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Li X.-W.,Zhejiang University | Meng X.-Q.,Zhejiang University | Jia H.-J.,Zhejiang University | Yu M.-L.,Jiangsu Academy of Agricultural Sciences | And 9 more authors.
BMC Genetics | Year: 2013

Background: Peach (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.Results: In 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.Conclusions: Our 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. © 2013 Li et al.; licensee BioMed Central Ltd.

Xie R.,Zhejiang University | Xie R.,Chinese Academy of Agricultural Sciences | Li X.,Zhejiang University | Chai M.,Zhejiang University | And 6 more authors.
Scientia Horticulturae | Year: 2010

A total of 94 peach accessions from the Zhejiang province of China were analyzed using 34 polymorphic single-locus simple sequence repeat (SSR) markers. Genetic distance analysis divided the accessions into two major clusters, one with mainly local accessions from the Fenghua region. Preselected lines from some crosses were exclusively clustered with the local ones, possibly related to maintaining the taste quality of the fruit. The number of alleles per locus at most loci was two or three, with an average of 2.85. The value of observed heterozygosity varied from 0.05 to 0.84 (average of 0.48). Diversity within the introduced accessions was higher than that of the Fenghua local accessions. Of the accessions analyzed in this study, 94% were individually identified. Those that could not be differentiated were all derived from the 'Yulu' cultivar, being either mutations or of identical origin.Our results suggest that Fenghua accessions are derived from limited parental materials and inbreeding over a long period of time. They will be useful for breeders to better manage their pre-breeding materials and choice of parents for further crossings. © 2010 Elsevier B.V.

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