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_SNP_Ga03_65303452CRI-A2_SNP_Ga03_65303452genetic_marker
CRI-A2_INDEL_Ga03_65303612CRI-A2_INDEL_Ga03_65303612genetic_marker
CRI-A2_SNP_Ga03_65481592CRI-A2_SNP_Ga03_65481592genetic_marker
CRI-A2_SNP_Ga03_66037929CRI-A2_SNP_Ga03_66037929genetic_marker
CRI-A2_SNP_Ga03_66038272CRI-A2_SNP_Ga03_66038272genetic_marker
CRI-A2_INDEL_Ga03_66308129CRI-A2_INDEL_Ga03_66308129genetic_marker
CRI-A2_INDEL_Ga03_66308307CRI-A2_INDEL_Ga03_66308307genetic_marker
CRI-A2_INDEL_Ga03_68523755CRI-A2_INDEL_Ga03_68523755genetic_marker
CRI-A2_INDEL_Ga03_68523759CRI-A2_INDEL_Ga03_68523759genetic_marker
CRI-A2_INDEL_Ga03_68524262CRI-A2_INDEL_Ga03_68524262genetic_marker
CRI-A2_SNP_Ga03_68710340CRI-A2_SNP_Ga03_68710340genetic_marker
CRI-A2_INDEL_Ga03_68819656CRI-A2_INDEL_Ga03_68819656genetic_marker
CRI-A2_INDEL_Ga03_68849454CRI-A2_INDEL_Ga03_68849454genetic_marker
CRI-A2_SNP_Ga03_69655006CRI-A2_SNP_Ga03_69655006genetic_marker
CRI-A2_SNP_Ga03_69931376CRI-A2_SNP_Ga03_69931376genetic_marker
CRI-A2_INDEL_Ga03_69932937CRI-A2_INDEL_Ga03_69932937genetic_marker
CRI-A2_INDEL_Ga03_70133664CRI-A2_INDEL_Ga03_70133664genetic_marker
CRI-A2_INDEL_Ga03_70133762CRI-A2_INDEL_Ga03_70133762genetic_marker
CRI-A2_SNP_Ga03_70174866CRI-A2_SNP_Ga03_70174866genetic_marker
CRI-A2_SNP_Ga03_70200123CRI-A2_SNP_Ga03_70200123genetic_marker
CRI-A2_SNP_Ga03_70541584CRI-A2_SNP_Ga03_70541584genetic_marker
CRI-A2_SNP_Ga03_70542632CRI-A2_SNP_Ga03_70542632genetic_marker
CRI-A2_SNP_Ga03_71116112CRI-A2_SNP_Ga03_71116112genetic_marker
CRI-A2_SNP_Ga03_73072446CRI-A2_SNP_Ga03_73072446genetic_marker
CRI-A2_SNP_Ga03_73100954CRI-A2_SNP_Ga03_73100954genetic_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