Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying

Abstract

European plum (Prunus domestica L.) is an ancient domesticated species cultivated in temperate areas worldwide whose genetic structure has been scarcely analyzed to date. In this study, a broad representation of Spanish European plum germplasm collected in Northeastern Spain and a representative set of reference cultivars were compared using nuclear and chloroplast markers. The number of alleles per locus detected with the SSR markers ranged from 8 to 39, with an average of 23.4 alleles, and 8 haplotypes were identified. Bayesian model-based clustering, minimum spanning networks, and the analysis of molecular variance showed the existence of a hierarchical structure. At the first level, two genetic groups were found, one containing ‘Reine Claude’ type reference cultivars altogether with ca. 25% of local genotypes, and a second one much more diverse. This latter group split in two groups, one containing most (ca. 70%) local genotypes and some old Spanish and French reference cultivars, whereas the other included 24 reference cultivars and only six local genotypes. A third partition level allowed a significant finer delineation into five groups. As a whole, the genetic structure of European plum from Northeastern Spain was shown to be complex and conditioned by a geographical proximity factor. This study not only contributes to genetic conservation and breeding for this species at the national level, but also supports the relevance of undertaking similar tasks of collection and characterization in other unexplored areas. Moreover, this kind of research could lead to future coordinated actions for the examination of the whole European plum diversity, to define conservation strategies, and could be used to better understand the genetic control of traits of horticultural interest through association mapping.

Identifying Pollen Donors and Success Rate of Individual Pollinizers in European Plum (Prunus domestica L.) Using Microsatellite Markers

“…A relatively high number of alleles, detected among a small set of genotypes, is a consequence of the hexaploid nature of plum as well as the fact that the analyzed cultivars have a very diverse pedigree. High values for the mean number of alleles per locus in plum is reported by numerous studies [19][20][21][22][23][24][25][26]. In the mentioned studies, this value ranged from 18.7 to 29 alleles.…”

“…Microsatellites or SSRs (simple sequence repeats) have previously been used for diversity studies of plum germplasm in France [19], Germany [20], Croatia [21], Sweden [22], Greece [23], Hungary [24], Spain [25], and Romania [26]. This marker system can also efficiently be used for parentage analyses in plum.…”

ECPGR recommended SSR loci for analyses of European plum (Prunus domestica) collections

“…Most of the hitherto published studies on SSR diversity in European plums are based on differing sets of loci (Horvath et al, 2011;Xuan et al, 2011;Öz et al, 2013;Gharbi et al, 2014;Halapija Kazija et al, 2014;Makovics-Zsohár et al, 2017;Merkouropoulos et al, 2017;Pop et al, 2018;Abdallah et al, 2019;Manco et al, 2019;Urrestarazu et al, 2018). In order to facilitate harmonization between future studies, we propose a standard set of nine SSR loci, approved by the ECPGR Prunus working group, for European plum (Table 1).…”

Genetic diversity analysis of Chinese plum (Prunus salicinaL.) based on whole-genome resequencing

“…Genetic variability is the prerequisite for any plant breeding program. Learning the extent and structure of genetic variation in germplasm collections is a crucial step for the efficient conservation and utilization of biodiversity in cultivated crops, and using diverse plum resources to broaden the genetic base of worldwide plum cultivars is the critical objective for plum breeders [2,7]. Previous efforts have been made to understand the genetic diversity of plum better.…”

“…Overcoming the above-mentioned problems, DNA-based markers became widely applied in plum genetic diversity analysis, including random amplified polymorphic DNAs (RAPDs) [5,10], simple sequence repeats (SSRs) [11][12][13], inter-simple sequence repeats (ISSRs) [2,14]. In addition, benefiting from the advances in next-generation sequencing (NGS) technologies, genotyping by sequencing (GBS), provides a great wealth of information that makes it possible to identify thousands of single nucleotide polymorphisms (SNPs), which, after adequate filtering, allow us to carry out detailed genetic diversity studies [7,[15][16][17].…”