SNP-Based Genetic Diversity Assessment in a Tropical japonica Rice Breeding Program.

The use of single nucleotide polymorphisms (SNPs) in plant breeding has increased in recent years due to their higher efficiency, stability, and cost-effectiveness relative to other types of DNA markers. We explored the potential use of SNP markers for the tropical japonica rice-based breeding program of Mississippi. Tropical japonica is the main subspecies of rice grown in the southern US that has been derived from only a few dozen progenitors. We, therefore, conducted a preliminary survey on the genetic diversity existing in a set of 101 varieties/breeding lines that comprise a part of the active breeding germplasm used in Mississippi rice breeding program. Leaf punch samples were collected from each variety at 4-5 weeks after planting. DNA extractions were done using the magnetic bead-based sbeadex® chemistry while SNP analysis was perform by KASP genotyping chemistry, both provided by LGC Genomics (http://www.lgcgroup.com). Potentially useful SNPs for tropical japonicas, were initially distilled from an earlier published dataset. A subset of 97 tropical japonicas from the 413 diverse panel was surveyed, and among the 36,901 SNPs, 5,912 SNPs or 16.0% were polymorphic among tropical japonica varieties. The SNPs were further reduced by retaining SNPs having an average of 329,000 bp interval across the 12 rice chromosomes, finally resulting in 1,054 SNPs that were used in the assays. Cluster analysis clearly separated the few indica entries from the mostly tropical japonica materials. Mississippi developed varieties and breeding lines were evenly spread within the tropical japonica group. Rex, the most popular conventional variety in Mississippi was the most genetically distinct among locally released conventional varieties. Knowing the genetic diversity in this breeding pool will be important in the planning and execution of future breeding strategies.