Peach genetic resources: diversity, population structure and linkage disequilibrium

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.

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

“…The rapid decay of LD in the wild and primitive diversity groups of cacao and the slow or non-existent decay in cultivated groups (Fig. 2) resemble similar patterns observed for peach (Li et al 2013) and cherry (Arunyawat et al 2012). In contrast, wild and cultivated varieties of grapevine exhibit very similar patterns of genome-wide LD (Myles et al 2011).…”

Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats

“…Forty-nine SSR markers distributed along 8 linkage groups of the Prunus reference map were used for genotyping ( Table S2). The SSRs that were used were similar to those in previous studies (Aranzana et al, 2010;Li et al, 2013). Polymerase chain reaction (PCR) amplifications were carried out as described by Aranzana et al (2003) using fluorescence-labeled primers.…”

“…Old varieties from Japan had the genetic background of Shanhai Suimitsuto (Yamamoto et al, 2003). However, genetic relationships, backgrounds, and evolution of local cultivars in China have not been emphasized in the previous studies (Cao et al, 2012;Li et al, 2013).…”

“…With the development of SSR markers (Cipriani et al, 1999;Testolin et al, 2000;Dirlewanger et al, 2002), many collections of peach were evaluated, including commercial varieties (Aranzana et al, 2010), rootstocks (Serrano et al, 2002), local varieties (Badenes et al, 2002;Cheng and Huang, 2009;Bouhadida et al, 2011), and a large set of accessions (Li et al, 2013). In addition, by using SSR markers, a better understanding of the diversity, genetic relationships, and evolution of peach genetic resources has been gained.…”

Characterization of the expression of the stress-responsive <i>PpERS1</i> gene from peach and analysis of its promoter using transgenic tomato

“…Peach is becoming a very promising climacteric drupe model to enhance our insight into ethylene biology and ripening, and for genomic analysis of fruit tree species (Li et al 2013;Verde et al 2013), even though transformation events in peach have been rarely reported (Pérez-Clemente et al 2004). Like other fruit species, stress restricts the yield and geographical area over which peach trees can be planted, and this continues to drive worldwide efforts to generate stress-tolerant cultivars using traditional and molecular genetic approaches ).…”