Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers

Abstract

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the ‘Germersdorfer-Ferrovia’ cluster, (iii) the ‘Burlat’ group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

“…The alignment efficiency between the results of this study and the reference genome is from 70.26% to 97.27%, which reveals that there are differences in the whole-genome sequence of the materials studied. The average ratio of Ts/Tv is 1.54; similar rates exist in other plants, like sweet cherry and sorghum [ 51 , 52 ]. Furthermore, some reports suggest that high Ts/Tv ratios indicate low levels of genetic differentiation in genomic comparisons [ 53 ].…”

“…The results of the NJ tree, ADMIXTURE structural and PCA analyses all divided 132 wild R. chingii resources into four subgroups. Regular patterns in the classification of germplasm resources are mostly influenced by known material lineages, geographical origins and dissemination patterns [ 51 ]. Pop1 is mainly located in the northeast of Jiangxi Province, while Pop3 distribution is concentrated in Jiangxi’s center; the main distribution of Pop4 is in Fujian, which borders Jiangxi; and Pop2 is dispersed across both Jiangxi and Fujian provinces, roughly 400 km apart, which is not consistent with the criteria of geographical origin of the first three subgroups.…”

Hilly, Semi-Mountainous and Mountainous Areas Harbor Landraces Diversity: The Case of Messinia (Peloponnese-Greece)

“…Hatziharissis et al [147] mentioned the cherries (P. avium) landraces "Karamela", "Lamboudi", "Petrokerasa", and especially the potential of "Lamboudi" to resist pathogens and dry conditions, an interesting feature for the climatic change that Earth is facing. The genetic affinities with other cherry landraces should be investigated, like in Basilicata (Southern Italy), where the landraces of that area exhibited genetic relationships with landraces from other Italian regions, especially Campania, and some genotypes were more closely related to foreign varieties [148]. Sour cherry (P. cerasus) presented the names "Mikro" (small), "Xino" (sour), "Xanthokokkino" (blond-reddish), and "Mavro" (black) [49].…”