Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively.

Background: Vitis viniferaL. is the most cultivated grapevine species worldwide.Erysiphe necatorSch., the causal agent of grape powdery mildew, is one of the main pathogens affecting viticulture.V. viniferahas little or no genetic resistances againstE. necatorand the grape industry is highly dependent on agrochemicals. Some CaucasianV. viniferaaccessions have been reported to be resistant toE. necatorand to have no genetic relationships to known sources of resistance to powdery mildew. The main purpose of this work was the study and mapping of the resistance toE. necatorin the Caucasian grapes ‘Shavtsitska’ and ‘Tskhvedianis tetra’.Results: The Caucasian varieties ‘Shavtsitska’ and ‘Tskhvedianis tetra’ showed a strong partial resistance toE. necatorwhich segregated in two cross populations: the resistant genotypes delayed and limited the pathogen mycelium growth, sporulation intensity and number of conidia generated. A total of 184 seedlings of ‘Shavtsitska’ x ‘Glera’ population were genotyped through the Genotyping by Sequencing (GBS) technology and two high-density linkage maps were developed for the cross parents. The QTL analysis revealed a major resistance locus, explaining up to 80.15% of the phenotypic variance, on ‘Shavtsitska’ linkage group 13, which was associated with a reduced pathogen infection as well as an enhanced plant necrotic response. The genotyping of 105 Caucasian accessions with SSR markers flanking the QTL revealed that the resistant haplotype of ‘Shavtsitska’ was shared by ‘Tskhvedianis tetra’ and a total of 25 Caucasian grape varieties, suggesting a widespread presence of this resistance in the surveyed germplasm. The uncovered QTL was mapped in the region where theRen1locus of resistance toE. necator, identified in theV. vinifera‘Kishmish vatkana’ and related grapes of Central Asia, is located. The genetic analysis conducted revealed that the Caucasian grapes in this study exhibit a resistant haplotype different from that of Central Asian grape accessions.Conclusions: The QTL isolated in ‘Shavtsitska’ and present in the CaucasianV. viniferavarieties could be a new candidate gene of resistance toE. necatorto use in breeding programmes. It co-localizes with theRen1locus but shows a different haplotype from that of grapevines of Central Asia. We therefore consider that the Caucasian resistance locus, namedRen1.2, contains a member of a cluster of R-genes, of which the region is rich, and to be linked with, or possibly allelic, toRen1.

The DNA fingerprinting of fruit crops, based on DNA microsatellite markers that are considered to be the key markers for the molecular analysis of germplasm collections, is reviewed. Simple sequence repeats (SSRs) remain the markers of choice for fingerprinting in humans, animals, plants, and other living organisms. This review, that considers 44 fruit species, provides a set of markers that are suitable for profiling accessions and that should make the databases produced in different laboratories more comparable. Every effort has been made to select SSR markers that are robust and easily scorable considering that such analyses are sometimes used in legal cases. The review first describes the basic protocols, procedures, and methods of data analyses; it then describes the fingerprinting of individual species or groups of species, providing a set of SSR markers and appropriate guidance based on the revised literature and on the authors’ experience.

Kiwifruit belong to the genus Actinidia with 54 species apparently all functionally dioecious. The sex-determinants of the type XX/XY, with male heterogametic, operate independently of the ploidy level. Recently, the SyGI protein has been described as the suppressor of female development. In the present study, we exploited the CRISPR/Cas9 technology by targeting two different sites in the SyGI gene in order to induce a stable gene knock-out in two tetraploid male accessions of Actinidia chinensis var. chinensis. The two genotypes showed a regenerative efficiency of 58% and 73%, respectively. Despite not yet being able to verify the phenotypic effects on the flower structure, due to the long time required by tissue-cultured kiwifruit plants to flower, we obtained two regenerated lines showing near fixation of a unique modification in their genome, resulting in both cases in the onset of a premature stop codon, which induces the putative gene knock-out. Evaluation of gRNA1 locus for both regenerated plantlets resulted in co-amplification of a minor variant differing from the target region for a single nucleotide. A genomic duplication of the region in proximity of the Y genomic region could be postulated.

Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which—the cultivar ‘Lito’ heterozygous for the resistance—has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A ‘Lito’ bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of ‘Lito’ was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar ‘Lito’ allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of ‘Lito’ is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.

Kiwifruit, with its unique flavor, nutritional value, and economic benefits, has gained significant attention in agriculture production. Kiwifruit plants have traditionally been propagated without grafting, but recently, grafting has become a more common practice. A new and complex disease called Kiwifruit Vine Decline Syndrome (KVDS) has emerged in different kiwifruit-growing areas. The syndrome was first recognized in Italy, although similar symptoms had been observed in New Zealand during the 1990s before subsequently spreading worldwide. While kiwifruit was not initially grafted in commercial orchards, the expansion of cultivation into regions with heavy soils or other challenging environmental conditions may make grafting selected kiwifruit cultivars onto KVDS-resistant or -tolerant rootstocks essential for the future of this crop. Grafting is a common horticultural practice, widely used to propagate several commercially important fruit crops, including kiwifruits, apples, grapes, citrus, peaches, apricots, and vegetables. Grafting methods and genetic compatibility have a crucial impact on fruit quality, yield, environmental adaptability, and disease resistance. Achieving successful compatibility involves a series of steps. During grafting, some scion/rootstock combinations exhibit poor graft compatibility, preventing the formation of a successful graft union. Identifying symptoms of graft incompatibility can be challenging, as they are not always evident in the first year after grafting. The causes of graft incompatibility are still largely unknown, especially in the case of kiwifruit. This review aims to examine the mechanisms of graft compatibility and incompatibility across different fruit crops. This review’s goal is to identify potential markers and techniques that could enhance grafting success and boost the commercial production of kiwifruit.