Population Structure and Phylogeny of Some U.S. Peach Cultivars

Abstract

Peach (Prunus persica) cultivars maintained at the U.S. Department of Agriculture program at Byron, GA, have never been characterized with any molecular markers. In this study, 20 microsatellite markers were used to genotype 112 cultivars and the data were analyzed to discern their population structure and phylogenetic relationships. STRUCTURE simulations revealed four K clusters and broad genetic admixture among the cultivars. Principal coordinate analysis (PCoA) showed the cultivar groups from western, northeastern, and southeastern U.S. states were adjacent to each other except cultivars from Michigan (close to most southeastern state groups) and Florida (most distant from the other groups). Principal component analysis (PCA) showed that these cultivars had no obvious PCA partitioning boundaries. The intertwined distribution in both PCoA and PCA partitions suggested many of them were genetically closely related to each other largely because most shared same ancestral parentages. Most pairwise distance means within and between the cultivar groups were relatively low, suggesting close phylogenetic relations among those cultivars, as were demonstrated in the phylogenetic tree. Limiting factors and perspectives relevant to peach breeding are discussed.

Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers

“…In the study of 195 peach genotypes from the breeding pools of the University of Florida using a set of 36 SSR markers, PIC value was practically the same as in our study and averaged 0.48 [13]. In another study of 112 cultivars from the US using 20 SSRs, the average PIC value (0.32) was lower [14]. As well as in the study of 94 Asian peach accessions using the set of 34 SSRs (mean PIC = 0.40) [18].…”

“…The study of 94 native Spanish and foreign peach cultivars using 15 SSRs revealed 6.73 alleles per locus with average observed heterozygosity 0.23 [24]. Four alleles per locus and the heterozygosity mean value 0.33 were detected in the study of 112 peach cultivars from public and private US breeding programs using 20 SSR markers [14]. While for the 168 peach and nectarine cultivars and advanced selections from the University of Florida, 6.41 alleles per locus were detected using 36 SSRs with an average H o = 0.41 [13].…”

“…Only two genotypes were identified for UDP98-405: two cultivars 'Kievskij Samyj Rannij' and 'Zheltoplodnyj Rannij' had one genotype and the remaining accessions had the other one. The largest number of genotypes (14) was identified using UDP96-005, BPPCT025, and CPPCT-022 markers. Polymorphism information content (PIC) varied from 0.04 (UDP98-405) to 0.68 (UDP98-022, CPPCT-022) and averaged 0.49.…”

“…Another study used 48 SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among more than 600 Chinese, North American, and European cultivars and demonstrated higher level of genetic diversity and relatively fast decay of LD in the Oriental peach germplasm [12]. Different sets of SSR markers were also used to determine the genetic diversity and population structure of the breeding peach germplasm in the USA [13][14][15] and Brazil [16], to evaluate the genetic variation and linkage disequilibrium in Chinese peach cultivars and landraces [17][18][19][20] and for peach and nectarine cultivars fingerprinting [21]. The molecular genetic studies of the Nikita Botanical Garden peach collection were fragmented and most of the peach cultivars bred in NBG have not been analyzed using SSR markers.…”