Genetics and Molecular Breeding of Fruit Tree Species

Fruit tree species contribute to human nutrition and health security by providing important beneficial compounds (e.g., micronutrients, antioxidants) and by playing a key role in the economies of many countries [1]. Global demand for varieties of fruit tree varieties with improved traits—such as enhanced fruit quality, higher yield, and increased resistance to biotic and abiotic stress—is steadily rising. In addition, climate change presents new challenges for perennial crops in many regions, necessitating the development of new varieties capable of adapting to changing environmental conditions, producing high-quality products under stress, and reducing environmental impact [2].

In this context, a thorough understanding of the genetic basis of agronomic traits is essential for both unraveling their regulatory mechanisms and supporting efficient breeding strategies.

However, genetic improvement in fruit trees through conventional methods—such as sexual hybridization and selection—is significantly constrained by the complex genetic and reproductive biology of woody plants. These challenges include a long juvenile period, large plant size, high levels of heterozygosity, and the presence of reproductive barriers (e.g., male or female sterility, incompatibility).

Recent advances in biotechnology and the emergence of genomics offer new opportunities for genetic studies and molecular breeding in fruit crops, helping to overcome the limitations of conventional strategies and enabling the exploitation of novel genetic resources.

The advent of high-throughput methods—such as next-generation sequencing (NGS) and genotyping-by-sequencing (GBS)—alongside genome-wide association studies, advanced phenotyping approaches, and integrated omics technologies (e.g., transcriptomics, proteomics, metabolomics, and hormonomics), has significantly enhanced our understanding of the genetic basis of agronomically important traits [3].

The use of these technologies facilitates the characterization of genetic variability within germplasm collections—an important source of traits for breeding—and contributes to the development of molecular markers. These markers can be used for fingerprinting (e.g., varietal identification, plant-derived products traceability) or for marker-assisted selection (MAS), which enables the early identification of new genotypes with superior traits in conventional breeding programs, thereby reducing time, space, and costs [4]. Additionally, these approaches support more efficient conservation of genetic resources, particularly in neglected species.

Last but not least, genes associated with desirable traits can be introduced or modified in elite cultivars using new plant breeding techniques (e.g., cisgenesis and genome editing), which allow point-specific mutations without introducing foreign genes, thereby preserving the genetic background [5,6]. However, the successful application of these technologies depends on the availability of efficient regeneration protocols, which remain a major bottleneck, as many cultivars within a species may be recalcitrant to regeneration [7].

This editorial provides an overview of the Special Issue “Genetics and Molecular Breeding of Fruit Tree Species”, which aims to highlight recent advances in the genetic and molecular breeding of fruit tree species for the selection or development of new genotypes with superior characteristics.

This Issue features nine original papers contributed by groups working on various tree species.

Vodiasova et al. (Contribution 1) analyzed the genetic diversity and population structure of 161 peach cultivars from a Russian collection using the GBS approach. They identified a total of 7803 single-nucleotide polymorphism (SNP) markers, which can be used to explore associations with agronomic traits.

Song et al. (Contribution 2) performed an in-depth comparative analysis of chloroplast genome structures across 21 Vitis cultivars, revealing valuable genomic resources that can support cultivar selection, breeding, and conservation efforts.

Jia et al. (Contribution 3) reported a novel and efficient pipeline for the development of multi-allelic insertion/deletion markers (InDels). Using NGS-based fingerprints, they successfully discriminated among 122 grape varieties.

Saensouk et al. (Contribution 4) carried out a cytological study on four edible and ornamental Zingiber species, generating insights that can inform plant breeding strategies for commercial purposes.

Simoni et al. (Contribution 5) provided a comprehensive characterization of transposable elements (TEs) in Punica granatum through a comparative analysis of the genome assemblies of four Tunisian pomegranate cultivars, providing information that can be leveraged for breeding and crop improvement in this species.

Wang et al. (Contribution 6) developed an effective plant regeneration protocol by inducing high-vigor somatic embryos from stem explants of pomegranate, leading to an essential advancement for genetic resource conservation and breeding efforts.

Gao et al. (Contribution 7) conducted a large-scale investigation on the callus induction and adventitious root development across peach germplasms. They identified a candidate gene potentially involved in the regulation of root formation and pinpointed cultivars more prone to regeneration protocols.

Guo et al. (Contribution 8) performed whole-genome resequencing of jujube cultivars to identify genome-wide SNP markers and constructed a high-density bin map, providing valuable tools for the selection of multiple traits in jujube breeding.

Odoi et al. (Contribution 9) carried out association mapping on a panel of 374 Shea tree (Vitellaria paradoxa) accessions using 7530 SNPs markers, offering a foundation for molecular breeding strategies aimed at improving oil yield in the species.