Fruit size is an important fruit quality trait that influences the production and commodity values of loquats (Eriobotrya japonica Lindl.). The Small Auxin Upregulated RNA (SAUR) gene family has proven to play a vital role in the fruit development of many plant species. However, it has not been comprehensively studied in a genome-wide manner in loquats, and its role in regulating fruit size remains unknown. In this study, we identified 95 EjSAUR genes in the loquat genome. Tandem duplication and segmental duplication contributed to the expansion of this gene family in loquats. Phylogenetic analysis grouped the SAURs from Arabidopsis, rice, and loquat into nine clusters. By analyzing the transcriptome profiles in different tissues and at different fruit developmental stages and comparing two sister lines with contrasting fruit sizes, as well as by functional predictions, a candidate gene (EjSAUR22) highly expressed in expanding fruits was selected for further functional investigation. A combination of Indoleacetic acid (IAA) treatment and virus-induced gene silencing revealed that EjSAUR22 was not only responsive to auxin, but also played a role in regulating cell size and fruit expansion. The findings from our study provide a solid foundation for understanding the molecular mechanisms controlling fruit size in loquats, and also provide potential targets for manipulation of fruit size to accelerate loquat breeding.

The MADS-box transcription factors have garnered substantial attention due to their crucial involvement in various biological processes, particularly in flower organogenesis. A comprehensive investigation into the MADS-box genes remains lacking in loquat (Eriobotrya japonica Lindl.). In the current study, to preliminarily explore the potential candidate genes related to flower and fruit development, a genome-wide analysis was carried out to identify and characterize the MADS-box gene family in loquat. Among the 125 identified EjMADS-box members, 49 genes belonged to type Ⅰ, which were subsequently assigned to three subfamilies: Mα (25 genes), Mβ (10 genes), and Mγ (14 genes). Additionally, 76 genes fell under type II, which were categorized into two groups: MIKC^C (70 genes) and MIKC* (6 genes). Through the collinearity analysis and comparison of the gene numbers between loquat and other Rosaceae genomes, it was revealed that the type Ⅱ MADS-box members were expanded in Maloideae after a whole genome duplication. The gene expression analysis utilizing various tissues during flower development revealed that the expression patterns of the ABCDE model homologs were conserved in loquat. In addition, several candidate genes potentially involved in flower bud differentiation (EjMADS107/109) and fruit expansion (EjMADS24/46/49/55/61/67/77/86) were identified. This analysis could serve as a fundamental basis for investigating the molecular functions of the MADS-box genes in the development of flowers as well as fruits in loquat.

Loquat (Eriobotrya japonica), an important subtropical fruit crop, blooms in autumn/winter, which is distinctive compared with other fruit trees such as apple, pear, and peach in Rosaceae. Currently, alternative splicing (AS) of flowering time genes remains understudied in loquat. In this study, full-length transcriptome sequencing of mixed tissues composed of leaves and shoot apical meristems/flower buds was performed and analyzed. A total of 94,194 high-quality isoforms and 44,186 complete open reading frames (ORFs) were obtained out of the 41.79 Gb of subread data. Further analysis revealed 25,988 AS events among 7461 genes, of which the most abundant type was intron retention (IR) occupying 55.32%. Importantly, 197 loquat genes homologous to Arabidopsis or Rosaceae flowering time genes were found to be alternatively spliced, including an important player CONSTANS (EjCO1) that contained three different isoforms (EjCO1-1, EjCO1-2, and EjCO1-3). To investigate the effect of AS on gene function, we overexpressed the three EjCO1 isoforms in Arabidopsis. The results showed that overexpression of EjCO1-1 and EjCO1-3 significantly promoted early flowering of transgenic Arabidopsis plants, whereas overexpressing EjCO1-2 did not significantly change the flowering time. Dual-luciferase reporter assays showed that EjCO1-1 and EjCO1-3 could significantly activate the expression of FLOWERING LOCUS T (EjFT2), while EjCO1-2 had no significant effect on the promoter activity of EjFT2. The results from this study systematically cataloged AS events of flowering time genes and illustrated the important effect of AS on gene functions, which provides insights into the molecular regulation of flowering time by AS in loquat.

Guava (Psidium guajava L.), a perennial species native to tropical regions of the Americas, holds significant economic value and plays an important role in the global fruit industry. Although several reference genomes have been published, population-level genomic studies remain limited, hindering genetic improvement efforts. In this study, we conducted whole genome re-sequencing of 62 guava accessions, primarily from Southern China and Brazil. A total of 4,887,006 high-quality SNPs and 731,469 InDels were identified for population genomic analyses. Phylogenetic and population structure analyses revealed subgroupings that largely corresponded to geographic origins. The data indicated that extensive hybridization between accessions from Brazil and or within China has contributed to the development of many dominant commercial varieties. Genetic diversity analyses showed that Brazilian accessions exhibited higher nucleotide diversity and more rapid linkage disequilibrium decay than those from China. Environmental factors and artificial selection likely imposed selective pressures that shaped guava’s adaptability and agronomic traits. A preliminary genome-wide association study (GWAS) identified PgMYB4 as a candidate gene potentially associated with fruit flesh color. These findings provide novel insights into the genetic diversity, population history, and domestication of guava, and lay a valuable foundation for future breeding and improvement strategies.

Loquat (Eriobotrya japonica), an economically important evergreen fruit tree, exhibits an unusual reproductive cycle characterized by autumn–winter flowering and spring fruit maturation. However, the endogenous hormonal basis underlying this distinctive developmental pattern remains poorly understood, partly due to the lack of reliable multi-hormone analytical platforms for complex perennial fruit tissues. In this study, we established a robust targeted UHPLC-QQQ-MS/MS method for the simultaneous quantification of 11 endogenous phytohormones and related metabolites, including indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellins (GA₁, GA₃, GA₄, and GA₇), and cytokinins (tZR, iPR, DHZ, iP, and zeatin). Sample preparation and chromatographic conditions were systematically optimized to improve extraction efficiency, to reduce matrix interference, and to maximize detection sensitivity. The method exhibited high linearity (R² > 0.990), satisfactory recoveries (80.02–120.09%), low limits of detection, and high repeatability. Application of this platform to eight different loquat tissues revealed pronounced tissue-specific patterns of phytohormone distribution. Seeds contained exceptionally high levels of GA₃ and zeatin, whereas stamens exhibited marked enrichment of IAA. Mature leaves showed relatively high ABA levels, whereas fruit flesh retained substantial cytokinin pools. These findings provide a reliable analytical workflow for phytohormone quantification in perennial fruit crops and establish a foundational dataset of tissue-specific hormone distribution in loquat, which may serve as a valuable reference for future studies on reproductive development and horticultural trait improvement.