ArticlePloS one2011
Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Uncovering the historic genetic diversity of Ugandan Robusta coffee germplasm: a foundation for core collection design.BMC plant biology · 2026Article
- A technique for measuring non-structural carbohydrate reserves in flag leaves of paddy rice using Fourier transform infrared spectroscopy (FTIR).Plant methods · 2025Article
- Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management.The plant genome · 2024Article
- Genetic profiles and phenotypic patterns in Taiwanese Phalaenopsis orchids: a two-step phenotype and genotype strategy using modified genetic distance algorithms.Frontiers in plant science · 2024Article
- Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Physiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids byPlants (Basel, Switzerland) · 2022Article
- Molecular Genetic Diversity and Combining Ability for Some Physiological and Agronomic Traits in Rice under Well-Watered and Water-Deficit Conditions.Plants (Basel, Switzerland) · 2022Article
- Evaluation of gene flow and genetic diversity in rice accessions across Kurdistan region-iraq using SSR markers.Molecular biology reports · 2022Article
- Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping.Frontiers in plant science · 2022Article
- Identification of Heterotic Groups and Patterns Based on Genotypic and Phenotypic Characteristics Among Rice Accessions of Diverse Origins.Frontiers in genetics · 2022Article
- Allele mining for a drought responsive genePhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing.Plant & cell physiology · 2021Article
- Population genetic structure and association mapping for iron toxicity tolerance in rice.PloS one · 2021Article
- Association of molecular markers with physio-biochemical traits related to seed vigour in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Genetic Diversity of Pineapple (Tropical life sciences research · 2020Article
- Diversity analysis of selected rice landraces from West Bengal and their linked molecular markers for salinity tolerance.Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Detection of mPing mobilization in transgenic rice plants.Genes & genomics · 2020Article
- Genetic Diversity, Population Structure, and Marker-Trait Association for Drought Tolerance in US Rice Germplasm.Plants (Basel, Switzerland) · 2019Article
- Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers.Plants (Basel, Switzerland) · 2019Article
- Association mapping reveals multiple QTLs for grain protein content in rice useful for biofortification.Molecular genetics and genomics : MGG · 2019Article
4 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
The assessment of genetic diversity and population structure of a core collection would benefit to make use of these germplasm as well as applying them in association mapping. The objective of this study were to (1) examine the population structure of a rice core collection; (2) investigate the genetic diversity within and among subgroups of the rice core collection; (3) identify the extent of linkage disequilibrium (LD) of the rice core collection. A rice core collection consisting of 150 varieties which was established from 2260 varieties of Ting's collection of rice germplasm were genotyped with 274 SSR markers and used in this study. Two distinct subgroups (i.e. SG 1 and SG 2) were detected within the entire population by different statistical methods, which is in accordance with the differentiation of indica and japonica rice. MCLUST analysis might be an alternative method to STRUCTURE for population structure analysis. A percentage of 26% of the total markers could detect the population structure as the whole SSR marker set did with similar precision. Gene diversity and MRD between the two subspecies varied considerably across the genome, which might be used to identify candidate genes for the traits under domestication and artificial selection of indica and japonica rice. The percentage of SSR loci pairs in significant (P<0.05) LD is 46.8% in the entire population and the ratio of linked to unlinked loci pairs in LD is 1.06. Across the entire population as well as the subgroups and sub-subgroups, LD decays with genetic distance, indicating that linkage is one main cause of LD. The results of this study would provide valuable information for association mapping using the rice core collection in future.
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