title: Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Plant Molecular Biology, Plant Breeding and Genetics Divison, International Rice Research Institute, Manila, Philippines. popvarun@gmail.com.
authors.forename: Vishnu Varthini
authors.initials: VV
authors.lastname: Nachimuthu
authors.affiliation: Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India. raveendrantnau@gmail.com.
authors.forename: Raveendran
authors.initials: R
authors.lastname: Muthurajan
authors.affiliation: Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India. dsudhakar@hotmail.com.
authors.forename: Sudhakar
authors.initials: S
authors.lastname: Duraialaguraja
authors.affiliation: Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India. rajisundar93@gmail.com.
authors.forename: Rajeswari
authors.initials: R
authors.lastname: Sivakami
authors.affiliation: Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India. aaron.agri@gmail.com.
authors.forename: Balaji Aravindhan
authors.initials: BA
authors.lastname: Pandian
authors.affiliation: International Crops Research Institute for the Semi-Arid-Tropics, Hyderabad, India. sanjay.626@gmail.com.
authors.forename: Govinthraj
authors.initials: G
authors.lastname: Ponniah
authors.affiliation: Crop Physiology laboratory, International Crops Research Institute for the Semi-Arid-Tropics, Hyderabad, India. karthi.tnau07@gmail.com.
authors.forename: Karthika
authors.initials: K
authors.lastname: Gunasekaran
authors.affiliation: Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India. swamimano@yahoo.co.in.
authors.forename: Manonmani
authors.initials: M
authors.lastname: Swaminathan
authors.affiliation: Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India. krishika_suji@yahoo.co.in.
authors.forename: Suji
authors.initials: S
authors.lastname: K K
authors.affiliation: Centre of Excellence in Molecular Breeding, Tamil Nadu Agricultural University, Coimbatore, India. robin.tnau@gmail.com.
authors.forename: Robin
authors.initials: R
authors.lastname: Sabariappan
keywords: Association mapping; Genetic diversity; Molecular variance; Polymorphism information content; Population structure; Rice