ArticlePLoS genetics2018
Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 101 citations in OpenAlex.
- Knockout of RRS1 Enhances Culm Mechanical Strength and Grain Yield in Rice.Plant, cell & environment · 2026Article
- Engineered diazotrophs with host-inducible nitrogen supply systems: Transforming rice farming through innovative nitrogen biofertilizers.Journal of integrative plant biology · 2026Review
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Article
- Unveiling genetic loci and natural alleles for seed iron accumulation in adzuki bean via genome-wide association study.BMC plant biology · 2026Article
- Genome-wide association analysis identifies SNP loci for multi-stage yield-related traits in wheat.Frontiers in plant science · 2026Article
- Rice cycles between drought and well-watered-adapted phenotypes by changing lateral root formation.Annals of botany · 2025Article
- Elite haplotype of STRONG1 enhances rice yield by improving lodging resistance, panicle and plant architecture.Nature communications · 2025Article
- Identifying Heat Adaptability QTLs and Candidate Genes for Grain Appearance Quality at the Flowering Stage in Rice.Rice (New York, N.Y.) · 2025Article
- Natural variation of CTB5 confers cold adaptation in plateau japonica rice.Nature communications · 2025Article
- Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice (International journal of molecular sciences · 2024Article
- Identification of genetic variants controlling diosgenin content in Dioscorea zingiberensis tuber by genome-wide association study.BMC plant biology · 2024Article
- Article
- Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding.Plant biotechnology journal · 2024Article
- Identification and characterization of candidate genes for primary root length in Asiatic cotton (Gossypium arboreum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.Rice (New York, N.Y.) · 2023Article
- Dissecting the genetic architecture of root-related traits in a grafted wild Vitis berlandieri population for grapevine rootstock breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genome-Wide Association Study Reveals the Genetic Basis of Total Flavonoid Content in Brown Rice.Genes · 2023Article
- Utilization of natural alleles for heat adaptability QTLs at the flowering stage in rice.BMC plant biology · 2023Article
- Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding.Journal of advanced research · 2022Article
Corrections and comments
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Authors and funding
20 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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