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_Ga07_8804817CRI-A2_SNP_Ga07_8804817genetic_marker
CRI-A2_INDEL_Ga07_8886702CRI-A2_INDEL_Ga07_8886702genetic_marker
CRI-A2_SNP_Ga07_8891427CRI-A2_SNP_Ga07_8891427genetic_marker
CRI-A2_INDEL_Ga07_8985962CRI-A2_INDEL_Ga07_8985962genetic_marker
CRI-A2_SNP_Ga07_9015938CRI-A2_SNP_Ga07_9015938genetic_marker
CRI-A2_SNP_Ga07_9024124CRI-A2_SNP_Ga07_9024124genetic_marker
CRI-A2_SNP_Ga07_9072421CRI-A2_SNP_Ga07_9072421genetic_marker
CRI-A2_INDEL_Ga07_9100525CRI-A2_INDEL_Ga07_9100525genetic_marker
CRI-A2_INDEL_Ga07_9100528CRI-A2_INDEL_Ga07_9100528genetic_marker
CRI-A2_SNP_Ga07_9129697CRI-A2_SNP_Ga07_9129697genetic_marker
CRI-A2_SNP_Ga07_9227779CRI-A2_SNP_Ga07_9227779genetic_marker
CRI-A2_INDEL_Ga07_9267100CRI-A2_INDEL_Ga07_9267100genetic_marker
CRI-A2_SNP_Ga07_9280006CRI-A2_SNP_Ga07_9280006genetic_marker
CRI-A2_INDEL_Ga07_9286535CRI-A2_INDEL_Ga07_9286535genetic_marker
CRI-A2_SNP_Ga07_9333023CRI-A2_SNP_Ga07_9333023genetic_marker
CRI-A2_SNP_Ga07_9390801CRI-A2_SNP_Ga07_9390801genetic_marker
CRI-A2_SNP_Ga07_9403476CRI-A2_SNP_Ga07_9403476genetic_marker
CRI-A2_SNP_Ga07_9431734CRI-A2_SNP_Ga07_9431734genetic_marker
CRI-A2_SNP_Ga07_9456505CRI-A2_SNP_Ga07_9456505genetic_marker
CRI-A2_SNP_Ga07_9479945CRI-A2_SNP_Ga07_9479945genetic_marker
CRI-A2_SNP_Ga07_9532393CRI-A2_SNP_Ga07_9532393genetic_marker
CRI-A2_SNP_Ga07_9539224CRI-A2_SNP_Ga07_9539224genetic_marker
CRI-A2_SNP_Ga07_9552211CRI-A2_SNP_Ga07_9552211genetic_marker
CRI-A2_SNP_Ga07_9553261CRI-A2_SNP_Ga07_9553261genetic_marker
CRI-A2_INDEL_Ga07_9586504CRI-A2_INDEL_Ga07_9586504genetic_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