International Journal of Horticulture, 2024, Vol.14, No.5, 283-296 http://hortherbpublisher.com/index.php/ijh 284 Additionally, we highlighted recent progress in developing molecular markers and genetic maps for breeding programs aimed at enhancing desirable traits. This review provides valuable insights for genetic research, gene discovery, and the development of superior cucumber varieties, thereby supporting the sustainable advancement of cucumber breeding. 2 Cucumber Genome Structure 2.1 Genome size and organization The cucumber genome is relatively small, with an estimated size of approximately 367 Mbp. Recent advancements in sequencing technologies have enabled the assembly of high-quality reference genomes. For instance, the research team generated a high-quality cucumber reference genome using advanced technologies such as PacBio, 10X Genomics, and Hi-C, resulting in a total length of 226.2 Mb and an N50 of 8.9 Mb (Li et al., 2019). This assembly revealed new features, including 1,374 full-length long terminal retrotransposons and 1,078 novel genes, showcasing many new characteristics of the cucumber genome (Li et al., 2019). Additionally, the genome of Cucumis hystrix, a wild species closely related to cucumber, was assembled to a size of 289 Mb, providing insights into the genetic diversity and potential for introgression in cucumber breeding (Qin et al., 2021). The study indicates that Cucumis hystrix is cross-compatible with cultivated cucumber, which offers the potential for enriching the cucumber gene pool and improving traits such as disease resistance and stress tolerance. 2.2 Chromosome mapping Chromosome mapping in cucumber has been significantly advanced through various genomic and cytogenetic techniques. Li et al. (2019) assembled a high-quality cucumber genome reference, which includes 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, providing 29.0 Mb more sequence data than previous versions. Through the use of 10X Genomics and Hi-C data, 89 contigs (approximately 211.0 Mb) were directly connected into 7 pseudomolecule sequences. This high-quality genome reveals new features of the cucumber genome and serves as a valuable resource for cucumber and plant comparative genomics studies (Li et al., 2019). Turek et al. (2023) conducted a structural analysis of the B10v3 cucumber genome by integrating biological and bioinformatics data. The study demonstrated that by aligning sequences with the reference genome, the RagTag program was used to reorder the sequenced contigs, confirming the chromosomal positions of approximately 98% of protein-coding genes. Additionally, BLAST analysis revealed similarities and differences between the B10v3 genome and other cucumber cultivar genomes (Turek et al., 2023). These studies indicate that by integrating advanced genomic sequencing technologies such as SMRT long-read sequencing, 10X Genomics, and Hi-C data, cucumber chromosomal mapping and genome assembly have reached a new level, providing a solid foundation for cucumber genomics research and breeding. 2.3 Gene content and distribution The cucumber genome contains a diverse array of genes, and significant progress has been made in the functional annotation of protein-coding genes. A recent study identified 94,486 pairs of homologous protein-coding genes between cucumber and 14 other angiosperm species (Song et al., 2018). These homologous genes were used as proxies for functional annotation, significantly improving the accuracy of gene function prediction in cucumber. The study ultimately assigned Gene Ontology (GO) terms to 10,885 cucumber protein-coding genes, demonstrating improved annotation accuracy compared to existing methods (Song et al., 2018). Genome-wide association studies (GWAS) have identified regions associated with important horticultural traits, providing valuable resources for crop improvement (Wang et al., 2018). Additionally, the identification of QTL and molecular marker genes has further deepened the understanding of the genetic basis of key phenotypic traits in cucumber (Wang et al., 2020).
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