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.

Features
This publication contains information about 25,394 features:
Feature NameUniquenameType
CRI-A2_INDEL_Ga07_58753225CRI-A2_INDEL_Ga07_58753225genetic_marker
CRI-A2_INDEL_Ga07_59086001CRI-A2_INDEL_Ga07_59086001genetic_marker
CRI-A2_INDEL_Ga07_59086002CRI-A2_INDEL_Ga07_59086002genetic_marker
CRI-A2_INDEL_Ga07_59109102CRI-A2_INDEL_Ga07_59109102genetic_marker
CRI-A2_INDEL_Ga07_59109111CRI-A2_INDEL_Ga07_59109111genetic_marker
CRI-A2_SNP_Ga07_59109570CRI-A2_SNP_Ga07_59109570genetic_marker
CRI-A2_INDEL_Ga07_59145932CRI-A2_INDEL_Ga07_59145932genetic_marker
CRI-A2_INDEL_Ga07_59146061CRI-A2_INDEL_Ga07_59146061genetic_marker
CRI-A2_SNP_Ga07_59281383CRI-A2_SNP_Ga07_59281383genetic_marker
CRI-A2_SNP_Ga07_59303845CRI-A2_SNP_Ga07_59303845genetic_marker
CRI-A2_INDEL_Ga07_60221020CRI-A2_INDEL_Ga07_60221020genetic_marker
CRI-A2_SNP_Ga07_60249114CRI-A2_SNP_Ga07_60249114genetic_marker
CRI-A2_INDEL_Ga07_60250350CRI-A2_INDEL_Ga07_60250350genetic_marker
CRI-A2_INDEL_Ga07_62732784CRI-A2_INDEL_Ga07_62732784genetic_marker
CRI-A2_INDEL_Ga07_62742715CRI-A2_INDEL_Ga07_62742715genetic_marker
CRI-A2_INDEL_Ga07_62955333CRI-A2_INDEL_Ga07_62955333genetic_marker
CRI-A2_SNP_Ga07_63879610CRI-A2_SNP_Ga07_63879610genetic_marker
CRI-A2_SNP_Ga07_64917548CRI-A2_SNP_Ga07_64917548genetic_marker
CRI-A2_SNP_Ga07_64927744CRI-A2_SNP_Ga07_64927744genetic_marker
CRI-A2_INDEL_Ga07_65570588CRI-A2_INDEL_Ga07_65570588genetic_marker
CRI-A2_SNP_Ga07_65588770CRI-A2_SNP_Ga07_65588770genetic_marker
CRI-A2_SNP_Ga07_66730240CRI-A2_SNP_Ga07_66730240genetic_marker
CRI-A2_SNP_Ga07_66732346CRI-A2_SNP_Ga07_66732346genetic_marker
CRI-A2_INDEL_Ga07_66737515CRI-A2_INDEL_Ga07_66737515genetic_marker
CRI-A2_INDEL_Ga07_66737523CRI-A2_INDEL_Ga07_66737523genetic_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