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Peach genetic resources: diversity, population structure and linkage disequilibrium

Xiong-wei Li1, Xian-qiao Meng1, Hui-juan Jia1, Ming-liang Yu2, Rui-juan Ma2, Li-rong Wang3, Ke Cao3, Zhi-jun Shen2, Liang Niu3, Jian-bao Tian4, Miao-jin Chen5, Ming Xie6, Pere Arus7, Zhong-shan Gao1* and Maria Jose Aranzana7*

Author Affiliations

1 Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou 310058, China

2 Horticultural Institute, Jiangsu Academy of Agricultural Sciences, Zhong-Lin Street 50, Nanjing 210014, China

3 Zhenzhou Fruit Research Institute, CAAS, Zhengzhou China

4 Pomology Institute, Shanxi Academy of Agricultural Sciences, Ke Yuan Road 1, Taigu, Shanxi 030815, China

5 Fenghua Honey Peach Institute, Xikou, Fenghua, Zhejiang Province 315521, China

6 Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

7 IRTA. Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Campus UAB – Edifici CRAG, Bellaterra - Cerdanyola del Vallès, 08193 Barcelona, Spain

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BMC Genetics 2013, 14:84  doi:10.1186/1471-2156-14-84

Published: 16 September 2013



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.


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.


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.