Assessment of the genetic diversity and population structure in temperate japonica rice germplasm used in breeding in Chile, with SSR markers

Viviana Becerra1*, Mario Paredes1, Marcio E. Ferreira2, Eduardo Gutiérrez1, and Lucy M. Díaz3
Rice Breeding Program (RBP) of the Instituto de Investigaciones Agropecuarias (INIA) at Chillán, Chile, has a rice (Oryza sativa L.) germplasm collection that consists of 1200 accessions, which are mainly temperate japonica rice accessions, well adapted to the local conditions. Most of the new accessions introduced in the country adapt very poorly to Chilean agroecological conditions because of the requirements of long days and cold tolerance. The objectives of this study were to use microsatellites to evaluate the level of polymorphism of a representative sample of the Chilean rice collection and determine its genetic diversity and relationships with cultivated germplasm from different geographical origin. A total of 249 genotypes were analyzed with 30 selected polymorphic microsatellites. The total number of alleles scored across the 249 genotypes was 183 with an overall mean of 6.1 alleles per locus, ranging from 2 to 14. The mean major allele (most common) frequency was 0.61 and the mean minor allele frequency was 0.028. The overall mean gene diversity across the 30 SSR loci was 0.52. Mean heterozygosity was 0.01, and mean polymorphism information content (PIC) value was 0.47. The accessions of this study were organized by the structure analysis into three main groups and revealed a fairly consistent genetic relationship with the dendrogram and the Principal Coordinates Analysis (PCoA). The temperate japonica accessions can be further subdivided into three subpopulations where the long and short Chilean varieties were grouped into different clusters. The three populations, showed different level of admixture, admixture probably due to the previous breeding work through years. Theresults indicate that polymorphism levels detected the Chilean rice temperate japonica collection has similar order of magnitude as temperate japonica germplasm reported in the literature.
Keywords: Genetic diversity, microsatellites, Oryza sativa, rice, temperate japonica germplasm.
1 Instituto de Investigaciones Agropecuarias, INIA Quilamapu, Av. Vicente Méndez 515, Chillán, Chile.
*Corresponding author (vbecerra@inia.cl).
2Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, SAIN Parque Estação Biológica, 70.770-917 Brasilia DF, Brasil.
3Centro Internacional de Agricultura Tropical, CIAT, Apartado aéreo 6713, Cali, Colombia.