Genetic characterization of Japanese plum (Prunus salicina L.) cultivars and segregant populations through Genotyping-By-Sequencing (GBS) and Simple Sequence Repeat (SSR) technologies

Next-generation sequencing technologies have dramatically accelerated the use of genetic information for genome diversity analysis and genetic mapping in plants. Genotyping-by-sequencing (GBS) is a next-generation DNA sequencing (NGS) technology that can analyzed hundreds of thousands of short reads from a genome, allowing a direct and inexpensive single nucleotide polymorphism (SNP) detection from germplasm collections. Our objective was to identify and characterize SNPs through commercial cultivars and segregant populations with known paternity relationships. We used the GBS technology to characterize a collection of 29 commercially important Japanese plum (Prunus salicina L.) cultivars plus 116 offspring derivated from controlled cross among Japanese plum cultivars. We analyzed 68 offspring from Angeleno (♀) by Aurora (♂) and 48 offspring from Flavor Rich (♀) by Larry Ann (♂). Previously, a paternity analysis was conducted in order to verify the filiations for individuals of each segregant population. We calculate the paternity index (PI), combinated paternity index (CPI) and probability of paternity (W) using 17 simple sequence repeat (SSR). The sequencing and filtering process gave 1,784,547 tags. The tags were aligned to the peach reference genome, where 50% aligned to unique position, 5% aligned to multiple position and 45% could not be aligned. Finally after filtering, 57,542 SNP were identified. We discussed the useful of high-throughput GBS to characterize the genetic diversity of commercial cultivars and segregant populations of Japanese plum. Acknowledgements: This research was supported by CONICYT, FONDECYT/Regular Nº1120261.