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

A 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, comprehe...

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Bibliographic Details
Published in:PLoS genetics 2018-08, Vol.14 (8), p.e1007521-e1007521
Main Authors: Zhao, 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, Li, Zichao
Format: Article
Language:English
Subjects:
Adaptation
Adaptation, Physiological - genetics
Aerobic conditions
Alleles
Analysis
Biology and Life Sciences
Biometeorology
Chromosome Mapping
Climate change
Cloning
Crop science
DNA, Bacterial - genetics
Domestication
Drought
Ecotype
Ecotypes
Education
Farmers
Gene Frequency
Gene mapping
Genetic Association Studies
Genetic diversity
Genetically altered foods
Genomes
Geographical distribution
Haplotypes
Intraspecific genetic variation
Laboratories
Oryza
Oryza - genetics
Oryza - physiology
Phenotyping
Phylogeny
Physiology
Plant Roots - genetics
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Research and Analysis Methods
Rice
Robustness (Statistics)
Single-nucleotide polymorphism
Supervision
T-DNA
Whole Exome Sequencing
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Summary:A 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 conditions.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1007521