Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers

Abstract

ABSTRACT. We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 East Anatolian plum and cherry plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars.

Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

“…The entire population was structured in seven groups and confirmed the genetic relationships observed in the UPGMA dendrogram. Although a higher number of accessions were analyzed herein, the genetic diversity was similar to that of previous studies [46,51,[53][54][55]. This may be due to the high number of modern cultivars and advanced selections of breeding programs analyzed, which reveal a bottleneck effect caused by the breeding system practices.…”

“…Currently, most SSR markers available derive from cherry [27][28][29][30] and peach [26,[31][32][33], although a small number have been developed in apricot [34] and Japanese plum [35]. They have been used to analyze the genetic diversity and to improve the management of plant genetic resources in almond [36][37][38][39], apricot [40,41], European plum [42,43], peach [44], and sweet cherry [45][46][47].…”

“…The significant variability observed in Japanese plum cultivars led to early diversity studies to estimate genetic relationships using isoenzymes [48], RAPDs [49,50], and SSR developed in Japanese plum [35] and other Prunus species [46,[51][52][53][54][55]. However, the genetic diversity of the cultivars currently grown globally is unknown, because the previous studies were mainly focused on traditional cultivars.…”

Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping

“…More recently, genetic diversity of Eurasian plum varieties and species has been studied using bi-parentally transmitted nuclear and maternal cytoplasmic (chloroplast, mitochondria) markers. Microsatellite (SSR) and Inter-simple Sequence Repeat (ISSR) markers were used for characterization of P. domestica germplasm across Europe in several geographically distant countries 21–24 , in Turkey 25 and China 9,26 . This approach enabled a reconstruction of parental lineages among related European plum cultivars 27 and molecular characterization of “Reine Claude” types in Spain 28 .…”

Molecular and morphological characterization of local apple cultivars in Southern Spain

“…DNA markers have been developed and are currently used for germplasm genotyping alone or as a complement to morphological characterization (Martinelli et al, 2008). Among these, simple sequence repeats (SSR) or microsatellites are the markers of choice in many fruit species (Bouhadida et al, 2010;Martín et al, 2011;Öz et al, 2013). In the case of apples, a high number of SSR markers have been described (Gianfranceschi et al, 1998;Hokanson et al, 1998;Liebhard et al, 2002;Silfverberg-Dilworth et al, 2006).…”