Comparative Genomic Analysis Across Multiple Species to Identify Candidate Genes Associated with Important Traits in Chickens

Abstract

Background: As one of the most important poultry species worldwide, chickens provide substantial amounts of meat, eggs, and other products for human consumption. With continuous improvements in living standards, consumer demand for high-quality animal products is increasing, making it essential to understand the genetic basis of key traits such as egg production, meat quality, and disease resistance for targeted genetic improvement. Methods: In this study, a number of the candidate genes associated with important traits in chickens were screened by various comparative genomics analysis methods. To further clarify the relationship between these candidate genes and important traits in chickens, they were functionally annotated through the KOG, GO, and KEGG databases. Results: These candidate genes are mainly concentrated in the functional categories of transcription and signal transduction mechanisms and are involved in biological processes such as cyclic nucleotide biosynthesis and intracellular signaling, which involve signaling pathways such as ECM-receptor interactions and calcium signaling. Conclusions: Based on the annotation results from various databases, a functional search of the candidate genes and related literature reports, the following results were obtained: genes such as TBX22, LCORL, and GH were associated with chicken growth traits; genes such as A-FABP, H-FABP, and PRKAB2 were associated with chicken meat quality; genes such as IGF-1, SLC25A29, and WDR25 were associated with chicken reproductive traits; and genes such as C1QBP, VAV2 and IL12B were associated with chicken disease resistance traits. Overall, the findings of this study provide novel insights and candidate genes for genetic improvements in chickens, laying a foundation for future research and breeding strategies targeting key economic traits.

Keywords: candidate genes; chicken; comparative genomics; functional annotation; gene families.

Figure 1

Distribution of gene families and gene copy numbers across eight species. (A,B) Distribution of gene copy numbers within all gene families across species. (C,D) Distribution of gene copy numbers at the gene level across species. Gene families and genes were categorized based on copy numbers (0, 1, 2, 3, 4, and >4), and the proportion in each category was calculated for each species.

Figure 2

Petal diagram of gene family clustering among eight species. The petal map illustrates the distribution of shared and species-specific gene families across the eight analyzed species: chickens, ducks, geese, cows, sheep, pigs, humans, and zebrafish. The central region represents the number of gene families common to all species, while each petal indicates the number of gene families unique to a specific species.

Figure 3

Phylogenetic trees show gene family expansion and contraction events across species. The evolutionary tree illustrates the relationships among the eight species analyzed, along with the number of gene families that have undergone significant expansion or contraction. Green numbers indicate the number of expanded gene families, while red numbers indicate the number of contracted gene families along each lineage.

Figure 4

Phylogenetic trees illustrate estimated species divergence times. The numbers at the top of the figure represent estimated divergence times (in millions of years ago, Mya), with larger values indicating earlier divergence events. The branches depict the evolutionary relationships among species, and the values along the branches represent the divergence time ranges between species, with specific intervals shown in parentheses. Abbreviations of geological periods are displayed at the bottom of the figure, including N. (Neoproterozoic), Ca. (Cambrian), S. (Silurian), De. (Devonian), Tr. (Triassic), Ju. (Jurassic), Cr. (Cretaceous), and P. (Paleoproterozoic).

Figure 5

Distribution of Ks values among chicken and other species. The x-axis (Ks) represents the synonymous substitution rate, while the y-axis (density) indicates the distribution density. Colored density curves correspond to the Ks distributions between chicken and each of the other species analyzed. By examining the peak positions of the Ks distributions, the timing of whole-genome duplication events and the evolutionary relationships between species can be inferred.

Figure 6

Genomic collinearity is plotted between chickens and closely related species. (A) Collinearity between chickens and geese. (B) Collinearity between chickens and ducks. The horizontal and vertical axes represent chromosomal positions in each species. Each dot indicates a pair of homologous genes exhibiting collinearity between the two genomes.

Figure 7

Distribution of LTR insertion times in the chicken genome. This figure illustrates the estimated insertion times and distribution density of LTR retrotransposons in Gallus gallus (chicken). The x-axis represents the insertion time in millions of years ago (Mya), while the y-axis indicates the density of LTR insertions across the genome.

Figure 8

Functional annotation and enrichment analysis of candidate genes. (A) KOG functional classification of candidate genes. (B) Gene Ontology (GO) functional enrichment analysis. (C) KEGG pathway enrichment analysis.