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

Abstract

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.

Keywords: CDCC171; Abdominal fat; GWAS; Goose; Ovarian transcriptome; Transposable elements.

Fig. 1

Genome-wide Distribution and Function of TE. A From outer to inner rings, the diagram represents chromosomal short-read mappability, distributions of reference genes and TE, as well as TIPs by superfamily (number of DNA TE, number of MITEs, and number of LTRs) across the 12 chromosomes of the goose genome. B The relationship between different types of TE and genes within the genome. C GO enrichment analysis of genes which promoter or gene region overlapping with TE. D Pfam domain enrichment analysis of genes which promoter or gene region overlapping with TE

Fig. 2

TAP were Conservative Across Varies Geese Breeds. A PCA of TAP. B Neighbor-joining tree based on TAP, showing the phylogenetic relationships among various goose populations. C Population structure analysis based on TAP. D Distribution of TAP numbers across different goose populations. E Fst values between different populations within TAP’s regions. F Gene flow analysis based on TAP

Fig. 3

Relationship between TAP and Trait Variation in Geese. A QQ plot of the GWAS analysis. B Manhattan plot of the TE-GWAS analysis. C Violin plot depicting the effect sizes of different TE types. D LD dot plot displaying the LD between the significant TE and SNPs within 50kb upstream and downstream

Fig. 4

Impact of CCDC171 on weight of abdominal fat. A Frequency histogram of the weight of abdominal fat in 180 resequencing samples. The y-axis represents the weight of abdominal fat, and the x-axis represents the number of samples with the phenotype in this range. The density plot below shows the density distribution of the sample phenotypes. The red line in the frequency histogram represents the density curve and the blue line represents the normal distribution curve. B The position of CCDC171_helitron in the CCDC171 gene (green regions represent exons of the gene, blue regions represent CCDC171_helitron) and the distribution of the weight of abdominal fat for different haplotypes

Fig. 5

Co-expression of TE and egg production-related genes. A Heatmap of the expression of egg production-related genes. C Heatmap of the expression levels of TE co-expressed with egg production-related genes. C Co-expression network diagram of TE and egg production-related genes