Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa.

Vishnu Varthini Nachimuthu,Manonmani Swaminathan,Rajeswari Sivakami,Balaji Aravindhan Pandian,Sudhakar Duraialaguraja,Karthika Gunasekaran,Raveendran Muthurajan,Govinthraj Ponniah,Robin Sabariappan,Suji K K

doi:10.1186/s12284-015-0062-5

Abstract

BackgroundGenetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining/association mapping. Association mapping based on LD (Linkage dis-equilibrium), non-random associations between causative loci and phenotype in natural population is highly useful in dissecting out genetic basis of complex traits. For any successful association mapping program, understanding the population structure and assessing the kinship relatedness is essential before making correlation between superior alleles and traits. The present study was aimed at evaluating the genetic variation and population structure in a collection of 192 rice germplasm lines including local landraces, improved varieties and exotic lines from diverse origin.ResultsA set of 192 diverse rice germplasm lines were genotyped using 61 genome wide SSR markers to assess the molecular genetic diversity and genetic relatedness. Genotyping of 192 rice lines using 61 SSRs produced a total of 205 alleles with the PIC value of 0.756. Population structure analysis using model based and distance based approaches revealed that the germplasm lines were grouped into two distinct subgroups. AMOVA analysis has explained that 14 % of variation was due to difference between with the remaining 86 % variation may be attributed by difference within groups.ConclusionsBased on these above analysis viz., population structure and genetic relatedness, a core collection of 150 rice germplasm lines were assembled as an association mapping panel for establishing marker trait associations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0062-5) contains supplementary material, which is available to authorized users.

Highlights

Genetic diversity is the main source of variability in any crop improvement program
Based on these above analysis viz., population structure and genetic relatedness, a core collection of 150 rice germplasm lines were assembled as an association mapping panel for establishing marker trait associations
Full list of author information is available at the end of the article and exploitation of rich genetic diversity existing in rice germplasm of India

Summary

Introduction

Genetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining/association mapping. Genetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining/. Association mapping based on LD (Linkage dis-equilibrium), non-random associations between causative loci and phenotype in natural population is highly useful in dissecting out genetic basis of complex traits. For any successful association mapping program, understanding the population structure and assessing the kinship relatedness is essential before making correlation between superior alleles and traits. 90 % of the world’s rice is produced in Asia and India contributes 20 % of the world’s production. This record level production and productivity is due to the availability.

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