# A Comparative Analysis of Transcriptome-Wide Differential Gene Expression and Alternative Polyadenylation in the Ovaries of Meat Ducks and Laying Ducks

## TL;DR

This study compares gene activity and alternative polyadenylation in the ovaries of meat and laying ducks to understand differences in egg production and growth.

## Contribution

The study reveals novel APA patterns and gene expression differences linked to ovarian function and egg-laying performance in ducks.

## Key findings

- Significant differences in alternative polyadenylation (APA) were found between Shaoxing and Qiangying ducks.
- Key genes related to hormone synthesis, lipid metabolism, and antioxidant defense were identified as differentially regulated.
- APA events were linked to pathways like mitochondrial energy metabolism and fatty acid degradation.

## Abstract

We aimed to understand why some duck breeds excel in egg production while others grow faster but lay fewer. Their ovaries are the key organs related to egg-laying, so we compared the complete set of active genes in the ovaries between the high-yielding Shaoxing ducks and the low-yielding Qiangying ducks. Using advanced full-length transcriptome sequencing, we discovered nearly a hundred thousand novel gene fragments and divergent patterns of alternative polyadenylation (APA), a key post-transcriptional regulatory process, in the two breeds. These differences affect energy use, hormone production, and cell protection. By linking these gene-level changes to ovarian function and breed phenotype, our work identifies candidate genes and regulatory mechanisms that may contribute to divergent egg-laying performance. These findings provide foundational insights and testable hypotheses for future breeding strategies aimed at enhancing lay efficiency in ducks.

Significant differences in reproductive performance exist between meat-type ducks (e.g., Qiangying Duck, QD) and laying-type ducks (e.g., Shaoxing Duck, SD). The molecular mechanisms underlying these differences, particularly concerning ovarian development and function, remain incompletely understood. This study aimed to comprehensively characterize the ovarian transcriptomes of these two duck types, focusing on differential gene expression and post-transcriptional regulatory events. We performed an integrated full-length transcriptome analysis of ovarian tissues from these two breeds using PacBio SMRT and Illumina sequencing. Bioinformatic analyses, including functional annotation, differential expression analysis, and the identification of APA events, were used. We discovered substantial breed-specific differences in alternative polyadenylation (APA), with SD ducks exhibiting significant 3′UTR shortening in 3799 genes and 3′UTR lengthening in 1626 genes compared to QD. The integrated analysis of differential gene expression and APA events highlighted key genes related to steroid hormone synthesis (HMGCS1, DHCR24), lipid metabolism (SCD), signal transduction (HRAS), and antioxidant defense (SOD1). The functional enrichment implicated critical pathways such as mitochondrial energy metabolism, oxidative phosphorylation, and fatty acid degradation. Our study provides a comprehensive atlas of post-transcriptional regulation in the duck ovary and reveals APA as a crucial process of gene regulation. APA may contribute to the differential ovarian function and egg-laying capacity between meat and laying ducks, thus offering valuable targets for genetic selection.