International Journal of Horticulture, 2024, Vol.14, No.3, 117-126 http://hortherbpublisher.com/index.php/ijh 119 2 Genomic Discoveries in Cucurbitaceae 2.1 Key genomic features and architectures discovered in different Cucurbitaceae species Recent studies have shed light on the genetic architecture of fruit size and shape variation in cucurbits, revealing a complex network of quantitative trait loci (QTL) and candidate genes. In cucumbers, melons, and watermelons, over 150 consensus QTLs for fruit size, shape, and weight have been identified, and a genome-wide survey has pinpointed 253 homologs of key fruit size/weight-related genes (Pan et al., 2019). These discoveries underscore the structural and functional conservation of fruit size/shape gene homologs across cucurbits, exemplified by genes such as CsSUN25-26-27a and CsTRM5 in cucumber, and CmOFP1a in melon (Pan et al., 2019). Additionally, the identification of 142 metal-tolerance proteins (MTPs) across eight Cucurbitaceae species highlights the importance of these transporters in plant metal tolerance and ion homeostasis (Jiang et al., 2021). The evolutionary analysis of these MTPs, which are under purifying selection, provides a basis for understanding ion transport functions and mechanisms in Cucurbitaceae (Jiang et al., 2021). 2.2 Comparative genomics: insights from comparing Cucurbitaceae genomes with other plant families Comparative genomics has been instrumental in understanding the evolution of mitochondrial genome size within the Cucurbitaceae family. The sequencing of the mitochondrial genomes of Citrullus lanatus and Cucurbita pepo revealed significant size variation, which is attributed to the accumulation of chloroplast sequences and short repeated sequences (Alverson et al., 2010). This variation is decoupled from mutation rate and RNA editing frequency, suggesting independent evolutionary pathways for these genomic features (Alverson et al., 2010). Furthermore, a multi-locus chloroplast phylogeny has provided insights into the character evolution and classification within the family, correlating well with flower characters such as the number of free styles and fusion of filaments and/or anthers (Kocyan et al., 2007). 2.3 Functional genomics: gene discoveries related to traits such as disease resistance, fruit quality, and stress tolerance The functional genomics landscape of Cucurbitaceae has expanded with the identification of calcium-dependent protein kinases (CDPKs) and CDPK-related kinases (CRKs) in six species. These kinases play crucial roles in plant growth, development, and stress response (Wei et al., 2019). Expression studies in watermelon have revealed genes that are induced by salinity and maintain high expression levels in male flowers, suggesting their potential roles in stress tolerance and reproductive development (Wei et al., 2019). Additionally, the complete chloroplast genome sequences of ten Cucurbitaceae species have been described, identifying genes under selection that are involved in chloroplast protein synthesis, gene transcription, energy transformation, and plant development (Zhang et al., 2018). These findings, along with the discovery of a large number of SSRs and SNPs in Cucurbita pepo, provide valuable resources for breeding programs aimed at improving disease resistance, fruit quality, and stress tolerance in cucurbits (Guo et al., 2020). 3 Applications of Genomic Research in Breeding 3.1 Marker-assisted selection (MAS): how genomic markers are used to accelerate breeding processes Marker-assisted selection (MAS) is a process where molecular markers are used to assist in the selection of desirable traits in crop improvement. In the context of Cucurbitaceae breeding, MAS has been significantly advanced by the development of high-throughput genotyping technologies and the identification of single nucleotide polymorphisms (SNPs). These advancements have facilitated the discovery of key genes and molecular markers linked to important traits in vegetables, including those in the Cucurbitaceae family (Mohan et al., 1997; He et al., 2014; Hao et al., 2019). Genotyping-by-sequencing (GBS) is one such technique that combines molecular marker discovery and genotyping, proving to be a cost-effective MAS tool in plant breeding (Figure 1) (He et al., 2014). 3.2 Genomic selection: principles and case studies in Cucurbitaceae Genomic selection (GS) is a breeding method that uses genome-wide marker data to predict the breeding values of individuals in a population. This approach is particularly useful for traits that are influenced by many genes, each
RkJQdWJsaXNoZXIy MjQ4ODYzNA==