Peach genetic resources: diversity, population structure and linkage disequilibrium
Research article Open Access
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 Gao1Email author and Maria Jose Aranzana7Email author
BMC Genetics201314:84
https://doi.org/10.1186/1471-2156-14-84
© Li et al.; licensee BioMed Central Ltd. 2013
Received: 30 March 2013Accepted: 11 September 2013Published: 16 September 2013
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.
Keywords
Linkage DisequilibriumPeach CultivarChinese LandraceBreeding CultivarSpanish Landrace
Background
Peach (Prunus persica (L) Batsch) is one of the most predominant commercially grown stone fruits in the Rosaceae family, subfamily Spiroideae because of its broad climate adaptation and high production in cultivation regions [1]. Its short juvenile period (2–3 years) and the ease of obtaining controlled crosses have made peach breeding programs quite successful: around 1,000 new cultivars were released during 1991–2001 [2]. In addition, because of its small genome size and the simple genetic basis of many morphological and economical traits [3], peach is a model fruit crop for traditional genetics and current genomics research, with subsequent applications in breeding and selection.
Being the centre of origin of peach, China has the longest history of peach cultivation (more than 4,000 years), and the richness of genetically diverse germplasm can provide useful genes to breed cultivars with enhanced resistance to pests and diseases, improved fruit size and quality, and a longer postharvest shelf-life. The ancestral form peach used as rootstock in south China still exists. Other wild related species are present in the north-western region of China: ‘P. mira Koehne’ , ‘P. kansuensis. Rehd’ , ‘P. davidiana. Franch’ and ‘P. potaninii Batal’. In China, the main peach germplasms are in three national collections, but regional and local collections are also established around the country. The national collections preserve 2,000 accessions from China and foreign countries, with about 600 cultivars of local origin [4]. Based on genetic fingerprint data, Chinese peach cultivars have more genetic diversity than has been reported for other peach germplasm collections [5]. The Chinese peach germplasm has had a great impact on breeding research in other countries. After introducing ‘Shanghai Shui Mi’ as parents in the early 20th century, Japan selected out ‘Hakuto’ [6, 7] and the USA released the famous cultivar ‘Elberta’. Both ‘Hakuto’ and ‘Elberta’ were extensively used as parents for further breeding of modern cultivars [8, 9]. Over the last few decades, considerable effort has been put into peach breeding in the USA, South Africa, Brazil, Argentina, Australia, China, Spain, Italy, France and Japan [10], producing almost 2,000 new cultivars; half of these have been registered in and come from the USA while only 5% are from China [11, 12].
As a self-pollinated species, peach retains a high degree of self-compatibility and homozygosity [13]. During the decade 1991–2001, peach and nectarine cultivars were generated through controlled crosses (43-61%), open pollination (15-21%) and bud mutation (4-5%), and the outcrossing range varied from 15 to 30% [14]. Most local Spanish varieties were self propagated; melting cultivars were usually produced by crossing two individuals and selecting from their progeny, and non-melting peaches were selected from seed-propagated populations [15]. Chinese breeding cultivars were mainly released using ‘Shanghai Shui Mi’(‘Chinese Cling’) and ‘Bai Hua Shui Mi’ as founders. ‘Okubo’ and ‘Hakuto’ from Japan were inter-crossed to produce white and low-acid peaches in Nanjing and Beijing germplasms. ‘NJN76’ , ‘Mayfire’ and ‘Legrant’ were also introduced and inter-crossed to produce nectarines. Chinese landrace reproduction was mainly based on seed propagation [4]. Most of the Japanese peaches were selections or mutations of ‘Hakuto’ and ‘Hakuho’ [6, 7]. New genetic backgrounds should be explored and intro (...truncated)
