From Population to Association Genetic Analyses in Prunus umbellata Elliot, Can GBS Do It All?—A Comparison of SSR and SNP Markers

Prunus umbellata is a diploid plum species native to the Southern US with a wide geographic range and adaptation to different soils and environments. Other species native to the Southern US include P. americana Marsh., P. angustifolia Marsh., and P. geniculata Harper. The objective of this research was to evaluate P. umbellata as a model plant for the identification of genomic regions associated with dormancy response. A total of 48 genotypes: 42 of P. umbellata ranging from central Georgia to south Florida, 2 of P. americana, 2 of P. angustifolia, and 2 of P. geniculata, were fingerprinted using 41 SSRs distributed across the peach genome (~15-25 cM). Similarly, genotype-by-sequencing (GBS) was used to identify SNPs across the genome of 48 multiplexed genotypes using Illumina HiSeq^® 2000 system. GBS produced up to 175 million reads in one flow cell lane, yielding approximately 40 Gb of data, with a filtered 101 million reads and an average of 2.1 million reads per genotype. SNP markers were detected using Stacks software and ranged from 30,411 markers (6x depth) for at least 33 genotypes (r=0.7 or 70% of genotypes required to process a locus) to 487 markers (6x depth) for all genotypes (r=1.0 or 100% of genotypes required to process a locus). Genetic diversity and population structure results based on SSR and SNP markers (using different depth coverage and r values) were comparable. SSR and SNPs markers allowed the identification of hybrid genotypes among species. Similarly, these markers were used to identify genomic regions associated with dormancy response.