Use of DArT-seq Markers to Study Genetic Diversity in Japanese Rice Accessions

To know the genetic diversity and population structure allows to explore alleles related to different characteristics, important for plant breeding. Rice germplasm bank of ESALQ - USP Genetics Department contains 192 Japanese accessions that were studied to understand their genetic diversity and population structure. Molecular characterization was carried out using DArTseq markers. After obtaining these markers, the data were filtered using some parameters: absence of missing data, allele frequency minimum, reading depth, reproducibility and linkage disequilibrium, which resulted 1.592 SNPs. Then R environment packages, adegenet and PopGenReport, were used in order to calculate the genetic diversity and how it is structured in the population. The estimated diversity parameters were: expected heterozygosity (H_S), observed heterozygosity (H_O) and inbreeding dependent on the reproductive system (F_IS). DAPC was used to obtain the population structure. H_O and H_S values found were 0.02 and 0.06, respectively. F_IS value found was 0.71. It is very common to find smaller H_O values than H_S values in rice, because it is a species with low outcrossing rate and loci tend to homozygosity. Due to the same reason we found high value for F_IS. The H_S values suggests that there is genetic diversity in the accessions, and it is structured in five clusters, containing 9, 42, 58, 40 and 43 accessions, with 59, 65, 65, 60 and 67 alleles, respectively. The existence of genetic structure in the studied population is expected, once the accessions are from different regions of Japan and went through different selection processes.