Genetic characterization of Japanese plum cultivars (Prunus salicina) using SSR and ISSR molecular markers

Abstract

B. Carrasco, C. Díaz, M. Moya, M. Gebauer and R. García-González. 2012. Genetic characterization of Japanese plum cultivars (Prunus salicina) using SSR and ISSR molecular markers. Cien. Inv. Agr. 39(3): 533-543. The genetic characterization of 29 elite Japanese plum cultivars (Prunus salicina) and 4 Prunus cultivars was carried out by analyzing 97 Simple Sequence Repeat (SSR) alleles and 232 binary Inter Simple Sequence Repeat (ISSR) loci. A high level of genetic variability was found for these two molecular markers among the Japanese plum cultivars compared to other Prunus species. On average, the variability found by analyzing the SSR alleles were Na = 12.1, Ne = 5.2, Ho = 0.9, He = 0.8 and F= -0.127, whereas ISSR yielded values of h = 0.15 and I = 0.27. The genetic relationship among cultivars was estimated with Principal Coordinate Analysis (PCA) and a Bayesian clustering approach using the software program Structure. This program identified two subgroups (k=2). The first group included cultivars of four Prunus species: P. salicina, P. armeniaca, P. domestica and P. ceracifera, whose memberships ranged between 0.74 and 1.0. The second group included 19 Japanese plum cultivars and one plumcot cultivar, with memberships between 0.57 and 0.99. With some exceptions, similar relationships among cultivars were foundPCA. The level of genetic differentiation between two groups was low (G st =0.055 and  ST =0.04), and a low level of linkage disequilibrium (LD) was observed for all allele combinations. These results suggest that the high level of genetic variability, the low level of LD and the scarce degree of differentiation detected by Structure between the two genetic groups can be explained by the self-incompatibility mechanism that favors the exchange between genetically distant Prunus cultivars and by the intra-and interspecific hybridization strategies frequently used in plum breeding programs.

Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to Water Stressed Environments

“…In this study, we detected high levels of diversity within 14 different plum landraces from the PRD region that have been selected through the years by local growers. The diversity indexes were lower than those described by Carrasco et al [14] (He = 0.80 and Ho = 0.90) and Ferrero Klabunde et al [15] (PIC = 0.80 and Ho = 0.77) with eight SSR markers. However, this was expected due to a higher number of P. salicina cultivars analyzed (29 and 47, respectively).…”

“…Mnejja et al [2] isolated 27 microsatellites or simple sequence repeats (SSRs) in P. salicina, whereas Carrasco et al [14] analyzed genetic diversity and correlation among 29 Japanese plum cultivars using a combination of inter simple sequence repeat (ISSR) and SSR markers. On the other hand, Klabunde et al [15] genotyped 47 cultivars with eight microsatellite markers.…”

Molecular characterization of twenty polymorphic microsatellite markers in the polyploid fruit tree species Syzygium samarangense (Myrtaceae)

“…The H E value was similar to that obtained for other tropical fruit trees, including mango cultivars and Indian jujube cultivars (Chiou et al, 2012). However, the Ne and H E values of wax apple were noticeably lower than those of Japanese plum cultivars (Carrasco et al, 2012) and apple cultivars (Sikorskaite et al, 2012). Both Japanese plum and apple cultivars have strong self-incompatibility (Okie and Weinberger, 1996;Hegedus, 2006) compared to the wax apple, which is a self-compatible species (Chantaranothai and Parnell, 1994).…”

Molecular characterization of the plum collection [Prunus domestica (L.) Borkh] of the Pedagogical and Technological University of Colombia

“…According to Wright (1978), values of 0.25 show high genetic differentiation, which may be reflected in the high degree of domestication that these materials have suffered, since most of them are commercial varieties. Carrasco et al, 2012 found an index fixation of F = -0.127, higher than those in other allogamous species such as the almond (F = 0.15; Fathi et al, 2008), and wild apple (F = 0.10; Coart et al, 2003). Excess heterozygosity could be explained by the negative selective mating related to the self-incompatibility system, such that the parental lines carry different favored alleles than the interspecific cross usually used in plum breeding programs.…”

“…In the plum, Carrasco et al (2012) molecularly characterized cultivars of the Japanese plum (Prunus salicina), using the molecular markers SSR and ISSR.…”