Identification of the YABBY Gene Family in Cerasus humilis and Analysis of Expression Patterns During Different Growth Stages

TL;DR

This study identifies and analyzes the YABBY gene family in Cerasus humilis and explores their expression during growth stages, linking them to fruit development.

Contribution

The first genome-wide investigation of the YABBY gene family in Cerasus humilis, revealing gene structure, expression patterns, and potential roles in fruit maturation.

Findings

Six ChYABBY genes were identified across five chromosomes in Cerasus humilis.

ChYABBY genes show tissue-specific expression and correlate with fruit growth and maturation.

ChYABBY genes share conserved motifs and are closely related to Malus pumila YABBY genes.

Abstract

We identified and analyzed the Cerasus humilis YABBY (ChYABBY) gene family and further explored the expression changes in ChYABBYs in different growth stages. At the same time, the changes in physiological indexes in different periods of fruit were measured, the correlation between them and YABBY gene expression was analyzed, and the possible regulatory mechanism was speculated. This research provides an important basis for further understanding the structure and function of the ChYABBY gene, and lays a foundation for the identification of YABBY genes in Rosaceae plants.

YABBY belongs to the family of plant-specific transcription factors, known for their role in plant morphology, growth, and development. Its name is derived from the first discovered member—the YABBY1 gene of Arabidopsis thaliana (named due to its mutated phenotype showing a “Y-shaped” bifurcation). Despite extensive research across various plant species, no studies have conducted a genome-wide investigation of the YABBY gene family in Cerasus humilis. This study identified six ChYABBY (Cerasus humilis YABBY) genes distributed across five chromosomes through a comprehensive bioinformatic analysis of the C. humilis genome. The gene expression during the four growth phases was confirmed using real-time-quantitative fluorescent PCR (qPCR). ChYABBY is segmented into five distinct subfamilies. Genetic lineage analysis determined the close genetic relationship between the YABBY genes of C. humilis and Malus pumila. An examination of the gene architecture and preserved motifs revealed that ChYABBY typically comprises 5–6 introns, with motif1, motif2, and motif3 being preserved domains across all ChYABBY protein sequences. Promoter analysis suggests that ChYABBY genes play various roles in the growth and maturation of C. humilis. An examination of the homology revealed the absence of tandem replication in the ChYABBY gene family, with a single pair of fragment-replicating genes. The heat map and q-PCR results indicate that the expression of the ChYABBY gene is tissue-specific and correlates with some aspects of the fruit growth and development. This suggests a potential role for this gene family in fruit maturation. The determination of total sugar and total flavonoid content indicated that the content of the two substances was high when the fruit was green. The antioxidant capacity of the fruit at each stage was different. This research provides an important basis for further understanding the structure and function of the ChYABBY gene, and lays a foundation for the identification of YABBY genes in Rosaceae plants.

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