Genomics and Biotechnology Empower Plant Science Research

Genomics and biotechnology play crucial roles in biological research, rapidly propelling the field of plant science. They provide the means to delve deeply into the understanding of plant genomics and functions, driving plant improvement and genetic studies, as well as deciphering mechanisms of plant responses to environmental stress. Furthermore, they further our comprehension and application of plant evolution and diversity. These advancements reported in this Special Issue, entitled “Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants”, contribute to the better utilization of plant resources, enhancing crop yield and quality, stress adaptations, as well as the preservation and conservation of plant species.

• Genomics and Biotechnologies in Horticulture

Horticultural plants encompass a diverse range of botanical species characterized by unique biological traits. They often necessitate controlled environments for optimal growth, rely on grafting techniques for propagation, and possess the ability for asexual reproduction. These plants hold immense economic and cultural significance for humankind. Currently, more than 200 horticultural plant species, including fruit trees, vegetables, flowers, medicinal plants, and beverage crops, have been subjected to genomic sequencing [1]. Remarkable strides have also been achieved in the fields of genome genotyping, pan-genomics, and the assembly of telomere-to-telomere genomes [2], marking an unprecedented advancement in our understanding of these plants.

Currently, the rapid development and application of multi-omics technologies, such as phenomics, metabolomics, and hormone profiling, as well as various gene editing technologies such as CRISPR-Cas, have greatly facilitated plant gene function research and the molecular breeding of new cultivars.

• The Molecular Mechanisms of Horticultural Plant Adaptation to the Environment

Environmental adaptation is a key characteristic of horticultural plants for their growth and reproduction under various environmental conditions. However, the study of horticultural plants lags behind model plants due to their diverse traits. With the decoding of the genomes of many horticultural plants and breakthroughs in various biotechnological approaches, significant progress has been made in the molecular genetics of horticultural plants. Identifying important genes is crucial in the face of various stresses. In this Special Issue, PebHLH56 in passion fruit was found to be involved in cold stress [3]; SOD in water lilies is associated with temperature stress and heavy metal stress [4]; and lncRNA participates in plant–pathogen interactions in tomatoes [5]. Furthermore, in addressing various disease and pest problems, Chae et al. identified key genomic loci and alleles that play critical roles in pepper disease resistance through quantitative trait locus (QTL) analysis. These research findings will provide references for the development of SNP markers associated with pepper disease resistance QTLs and the breeding of disease-resistant pepper cultivars [6]. Shao et al., exploring the duplication/loss of NLR genes in Asteraceae species, discovered a unique evolutionary pattern of “expansion followed by contraction” in NLR genes, thus establishing the NLR gene repertoire in Asteraceae plants and revealing the genetic basis of disease resistance in Asteraceae plants [7].

• The Molecular Mechanisms Underlying the Formation of Quality Traits in Horticultural Crops

The formation of quality traits in horticultural crops is a complex process involving the regulation of multiple molecular mechanisms. These mechanisms directly or indirectly influence the crop’s appearance, taste, aroma, and nutritional value, among other quality features. The accumulation of sugars in fruits is crucial for quality formation, and sugar accumulation is associated with several molecular mechanisms. Shui et al. [8] investigated lychee fruit quality by applying excessive calcium fertilizer and found that downregulation and expression of the CHS gene family may lead to the reduced accumulation of chalcones, resulting in oxidative damage to fruit flesh and the inhibition of soluble sugar accumulation in the tissue. Xu et al. utilized transcriptomic approaches to study the gene expression profile underlying grape skin color formation and identified key MYB genes involved in skin color transitions [9]. Sun et al. [10] performed cluster analyses on chrysanthemum varieties, dividing them into five categories and summarizing the typical plant configurations of each variety. Finally, they conducted genome-wide association studies (GWASs) to identify potential functional genes. A comprehensive understanding of these mechanisms contributes to optimizing the quality and yield of horticultural crops.

• Big Data Tools for Horticulture Research

Genomics, through high-throughput sequencing technologies such as whole-genome sequencing and transcriptome sequencing, enables us to rapidly and comprehensively develop understanding of the composition, structure, and function of plant genomes. This provides a powerful tool for uncovering the functions, genetic variations, and evolution of plant genes. However, genomic data have not been effectively utilized. To address this gap and efficiently utilize big data, Zhou et al. [11] established the first multi-omics database focused on strawberries, storing all available genomic and transcriptomic data. They developed a series of bioinformatics tools, creating an integrated platform that will facilitate genetic and breeding research in strawberries. RNA-Seq analysis is a fundamental transcriptomics research method; Shi et al. [12] proposed a clustering-based correlation analysis method (C-CorA), which is an efficient approach for analyzing the correlation of various types of data across different dimensions. This method can be applied to RNA-Seq data for candidate gene detection in fruit quality research. Jin et al. [13] conducted genome re-sequencing of Gypsophila paniculata, constructed a whole-genome InDel marker system, and established the first genome-wide genetic map for Gypsophila paniculata, providing a complete marker system for molecular studies. This technology enables us to study and improve important traits in plants, such as disease resistance, stress tolerance, and yield.

Genomics and biotechnology have provided abundant data and tools for studying genetic diversity and evolution in plants. By comparing the genome sequences and conducting functional genomics studies of different plant species, we can determine the patterns and mechanisms of plant evolution, infer species relationships, and understand the genomic bases of plant adaptations to different environments. Using biotechnological tools such as gene knockout, gene expression regulation, and transgenic techniques, we can identify and validate the functions of plant genes, thus revealing their roles in biological processes.