Peach genetic resources: diversity, population structure and linkage disequilibrium
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Author
Li, Xiong-wei
Meng, Xian-qiao
Jia, Hui-juan
Yu, Ming-liang
Ma, Rui-juan
Wang, Li-rong
Cao, Ke
Shen, Zhi-jun
Niu, Liang
Tian, Jian-bao
Chen, Miao-jin
Xie, Ming
Arús, Pere
Gao, Zhong-shan
Publication date
2013-09-16ISSN
1471-2156
Abstract
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
16
Publisher
BMC
Is part of
BMC Genetics
Citation
Li, Xiong-wei, Xian-qiao Meng, Hui-juan Jia, Ming-liang Yu, Rui-juan Ma, Li-rong Wang, and Ke Cao et al. 2013. "Peach Genetic Resources: Diversity, Population Structure And Linkage Disequilibrium". BMC Genetics 14 (1). doi:10.1186/1471-2156-14-84.
Grant agreement number
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2009-07305/ES/Evaluacion E Introgresion De Nuevas Fuentes De Variabilidad Genetica En Germoplasma De Melocotonero Europeo Y Norte-Americano/
INIA/Programa Nacional de Proyectos de Investigación Fundamental/RF2009-00002/ES/Prospección, recolección, conservación y caracterización de nuevo germoplasma de melocotonero/
Program
Genòmica i Biotecnologia
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