Identification of the Auxin Response Factor gene family in kernel consumption apricot and association analysis of related genes regulating fruit size in distant hybridization.

backgroundDistant hybridization is pivotal for fruit tree germplasm enhancement. Although successful hybridization has been achieved between kernel consumption apricot and almond, the hybrid progeny exhibits a consistent fruit size diminution compared to the maternal parent. Auxin Response Factor (ARF) is a key regulator of fruit size. However, the role of ARF family in regulating fruit size in kernel consumption apricot × almond distant hybridization remains uncharaterized.

resultsA total of 14 PaARF genes were identified in the kernel consumption apricot genome ('Longwangmao') and phylogenetically classified into five groups. All encoded conserved B3 and Auxin_resp domains, with seven containing an AUX_IAA domain. All PaARF genes exhibit a dispersed distribution pattern across seven chromosomes, and their promoters were enriched with cis-elements for light, hormone, and stress responses. Collinearity analysis identified PaARF genes show high functional conservation and lack recent duplications, with interspecific collinearity identifying only nine localized orthologous pairs in Arabidopsis. RNA-seq and RT-qPCR revealed that PaARF4, PaARF11B, PaARF16, and PaARF17 were differentially expressed between large and small hybrid fruits. Tissue-specific expression analysis across different apricot tissues revealed that PaARF4, PaARF11B,and PaARF17 were highly expressed in fruit, peaking at 55, 45, and 75 days after flowering, respectively. Weighted gene co-expression network analysis (WGCNA) revealed direct interactions of PaARF4 with 12 genes in the turquoise module, while PaARF11B and PaARF17 connected to 3 and 19 genes, respectively. A combinatorial bioinformatics analysis utilizing PlantRegMap, PlantPAN, and MEME further identified a candidate transcription factor (WRKY7) for PaARF4 and predicted eight downstream target genes along with their corresponding binding motifs for three PaARF genes.

conclusionsOur results suggest that PaARF4, PaARF11B, and PaARF17 are key regulators of fruit growth and development in kernel consumption apricot × almond hybrids, with PaARF11B is a particularly promising candidate gene for the regulation of fruit size. Further, the identified candidate transcription factors and downstream target genes provide a foundational regulatory network for understanding auxin-mediated fruit development. This work provides valuable genetic resources and candidate genes for future research on fruit size, facilitating the genetic improvement of fruit trees through distant hybridization.