Genomic Characterization, Relatedness, and Analysis of Luther Burbank’s Plum (Prunus sp) Introductions using Genotyping by Sequencing (GBS)
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Genomic Characterization, Relatedness, and Analysis of Luther Burbank’s Plum (Prunus sp) Introductions using Genotyping by Sequencing (GBS)


Historic breeding populations often have limited pedigree notation and genomic data associated with them. A prime example of this is the Plum Collection of over 150 cultivars introduced by Luther Burbank between the 1880’s-1920’s which consisted of many different Prunus species, the most prominent of which were combinations of the diploid species P. salicina, P. simonii, P. americana, and the hexaploid species P. domestica. The primary goals of this study were to locate as many of Burbank’s introductions as possible and to investigate their pedigrees and genetic diversity. Fifty-three cultivars were located at three California sites; the USDA-ARS-National Clonal Germplasm Repository at the Wolfskill Experimental Orchard , Luther Burbank Home & Gardens, Gold Ridge Experiment Farm, and at numerous scion exchanges held by the California Rare Fruit Growers. These taxa were analyzed using genotyping by sequencing (GBS) which retrieved over 24,000 SNPs spread over eight chromosomes with degrees of heterozygosity that ranged from 5.33% - 30.90%, with an average of 13.28%. The transition/transversion rates of SNPs retrieved were 60.99% and 33.73% respectively The remaining SNPs are indels.SNP data were visualized using Identity by Descent (IBD) heatmaps, dendrograms, kinship matrices, and phylogenetic admixture plots. Eight distinct kinship groups emerged as significant using approximately unbiased bootstrapping on a dendrogram. Phylogenetic admixture analyses optimized at K=4 corresponded to P. salicina, P. simonii, European plums (P. domestica and P. cerasifera), and North American plums (P. americana and P. rivularis). The heatmap visualized shared rare alleles. Combined with phylogenetic admixture, the IBD analyses show how the taxa are related to each other. Lastly, fruits scored for exocarp color, mesocarp color, free or cling-stone endocarps, and general shape were compared to genotypic data using genome-wide association studies (GWAS) and integrated haplotype scoring (iHS). Using Bonferroni-corrected and false discovery rate (FDR) p-values as a threshold of significance at alpha=0.05, GWAS showed exocarp color significantly correlated to a SNP on chromosome 2. Mesocarp color showed SNPs on chromosomes 2 and 3 that surpassed significance thresholds for association at FDR alpha=0.15. Similarly, free and cling-stone endocarps have a prominent, non-significant SNP on chromosome 7, and shape appears to be a multi-genic trait with SNP areas of interest on chromosomes 1, 3, 4,and 6. These results await confirmation in a larger sample. The iHS showed areas of improvement via long haplotypes on chromosomes 2, 4, and 7. Traits being selected against, as indicated by short haplotypes, were detected on chromosomes 1, 2, 3, 5, and 6. Taken together, these analyses provide new insights into the identities among Burbank’s Prunus introductions and the potential of these valuable genetic resources for further development in the horticultural industry.

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