Population Structure and Genetic Diversity in a Rice Core Collection (Oryza sativa L.) Investigated with SSR Markers

Peng Zhang; Jinquan Li; Xiaoling Li; Xiangdong Liu; Xingjuan Zhao; Yonggen Lu
December 2011
PLoS ONE;2011, Vol. 6 Issue 12, p1
Academic Journal
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.


Related Articles

  • Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. Nhung Thi Phuong Phung; Chung Duc Mai; Mournet, Pierre; Frouin, Julien; Droc, Gaëtan; Nhung Kim Ta; Jouannic, Stefan; Loan Thi Lê; Vinh Nang Do; Gantet, Pascal; Courtois, Brigitte // BMC Plant Biology;2014, Vol. 14 Issue 1, p603 

    Background The development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide...

  • A first insight into population structure and linkage disequilibrium in the US peanut minicore collection. Belamkar, Vikas; Selvaraj, Michael; Ayers, Jamie; Payton, Paxton; Puppala, Naveen; Burow, Mark // Genetica;Apr2011, Vol. 139 Issue 4, p411 

    Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore...

  • Dissecting the genetic make-up of North-East Sardinia using a large set of haploid and autosomal markers. Pardo, Luba M; Piras, Giovanna; Asproni, Rosanna; van der Gaag, Kristiaan J; Gabbas, Attilio; Ruiz-Linares, Andres; de Knijff, Peter; Monne, Maria; Rizzu, Patrizia; Heutink, Peter // European Journal of Human Genetics;Sep2012, Vol. 20 Issue 9, p956 

    Sardinia has been used for genetic studies because of its historical isolation, genetic homogeneity and increased prevalence of certain rare diseases. Controversy remains concerning the genetic substructure and the extent of genetic homogeneity, which has implications for the design of...

  • LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. Machiela, Mitchell J.; Chanock, Stephen J. // Bioinformatics;11/1/2015, Vol. 31 Issue 21, p3555 

    Summary: Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules...

  • Different models of genetic variation and their effect on genomic evaluation. Clark, Samuel A.; Hickey, John M.; Van der Werf, Julius H. J. // Genetics Selection Evolution;May2011, Vol. 43 Issue 5, p1 

    Background: The theory of genomic selection is based on the prediction of the effects of quantitative trait loci (QTL) in linkage disequilibrium (LD) with markers. However, there is increasing evidence that genomic selection also relies on "relationships" between individuals to accurately...

  • Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens. Wragg, D; Mwacharo, J M; Alcalde, J A; Hocking, P M; Hanotte, O // Heredity;Jul2012, Vol. 109 Issue 1, p6 

    Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken...

  • Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates. Freyer, Gertraude; Hernández-Sánchez, Jules; Vukasinovic, Natascha // BMC Genetics;2010, Vol. 11, p85 

    Background: A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker...

  • HLA class II, MICA and PRL gene polymorphisms: the common contribution to the systemic lupus erythematosus development in Czech population. Fojtíková, Markéta; Novota, Peter; Čejková, Pavlína; Pešičková, Satu; Tegzová, Dana; Černá, Marie // Rheumatology International;Sep2011, Vol. 31 Issue 9, p1195 

    The genetic components contribute to the systemic lupus erythematosus development. This study for the first time determined the distribution of the polymorphisms and linkage disequilibrium in HLA class II, MICA and PRL gene among patients suffering from SLE and healthy Czech individuals. DNA was...

  • The Spatial Mixing of Genomes in Secondary Contact Zones. Sedghifar, Alisa; Brandvain, Yaniv; Ralph, Peter; Coop, Graham // Genetics;9/1/2015, Vol. 201 Issue 1, p243 

    Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. These...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics