Genetically Distinct Rice Lines for Specific Characters as Revealed by Gene-Associated Average Pairwise Dissimilarity

Broadening the genetic base of an elite breeding gene pool is one important goal in a successful long-term plant breeding program. This goal is largely achieved through the search for and introgression of exotic germplasm with adaptive traits. However, little is known about the genetic backgrounds of acquired exotic germplasm, as germplasm selection is mainly based on trait information. Here, we expanded an average pairwise dissimilarity (APD) analysis to samples with SNP genotypes associated with genes for specific characters of breeding interest. Specifically, we explored a gene-associated APD analysis in a genomic characterization of 2643 rice lines based on their published FASTQ data. Published contigs for cloned genes conditioning heat tolerance, cold tolerance, fertility, and seed size were downloaded as gene reference sequences for SNP calling, along with those SNP calls based on the rice reference genome and published indels. Totally, eight SNP or indel data sets were formed for each of three sample groups (All2643, Indica1789, and Japonica854). APD estimation was made for each of the 24 data sets. For each sample group, four novel sets of the 25 most genetically distinct rice lines, each for an assayed character, were identified. Further analyses of APD estimates also revealed some interesting APD properties. Four contig-based SNP data sets for four specific characters displayed similar APD frequency distributions and positive high correlations of APD estimates. Contig-based APD estimates were negatively correlated with genome-based APD estimates and nearly uncorrelated with indel-based APD estimates. These findings are significant for plant germplasm characterization and germplasm utilization in plant breeding.