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_SNP_Ga05_96614289CRI-A2_SNP_Ga05_96614289genetic_marker
CRI-A2_SNP_Ga05_96614504CRI-A2_SNP_Ga05_96614504genetic_marker
CRI-A2_INDEL_Ga05_96614642CRI-A2_INDEL_Ga05_96614642genetic_marker
CRI-A2_INDEL_Ga05_96614645CRI-A2_INDEL_Ga05_96614645genetic_marker
CRI-A2_SNP_Ga05_96614647CRI-A2_SNP_Ga05_96614647genetic_marker
CRI-A2_INDEL_Ga05_96614651CRI-A2_INDEL_Ga05_96614651genetic_marker
CRI-A2_SNP_Ga05_96615810CRI-A2_SNP_Ga05_96615810genetic_marker
CRI-A2_SNP_Ga05_96615845CRI-A2_SNP_Ga05_96615845genetic_marker
CRI-A2_INDEL_Ga05_96721374CRI-A2_INDEL_Ga05_96721374genetic_marker
CRI-A2_INDEL_Ga05_96779821CRI-A2_INDEL_Ga05_96779821genetic_marker
CRI-A2_INDEL_Ga05_96780218CRI-A2_INDEL_Ga05_96780218genetic_marker
CRI-A2_INDEL_Ga05_96780222CRI-A2_INDEL_Ga05_96780222genetic_marker
CRI-A2_INDEL_Ga05_96780303CRI-A2_INDEL_Ga05_96780303genetic_marker
CRI-A2_INDEL_Ga05_96780559CRI-A2_INDEL_Ga05_96780559genetic_marker
CRI-A2_INDEL_Ga05_96780566CRI-A2_INDEL_Ga05_96780566genetic_marker
CRI-A2_INDEL_Ga05_96780571CRI-A2_INDEL_Ga05_96780571genetic_marker
CRI-A2_INDEL_Ga05_96780573CRI-A2_INDEL_Ga05_96780573genetic_marker
CRI-A2_INDEL_Ga05_96780575CRI-A2_INDEL_Ga05_96780575genetic_marker
CRI-A2_INDEL_Ga05_96780723CRI-A2_INDEL_Ga05_96780723genetic_marker
CRI-A2_SNP_Ga05_96781055CRI-A2_SNP_Ga05_96781055genetic_marker
CRI-A2_INDEL_Ga05_96781089CRI-A2_INDEL_Ga05_96781089genetic_marker
CRI-A2_SNP_Ga05_96781280CRI-A2_SNP_Ga05_96781280genetic_marker
CRI-A2_INDEL_Ga05_96781637CRI-A2_INDEL_Ga05_96781637genetic_marker
CRI-A2_SNP_Ga05_96781928CRI-A2_SNP_Ga05_96781928genetic_marker
CRI-A2_INDEL_Ga05_96831001CRI-A2_INDEL_Ga05_96831001genetic_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