Tree Genetics and Molecular Breeding 2024, Vol.14, No.6, 286-294 http://genbreedpublisher.com/index.php/tgmb 288 3.2 Advances in next-generation sequencing (NGS) technologies The advent of next-generation sequencing (NGS) technologies has significantly advanced loquat genomics. NGS has enabled high-throughput sequencing and comprehensive transcriptome analysis, facilitating the identification of thousands of differentially expressed genes (DEGs) involved in fruit development and ripening (Song et al., 2016). This technology has also allowed for the assembly of high-quality reads into unigenes, providing a deeper understanding of the genetic networks regulating loquat fruit development. The integration of NGS with other omics approaches, such as metabolomics, has further enhanced the ability to map complex traits and identify candidate genes for molecular breeding (Peng et al., 2022b). 3.3 High-quality reference genome and assembly techniques Recent efforts have focused on generating high-quality reference genomes for loquat, which are essential for accurate genome mapping and molecular breeding. The first high-quality chromosome-level genome assembly of wild loquat has been completed, revealing insights into the genomic evolution and domestication of the species (Jing et al., 2022). This reference genome includes a comprehensive set of predicted protein-coding genes and has facilitated the identification of genomic regions associated with important traits such as fruit quality and size. Advanced assembly techniques, combined with large-scale transcriptome and metabolome analyses, have provided valuable resources for elucidating the genetic basis of domestication and for guiding future breeding efforts in loquat. 4 Genomic Insights into Key Traits in Loquat 4.1 Genes and QTLs for fruit size and quality Recent genomic studies have significantly advanced our understanding of the genetic basis of fruit size and quality in loquat. The identification of 95 EjSAUR genes, which are involved in auxin signaling, has been pivotal in understanding fruit size regulation. Specifically, the EjSAUR22 gene has been identified as a key player in fruit expansion, responding to auxin and influencing cell size. Additionally, a multi-omics approach has identified major loci associated with fruit weight, including homologs of ETHYLENE INSENSITIVE 4 (EjEIN4) and TORNADO 1 (EjTRN1), which are crucial for fruit development (Peng et al., 2022b). Furthermore, the EjBZR1 gene has been shown to repress fruit enlargement by binding to the EjCYP90 promoter, highlighting its role in regulating brassinosteroid biosynthesis and cell expansion (Nadeem et al., 2018; Su et al., 2021). These insights provide a foundation for molecular breeding aimed at improving fruit size and quality in loquat. 4.2 Genetic regulation of flowering and fruiting time The genetic regulation of flowering and fruiting time in loquat is closely linked to the MADS-box gene family. A comprehensive genome-wide analysis has identified 125 EjMADS-box genes, which are crucial for flower and fruit development. These genes are categorized into various subfamilies, with several candidates like EjMADS107/109and EjMADS24 / EjMADS46 / EjMADS49 / EjMADS55 / EjMADS61 / EjMADS67 / EjMADS77/ EjMADS86 being potentially involved in flower bud differentiation and fruit expansion (Figure 2) (Li et al., 2023). The expression patterns of these genes during different developmental stages suggest their conserved roles in regulating flowering and fruiting time, providing valuable targets for breeding programs aimed at optimizing these traits (Xu et al., 2012). 4.3 Disease resistance genes in loquat Disease resistance in loquat is a critical trait for ensuring crop resilience and productivity. Genomic studies have identified several genes that may contribute to disease resistance. For instance, genes involved in sugar biosynthesis have been enriched in regions undergoing selective sweeps, indicating their potential role in disease resistance (Wang and Paterson, 2021). Additionally, transcriptomic analyses under cold stress conditions have revealed differentially expressed genes (DEGs) such as UDP-glycosyltransferase and glycosyltransferase, which are implicated in stress responses and may contribute to enhanced disease resistance (Zhang et al., 2022). These findings underscore the importance of integrating genomic data to identify and utilize disease resistance genes in loquat breeding programs.
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