Genomic regions and candidate genes selected during the breeding of rice in Vietnam

Higgins, Janet; Santos, Bruno; Khanh, Tran Dang; Trung, Khuất Hữu; Duong, Tran Duy; Doai, Nguyen Thi Phuong; Hall, Anthony; Dyer, Sarah; Hàm, Lê Huy; Cáccamo, Mario; Vega, Jose J De

doi:10.1111/eva.13433

Cited by 4 publications

(1 citation statement)

References 102 publications

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“…The deep sequencing of six elite rice varieties and the use of two large control panels led to the identification of elite variety-tagged SNP alleles and the validation of an important allele in upland rice for denser lateral roots using transgenic plants [12]. Sixty-five genes in a Indica-5 subpopulation with characteristics of novelty and differential evolution were identified by genomic selection analysis among Vietnamese rice varieties [26]. Although information regarding many genomic variations is available for rice, there has been limited research on complex traits, such as drought and salt tolerance.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Scan for Genetic Signatures Based on the Whole-Genome Resequencing of Salt- and Drought-Tolerant Rice Varieties

et al. 2023

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Identifying elite stress-tolerant varieties and elucidating the genetic mechanisms mediating stress resistance can help breeders develop and exploit new rice germplasm resources. In this study, we identified five salt-tolerant varieties and five drought-tolerant upland rice varieties by survival rate and drought tolerance grade and constructed variation maps of the resistance using a deep-sequencing approach. Using 116 rice accessions from the 3000 Rice Genomes Project, we characterized the population structure of sequenced varieties. Through comparative genomics and transcriptome analysis, we screened 39 salt-response candidate genes. Natural variation analysis on root length-related drought candidate gene showed that Hap1 and Hap4 were the predominant haplotypes in indica, while Hap5 was the predominant haplotype in japonica. Gene Ontology (GO) analysis showed that carbohydrate metabolic process, defense response, and response to stimulus were the common GO terms associated with salt and drought tolerance. Selective signatures in elite stress-tolerant varieties indicated that multiple important stress tolerance genes, namely OsRac1, Pikp-2, Xa26, OsSIRP4, and wsl1, were selected and utilized in these sequenced rice varieties. These findings may be useful for clarifying the genetic variations among elite stress-tolerant varieties, while also laying the foundation for a more comprehensive investigation of the genetic basis of salt and drought tolerance.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Scan for Genetic Signatures Based on the Whole-Genome Resequencing of Salt- and Drought-Tolerant Rice Varieties

et al. 2023

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A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants

Wang,

He,

et al. 2023

Nucleic Acids Research

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Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a large rice population with a total of 10 548 accessions to construct a rice super-population variation map (RSPVM), consisting of 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations and 184 736 presence/absence variations . Assessment of variation detection efficiency for different population sizes revealed a sharp increase of all types of variation as the population size increased and a gradual saturation of that after the population size reached 10 000. Variant frequency analysis indicated that ∼90% of the obtained variants were rare, and would therefore likely be difficult to detect in a relatively small population. Among the rare variants, only 2.7% were predicted to be deleterious. Population structure, genetic diversity and gene functional polymorphism of this large population were evaluated based on different subsets of RSPVM, demonstrating the great potential of RSPVM for use in downstream applications. Our study provides both a rich genetic basis for understanding natural rice variations and a powerful tool for exploiting great potential of rare variants in future rice research, including population genetics and functional genomics.

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Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes

Schläppi,

Jessel,

Jackson

et al. 2023

Front. Plant Sci.

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Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.

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Genomic regions and candidate genes selected during the breeding of rice in Vietnam

Cited by 4 publications

References 102 publications

Genome-Wide Scan for Genetic Signatures Based on the Whole-Genome Resequencing of Salt- and Drought-Tolerant Rice Varieties

Genome-Wide Scan for Genetic Signatures Based on the Whole-Genome Resequencing of Salt- and Drought-Tolerant Rice Varieties

A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants

Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes

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