Tree Genetics and Molecular Breeding 2024, Vol.14, No.6, 286-294 http://genbreedpublisher.com/index.php/tgmb 290 6 Case Study: Genomic Dissection of Loquat Fruit Ripening 6.1 Background and importance of fruit ripening in loquat cultivation Loquat (Eriobotrya japonica Lindl.) is a non-climacteric fruit known for its rich nutritional profile, including essential minerals and carotenoids. The ripening process in loquat is crucial as it affects the fruit's taste, texture, and overall marketability. Understanding the molecular mechanisms underlying fruit ripening can significantly enhance loquat cultivation by improving fruit quality and extending shelf life. The ripening process involves complex physiological and biochemical changes driven by differentially expressed genes (DEGs) across various metabolic pathways, including carbohydrate metabolism and hormone signaling (Jing et al., 2020). 6.2 Identification of candidate genes through transcriptomic analysis Transcriptomic analysis has been instrumental in identifying candidate genes involved in loquat fruit ripening. High-throughput RNA sequencing has revealed thousands of DEGs during fruit development, with significant involvement in pathways such as cell-wall degradation and hormone signaling. Notably, genes related to auxin and ethylene response have been differentially expressed, indicating their roles in the ripening process. Additionally, several transcription factor families have been identified, which may regulate these pathways (Gisbert et al., 2009; Jing et al., 2020). The integration of genomics and transcriptomics has further identified key loci and genes, such as Ethylene Insensitive 4 (EjEIN4), that are potentially involved in fruit development and ripening (Figure 3) (Peng et al., 2022a). Figure 3 Observation of fruit development and DEGs identified from the RNA-seq experiment (Adopted from Peng et al., 2022a) Image caption: (A) Observations of fruit development of ZP44 and ZP65 at 10 time points, including 0 days past anthesis (0D, S1), 7D (S2), 14D, 28D (S4), 42D, 56D (S6), 63D, 77D (S8), 84D, and 91D. (B) Comparison of fruit diameter (transverse diameter) between ZP44 and ZP65. The values are the mean fruit diameter of 15 fruits. Bars are standard errors. (C) Principal component analysis using transcriptome profiles of all 30 replicates. (D) Summary of DEGs between ZP44 and ZP65 at each stage. (E) Comparison of DEGs at each stage (Adopted from Peng et al., 2022a)
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