Genome and population dynamics under selection and neutrality: an example of S-allele diversity in wild cherry (Prunus avium L.)

Self-incompatibility, a common attribute of plant development, forms a classical paradigm of balancing selection in natural populations, in particular negative frequency-dependent selection. Under negative frequency-dependent selection population genetics theory predicts that the S-locus, being in command of self-incompatibility, keeps numerous alleles in equal frequencies demonstrating a wide allelic range. Moreover, while natural populations exhibit a higher within population genetic diversity, a reduction of population differentiation and increase of effective migration rate is expected in comparison to neutral loci. Allelic frequencies were investigated in terms of distribution and genetic structure at the gametophytic self-incompatibility locus in five wild cherry (Prunus avium L.) populations. Comparisons were also made between the differentiation at the S-locus and at the SSR loci. Theoretical expectations under balancing selection were congruent to the results observed. The S-locus showed broad multiplicity (16 S-alleles), high genetic diversity, and allelic isoplethy. Genetic structure at the self-incompatibility locus was almost four times lower than at 11 nSSR loci. Analysis of molecular variance revealed that only 5?% of the total genetic variation concerns differentiation among populations. In conclusion, the wealth of S-allelic diversity found in natural wild cherry populations in Greece is useful not only in advancing basic population genetics research of self-incompatibility systems in wild cherry but also in the development of breeding programs.     

Universal ITS2 Barcoding DNA Region Coupled with High-Resolution Melting (HRM) Analysis for Seed Authentication and Adulteration Testing in Leguminous Forage and Pasture Species

Legume species are part of a very important agricultural family, second only to cereals. Their importance for sustainable agriculture worldwide comes from their nitrogen-fixing ability. They include mainly annual grain crops and also very important perennial forage and pasture species. Given their small size, seed admixture and adulteration are a common problem, lowering the forage value, creating weed components in the grassland and causing digestive problems to animals. Here we report the application of the Barcode-DNA High-Resolution Melting (Bar-HRM) analysis method using the universal nuclear plant DNA barcoding region ITS2 for the identification, adulteration and quantification of the main pasture species. Bar-HRM detected Medicago lupulina adulterants in Trifolium pratense seeds as low as 1:100. In conclusion, Bar-HRM analysis could be a faster with higher resolution and cost-effective alternative method to authenticate forage and pasture species and quantitatively detect the purity of their seeds or their feed products.     

Genetic differentiation and gene flow between wild and cultivated Prunus avium: An analysis of molecular genetic evidence at a regional scale

The presence of conspecific wild-type and cultivar populations has been a common landscape feature for centuries. As orchards generally continue to expand towards the natural forest, two important issues are raised: the potential reduction of cultivar genetic diversity compared to wild populations and the extent of gene flow between the two population types. These questions were addressed in a study of Prunus avium in northern Greece using nine simple sequence repeat loci to analyse genetic variation in 93 wild-type individuals and 21 cultivars representing the local cultivated germplasm. Results showed a significant reduction of genetic diversity parameters in the cultivated germplasm compared to natural populations. Bayesian, frequency-based and Markov chain – Monte Carlo analyses have revealed that the wild and cultivar groups are genetically divergent and that realized between-group gene flow is almost completely absent. This result was further verified by a principal component analysis showing a clear separation of the two groups in low multivariate space after a principal coordinate analysis. The significant disjunction in flowering time and a considerable geographic distance between the two groups could primarily account for the absence of substantial gene flow. These findings indicate that local wild cherry can provide a source of genetic variation for future breeding in the genetically restricted cultivar group.     

DNA barcode ITS2 coupled with high resolution melting (HRM) analysis for taxonomic identification of Sideritis species growing in Greece

Identification of genotypes in Sideritis is complicated owing to the morphological similarity and common occurrence of natural hybridisation within Sideritis species. Species- and genotype-specific DNA markers are very useful for plant identification, breeding and preservation programs. Herein, a real-time polymerase chain reaction (PCR) of ITS2 barcode region coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on seven Sideritis species growing in Greece. The HRM assay developed in this study is a rapid and straightforward method for the identification and discrimination of the investigated Sideritis species. This assay is simple compared to other genotyping methods as it does not require DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of Sideritis species.     

Summer Squash Identification by High-Resolution-Melting (HRM) Analysis Using Gene-Based EST–SSR Molecular Markers

Cucurbita pepo (squash, pumpkin, gourd), a worldwide cultivated vegetable of American origin, is extremely variable in fruit characteristics. Most of its widely grown commercial types are known as summer squashes and belong to the elongated forms of C. pepo ssp. pepo (Cocozelle, Vegetable marrow and Zucchini groups). Here, we have integrated the high-resolution-melting (HRM) analysis method with expressed sequence tags–simple sequence repeat (EST–SSR) marker genotyping, in order to facilitate the identification of 36 summer squash landraces originated from Greece. The six EST–SSR loci used were informative and generated a unique melting curve profile of EST-derived microsatellites for each accession allowing their comparison and classification. Moreover, HRM was highly informative, as by using only four microsatellite markers we were able to discriminate 36 summer squash landraces and by using six EST–SSRs. We were able to construct a highly informative and discriminative dendrogram where the 36 genotypes were classified in six distinct clusters. Furthermore, we acquired information about the genes containing the EST–SSRs using bioinformatics tools. We found that the EST–SSRs used in this study were hybridizing to genes involved in stress response to heavy metals and biotic stresses or the production of flavonoids or symporters of important nitrogen sources, like xanthine and uric acid amongst others. The results presented here suggest that the panel of EST–SSR markers used in combination with HRM analysis could be useful in a variety of applications, like squash biodiversity assessment but most importantly in managing squash germplasm to improve breeding programs.     

Novel insights into the calcium action in cherry fruit development revealed by high-throughput mapping

Plant Molecular Biology - This work provides the first system-wide datasets concerning metabolic changes in calcium-treated fruits, which reveal that exogenously applied calcium may specifically...     

A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.