title: Peach genetic resources: diversity, population structure and linkage disequilibrium.
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.
authors.affiliation: Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou 310058, China. gaozhongshan@zju.edu.cn.
authors.forename: Xiong-wei
authors.initials: XW
authors.lastname: Li
authors.forename: Xian-qiao
authors.initials: XQ
authors.lastname: Meng
authors.forename: Hui-juan
authors.initials: HJ
authors.lastname: Jia
authors.forename: Ming-liang
authors.initials: ML
authors.lastname: Yu
authors.forename: Rui-juan
authors.initials: RJ
authors.lastname: Ma
authors.forename: Li-rong
authors.initials: LR
authors.lastname: Wang
authors.forename: Ke
authors.initials: K
authors.lastname: Cao
authors.forename: Zhi-jun
authors.initials: ZJ
authors.lastname: Shen
authors.forename: Liang
authors.initials: L
authors.lastname: Niu
authors.forename: Jian-bao
authors.initials: JB
authors.lastname: Tian
authors.forename: Miao-jin
authors.initials: MJ
authors.lastname: Chen
authors.forename: Ming
authors.initials: M
authors.lastname: Xie
authors.forename: Pere
authors.initials: P
authors.lastname: Arus
authors.forename: Zhong-shan
authors.initials: ZS
authors.lastname: Gao
authors.forename: Maria Jose
authors.initials: MJ
authors.lastname: Aranzana
mesh_terms: D000483:Alleles; D001499:Bayes Theorem; D001947:Breeding; D002874:Chromosome Mapping; D016000:Cluster Analysis; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D005838:Genotype; D006579:Heterozygote; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D010802:Phylogeny; D025341:Principal Component Analysis; D027861:Prunus / Q000145:classification / Q000235:genetics*
references.citation: PLoS Genet. 2007 Nov;3(11):e185
references.pmid: 18039031
references.citation: Genetics. 2005 Nov;171(3):1305-9
references.pmid: 16118196
references.citation: Mol Ecol. 2005 Jul;14(8):2611-20
references.pmid: 15969739
references.citation: Nat Genet. 2002 Feb;30(2):190-3
references.pmid: 11780140
references.citation: Plant Mol Biol. 2005 Mar;57(4):461-85
references.pmid: 15821975
references.citation: BMC Evol Biol. 2011 Feb 10;11:42
references.pmid: 21310063
references.citation: BMC Genet. 2010 Jul 20;11:69
references.pmid: 20646280
references.citation: Nat Genet. 2013 May;45(5):487-94
references.pmid: 23525075
references.citation: Nat Genet. 1999 Jun;22(2):139-44
references.pmid: 10369254
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: BMC Evol Biol. 2010 Feb 15;10:44
references.pmid: 20156342
references.citation: Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269-73
references.pmid: 291943
references.citation: Theor Appl Genet. 2002 Jul;105(1):127-138
references.pmid: 12582570
references.citation: Bioinformatics. 2012 Oct 1;28(19):2537-9
references.pmid: 22820204
references.citation: Bioinformatics. 2005 May 1;21(9):2128-9
references.pmid: 15705655
references.citation: Theor Appl Genet. 2006 Feb;112(4):708-16
references.pmid: 16402190
references.citation: Comput Appl Biosci. 1994 Sep;10(5):569-70
references.pmid: 7828077
references.citation: Genome. 2000 Jun;43(3):512-20
references.pmid: 10902716
references.citation: Poult Sci. 2010 Mar;89(3):420-7
references.pmid: 20181856
references.citation: Heredity (Edinb). 2010 May;104(5):431-7
references.pmid: 19844269
references.citation: Mol Ecol Resour. 2010 May;10(3):564-7
references.pmid: 21565059
references.citation: Theor Appl Genet. 2003 May;106(8):1341-52
references.pmid: 12750778
references.citation: Bioinformatics. 2007 Jul 15;23(14):1801-6
references.pmid: 17485429
references.citation: Int J Plant Genomics. 2008;2008:574927
references.pmid: 18551188