Abstract
BackgroundPeach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars.ResultsIn total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: ‘Yu Lu’ and ‘Hakuho’. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the ‘Yu Lu’ subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations.ConclusionsOur study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach.
Highlights
Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family
Genetic diversity of the accessions The 48 simple sequence repeat markers (SSRs) selected in this research were polymorphic in both Oriental and Occidental samples, amplifying a total of 588 alleles (Table 1), with an average of 12.25 alleles per locus
Loci were highly informative: the highest power of discrimination (PD) between two random cultivars was observed in BPPCT006 (PD = 0.95), and the lowest in PMS02 (PD = 0.28)
Summary
Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. Being the centre of origin of peach, China has the longest history of peach cultivation (more than 4,000 years), and the richness of genetically diverse germplasm can provide useful genes to breed cultivars with enhanced resistance to pests and diseases, improved fruit size and quality, and a longer postharvest shelf-life. After introducing ‘Shanghai Shui Mi’ as parents in the early 20th century, Japan selected out ‘Hakuto’ [6,7] and the USA released the famous cultivar ‘Elberta’. Both ‘Hakuto’ and ‘Elberta’ were extensively used as parents for further breeding of modern cultivars [8,9]. Over the last few decades, considerable effort has been put into peach breeding in the USA, South Africa, Brazil, Argentina, Australia, China, Spain, Italy, France and Japan [10], producing almost 2,000 new cultivars; half of these have been registered in and come from the USA while only 5% are from China [11,12]
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