetic_marker
CRI-A2_INDEL_Ga01_40149332CRI-A2_INDEL_Ga01_40149332genetic_marker
CRI-A2_INDEL_Ga01_40166297CRI-A2_INDEL_Ga01_40166297genetic_marker
CRI-A2_SNP_Ga01_40309724CRI-A2_SNP_Ga01_40309724genetic_marker
CRI-A2_SNP_Ga01_40320315CRI-A2_SNP_Ga01_40320315genetic_marker
CRI-A2_SNP_Ga01_40527915CRI-A2_SNP_Ga01_40527915genetic_marker
CRI-A2_INDEL_Ga01_40527920CRI-A2_INDEL_Ga01_40527920genetic_marker
CRI-A2_SNP_Ga01_40528111CRI-A2_SNP_Ga01_40528111genetic_marker
CRI-A2_SNP_Ga01_41305159CRI-A2_SNP_Ga01_41305159genetic_marker
CRI-A2_SNP_Ga01_41305287CRI-A2_SNP_Ga01_41305287genetic_marker
CRI-A2_SNP_Ga01_41790382CRI-A2_SNP_Ga01_41790382genetic_marker
CRI-A2_INDEL_Ga01_41901184CRI-A2_INDEL_Ga01_41901184genetic_marker
CRI-A2_INDEL_Ga01_41901622CRI-A2_INDEL_Ga01_41901622genetic_marker
CRI-A2_INDEL_Ga01_41901671CRI-A2_INDEL_Ga01_41901671genetic_marker
CRI-A2_INDEL_Ga01_42287970CRI-A2_INDEL_Ga01_42287970genetic_marker
CRI-A2_INDEL_Ga01_42287972CRI-A2_INDEL_Ga01_42287972genetic_marker
CRI-A2_INDEL_Ga01_42617087CRI-A2_INDEL_Ga01_42617087genetic_marker
CRI-A2_INDEL_Ga01_43037823CRI-A2_INDEL_Ga01_43037823genetic_marker
CRI-A2_SNP_Ga01_44040690CRI-A2_SNP_Ga01_44040690genetic_marker
CRI-A2_SNP_Ga01_44966622CRI-A2_SNP_Ga01_44966622genetic_marker
CRI-A2_INDEL_Ga01_44966924CRI-A2_INDEL_Ga01_44966924genetic_marker
CRI-A2_INDEL_Ga01_45865439CRI-A2_INDEL_Ga01_45865439genetic_marker
CRI-A2_SNP_Ga01_45866110CRI-A2_SNP_Ga01_45866110genetic_marker
CRI-A2_SNP_Ga01_46043009CRI-A2_SNP_Ga01_46043009genetic_marker
CRI-A2_INDEL_Ga01_46043099CRI-A2_INDEL_Ga01_46043099genetic_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