Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

Simple item page
cg.identifier.doihttps://doi.org/10.1371/journal.pgen.1007521
cg.issn1553-7404
cg.issue8
cg.journalPLOS Genetics
cg.numbere1007521
cg.volume14
dc.contributor.authorZhao, Yan
dc.contributor.authorZhang, Hongliang
dc.contributor.authorXu, Jianlong
dc.contributor.authorJiang, Conghui
dc.contributor.authorYin, Zhigang
dc.contributor.authorXiong, Haiyan
dc.contributor.authorXie, Jianyin
dc.contributor.authorWang, Xueqiang
dc.contributor.authorZhu, Xiaoyang
dc.contributor.authorLi, Yang
dc.contributor.authorZhao, Weipeng
dc.contributor.authorRashid, Muhammad Abdul Rehman
dc.contributor.authorLi, Jinjie
dc.contributor.authorWang, Wensheng
dc.contributor.authorFu, Binying
dc.contributor.authorYe, Guoyou
dc.contributor.authorGuo, Yan
dc.contributor.authorHu, Zhiqiang
dc.contributor.authorLi, Zhikang
dc.contributor.authorLi, Zichao
dc.date.accessioned2024-12-19T12:54:20Zen
dc.date.available2024-12-19T12:54:20Zen
dc.identifier.urihttps://hdl.handle.net/10568/164819
dc.titleLoci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditionsen
dcterms.abstractA robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditionsen
dcterms.accessRightsOpen Access
dcterms.available2018-08-10
dcterms.bibliographicCitationZhao, Yan; Zhang, Hongliang; Xu, Jianlong; Jiang, Conghui; Yin, Zhigang; Xiong, Haiyan; Xie, Jianyin; Wang, Xueqiang; Zhu, Xiaoyang; Li, Yang; Zhao, Weipeng; Rashid, Muhammad Abdul Rehman; Li, Jinjie; Wang, Wensheng; Fu, Binying; Ye, Guoyou; Guo, Yan; Hu, Zhiqiang; Li, Zhikang and Li, Zichao. 2018. Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions. PLoS Genet, Volume 14 no. 8 p. e1007521en
dcterms.issued2018-08-10
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherPublic Library of Science
dcterms.subjectaerobiosisen
dcterms.subjectallelesen
dcterms.subjectcloningen
dcterms.subjectdomesticationen
dcterms.subjectlocien
dcterms.subjectquantitative trait locien
dcterms.typeJournal Article

Files

Collections

IRRI Journal Articles