Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations

Tâm, Nguyễn Thành; Dwiyanti, Maria Stefanie; Koide, Yohei; Nagano, Atsushi J.; Kỳ, Huỳnh; Tin, Huynh Quang; Hiền, Nguyễn Lộc; Dung, Le Viet; Kishima, Yuji

doi:10.3835/plantgenome2019.06.0042

Cited by 8 publications

(18 citation statements)

References 60 publications

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“…Numerous techniques can be used to determine rice genetic variations in order to comprehend and use accessible gene bank accessions. Initially, isozyme markers were used to evaluate rice genetic diversity [12]; however, these have now been replaced with DNA markers, such as simple sequence repeats (SSRs), microsatellites [13,14], and single nucleotide polymorphisms (SNPs) [15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

et al. 2021

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Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to indica and japonica groups. The indica group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise FST showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.

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Section: Introductionmentioning

confidence: 99%

Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

et al. 2021

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“…Previous findings suggested that lower genetic diversity was experienced in a recent bottleneck during the domestication selection of the waxy locus in the waxy rice genome [69][70][71]. On the other hand, the remaining cultivated subgroups, indica, aus, and admixture (representing higher diversity landrace, weedy, and bred groups in another way) were higher in nucleotide diversity than that of the wild group, suggesting positive artificial selection due to the high π-value regions in each of these classified populations [68].…”

Section: Discussionmentioning

confidence: 97%

“…Of which, many starch synthesis genes have been studied on their genetics and genomics [47,66] but GBSSII is the only exception. Analysis of nucleotide diversity is important to highlight the functional importance of genomic regions [67] and it has also appeared to be useful to characterize local populations, representing the whole genome distribution of each population using π-values [68]. In our study, the nucleotide diversity analysis based on the classified ecotypes of 475 rice accessions revealed the lowest diversity values in japonica ecotypes (temperate japonica, 0.0029, and tropical japonica, 0.0030) despite the wild group representing its lowest diversity value (0.0045) on a variety basis, suggesting no significant differences between the wild group and any of the identified cultivated subgroups (Figure 3 and Table S3).…”

Section: Discussionmentioning

confidence: 99%

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Maung

Chu

Park

2021

Foods

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Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1–C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima’s D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima’s D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.

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“…Ninety-seven rice accessions consisting of 79 landraces and 18 improved accessions were selected from the Genebank of Mekong Delta Development Research Institute (MDI), Can Tho University, Vietnam (Supplementary Table 1) (Tam et al 2019). 'Nipponbare' and 'Pokkali' were added as sensitive and tolerant cultivar controls, respectively, for salinity stress.…”

Section: Plant Materialsmentioning

confidence: 99%

“…In this study, we investigated the salt tolerance and physiological characteristics of a diverse panel of landrace rice accessions cultivated in the Mekong Delta region (Tam et al 2019). We focused on the rice landrace variety 'Doc Phung', known to be particularly resistant to salt in the Mekong Delta (Ho et al 2018;Le 1999;Tin et al 2021).…”

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confidence: 99%

Identification of a Saltol-independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung

Tâm

Dwiyanti

Sakaguchi

et al. 2021

Preprint

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The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from –0.68 to –0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na+ in roots, stems, and leaves and Ca2+ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity (CEC) in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance–related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies (GWASs) using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3′ untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salt-tolerant varieties in the Mekong Delta population and a promising new genetic resource.

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Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations

Cited by 8 publications

References 60 publications

Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

Identification of a Saltol-independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung

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