Tree Genetics and Molecular Breeding 2024, Vol.14, No.4, 185-193 http://genbreedpublisher.com/index.php/tgmb 186 improvement, addressing current challenges in horticultural production, and exploring new paths for future development. 2 Genomic Resources for Loquat 2.1 Progress in genome sequencing The advancement in genome sequencing has significantly contributed to the understanding of loquat (Eriobotrya japonica) genetics. The first high-quality chromosome-level genome assembly of wild loquat has been generated, revealing 45 791 predicted protein-coding genes. This assembly has provided insights into the genomic evolution and domestication of loquat, showing a recent whole-genome duplication event prior to its divergence from a common ancestor shared with apple and pear (Jing et al., 2022). Additionally, genome resequencing has distinguished loquat germplasms into wild and cultivated groups, highlighting the genetic diversity and selective sweeps related to fruit quality and size during domestication (Jing et al., 2022). 2.2 Transcriptomics and proteomics Transcriptomic and proteomic analyses have been pivotal in identifying key genes and metabolic pathways involved in loquat fruit development and ripening. High-throughput RNA-seq has identified thousands of differentially expressed genes (DEGs) across various metabolic pathways, including carbohydrate metabolism and hormone signaling, which are crucial for fruit development (Song et al., 2016). Furthermore, a comprehensive analysis of expressed sequence tags (ESTs) from a normalized full-length cDNA library has revealed significant functional genes related to loquat fruit development, such as ethylene receptors and cell wall expansin genes. Proteomic studies have also highlighted the role of differentially accumulated proteins in starch and sucrose metabolism during flower development (Jing et al., 2020). 2.3 Comparative genomics Comparative genomics has provided valuable insights into the genetic relationships and evolutionary history of loquat. Analysis has shown that loquat shares a common ancestor with other members of the Rosaceae family, such as apple and pear, and has undergone a whole-genome duplication event (Jing et al., 2022). This comparative approach has also been used to identify quantitative trait loci (QTLs) associated with important traits in other crops, which can be applied to loquat for genetic improvement (Shariatipour et al., 2021). Additionally, the identification of single nucleotide polymorphisms (SNPs) from transcriptome sequences has facilitated genetic diversity analyses and marker-assisted selection breeding in loquat (Li et al., 2015). 3 Identification of Key Genes 3.1 Genes controlling agronomic traits In loquat, several genes have been identified that play crucial roles in controlling agronomic traits such as fruit size, flesh color, and development. The genome assembly of wild loquat has revealed key differentially expressed genes (DEGs) involved in carbohydrate metabolism and plant hormone signal transduction, which are significantly regulated during fruit development in cultivated loquats (Table 1) (Jing et al., 2022). Additionally, the MADS-box gene family, particularly the ABCDE model homologs, has been associated with flower and fruit development, indicating their potential role in agronomic trait regulation (Li et al., 2023). Furthermore, quantitative PCR (qPCR) techniques have been developed to genotype polyploid loquats, allowing for the identification of flesh color genotypes, which is a key agronomic trait (Wang et al., 2021). 3.2 Genes involved in stress responses Loquat plants have developed various genetic mechanisms to respond to environmental stresses. The SWEET gene family, identified in loquat, plays a significant role in sugar transport and is involved in various physiological processes, including stress responses (Li et al., 2022). The expression patterns of EjSWEET genes in different tissues suggest their potential roles in plant development and stress adaptation. Moreover, the circadian clock genes in loquat, such as EjLHY, EjTOC1, and EjGIGANTEA, have been linked to heterosis and stress resistance, indicating their involvement in stress response mechanisms (Liu et al., 2019).
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