Journal Article

Investigating the role of transposable elements in shaping abdominal fat and egg production phenotypic traits in geese

Chen, Zhuping, Chao, Wang, Chen, Ying, Gao, Guangliang, Ma, Lin, Zhang, Keshan, Hu, Silu, Wang, Qigui, Kuang, Shaoxiang, Xie, Youhui, Wang, Lihui, Zhao, Xianzhi, Xue, Jiajia, Luo, Yi, Wang, Haiwei, Wu, Xianwen

2025

Overview

While transposable elements (TE) are critical drivers of genomic diversity, their influence on phenotypic traits in geese remain largely unexplored, primarily because most research has focused on single nucleotide polymorphisms (SNP). In this study, we identified 157,044 TE absence polymorphisms (TAP) in the genome of 566 Sichuan White geese through whole-genome resequencing (with an average coverage depth of 12.44 ×) to evaluate their influence across different populations, and we extended our investigation to include a TE genome-wide association study (TE-GWAS) encompassing 48 traits, with a particular focus on abdominal fat weight. Notably, a TE within an intron of the CDCC171 gene was identified and significantly affects abdominal fat deposition, exhibiting minimal Linkage with SNPs within a 100 kb region. Additionally, co-expression analysis of ovarian transcriptome data from four geese populations revealed significant correlations between long terminal repeat (LTR) and terminal inverted repeat (TIR) elements and genes related to egg production. Collectively, these findings highlight the potential of TE as key drivers of phenotypic variation in geese, presenting new opportunities for targeted breeding strategies.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abdomen / Abdominal fat / Abdominal Fat - metabolism / Animal genetics / Animal Genetics and Genomics / Animals / Aquatic birds / Biomedical and Life Sciences / CDCC171 / Datasets / DNA Transposable Elements / Domestication / Egg (Biology) / Egg production / Eggs / Fat / Female / Fertility / Geese / Geese - genetics / Geese - physiology / Gene expression / Genetic aspects / Genetic research / Genome-wide association studies / Genome-Wide Association Study / Genomics / Genomics of domestication / Goose / GWAS / Immune response / Inverted repeat / Life Sciences / Long terminal repeat / Metabolism / Microarrays / Microbial Genetics and Genomics / Nucleotides / Ovarian transcriptome / Ovaries / Phenotype / Phenotypic variations / Physiological aspects / Plant Genetics and Genomics / Polymorphism / Polymorphism, Single Nucleotide / Populations / Proteomics / Single-nucleotide polymorphism / Software / Transcriptomes / Transposable elements / Transposons / Waterfowl / Whole genome sequencing / Wildfowl