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_SNP_Ga02_38399104CRI-A2_SNP_Ga02_38399104genetic_marker
CRI-A2_SNP_Ga02_38597054CRI-A2_SNP_Ga02_38597054genetic_marker
CRI-A2_INDEL_Ga02_38597454CRI-A2_INDEL_Ga02_38597454genetic_marker
CRI-A2_SNP_Ga02_38630175CRI-A2_SNP_Ga02_38630175genetic_marker
CRI-A2_INDEL_Ga02_38631066CRI-A2_INDEL_Ga02_38631066genetic_marker
CRI-A2_INDEL_Ga02_38631089CRI-A2_INDEL_Ga02_38631089genetic_marker
CRI-A2_INDEL_Ga02_38640045CRI-A2_INDEL_Ga02_38640045genetic_marker
CRI-A2_INDEL_Ga02_38640083CRI-A2_INDEL_Ga02_38640083genetic_marker
CRI-A2_SNP_Ga02_38640300CRI-A2_SNP_Ga02_38640300genetic_marker
CRI-A2_INDEL_Ga02_39577078CRI-A2_INDEL_Ga02_39577078genetic_marker
CRI-A2_SNP_Ga02_40502322CRI-A2_SNP_Ga02_40502322genetic_marker
CRI-A2_INDEL_Ga02_40503619CRI-A2_INDEL_Ga02_40503619genetic_marker
CRI-A2_SNP_Ga02_40653067CRI-A2_SNP_Ga02_40653067genetic_marker
CRI-A2_SNP_Ga02_40655998CRI-A2_SNP_Ga02_40655998genetic_marker
CRI-A2_SNP_Ga02_41530073CRI-A2_SNP_Ga02_41530073genetic_marker
CRI-A2_SNP_Ga02_41534218CRI-A2_SNP_Ga02_41534218genetic_marker
CRI-A2_INDEL_Ga02_44666781CRI-A2_INDEL_Ga02_44666781genetic_marker
CRI-A2_SNP_Ga02_45445066CRI-A2_SNP_Ga02_45445066genetic_marker
CRI-A2_INDEL_Ga02_47208459CRI-A2_INDEL_Ga02_47208459genetic_marker
CRI-A2_SNP_Ga02_47435298CRI-A2_SNP_Ga02_47435298genetic_marker
CRI-A2_SNP_Ga02_47435317CRI-A2_SNP_Ga02_47435317genetic_marker
CRI-A2_SNP_Ga02_47688278CRI-A2_SNP_Ga02_47688278genetic_marker
CRI-A2_SNP_Ga02_47689497CRI-A2_SNP_Ga02_47689497genetic_marker
CRI-A2_SNP_Ga02_47840847CRI-A2_SNP_Ga02_47840847genetic_marker
CRI-A2_SNP_Ga02_47841147CRI-A2_SNP_Ga02_47841147genetic_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