GWAS & Selection signatures

Identifying the drivers of new genetic variation in chickens

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Abstract

To understand the contribution of new mutations to functional genetic variation, we quantified the rate, spectrum, and genomic determinants of germline mutations in a commercial chicken pedigree line. Using whole-genome sequencing data from 194 trios, we estimated a rate of µ = 3.49×10-9 mutations per nucleotide site per generation. A goodness-of-fit test (χ213 = 10.97, P = 0.61) indicated that the number of new mutations per generation follows a Poisson distribution with a rate parameter λ = 6.22. A read-based phasing approach revealed a strong sex bias, with males contributing approximately twice as many mutations to their offspring as females. We also found an 8% higher mutation rate in microchromosomes compared with macrochromosomes, which was explained by their higher GC content (~50% vs. 40%) and a mutation spectrum dominated by C→T transitions. Using this spectrum to build a codon transition matrix, we identified glutamic acid and glutamine codons among the most prone to non-silent mutations. To assess gene-level contributions to mutational variance (Vm), we scored protein-coding genes based on their codon composition and their likelihood of incurring moderate-effect (M, missense) or high-effect (H, nonsense) mutations as predicted from the mutation spectrum by calculating, for each protein-coding gene i of length L, the sum over all amino acids j of the probability that a mutation affecting amino acid j produces an effect of a given magnitude (M or H). These scores therefore capture gene-specific differences in Vm by integrating both the probability that a new mutation affects a protein and the expected magnitude of that effect. Because Vm determines the rate at which genetic variation is introduced each generation, genes with higher scores are expected to contribute disproportionately to the mutational input of potentially selectable variation. Gene ontology enrichment analysis of high-scoring genes revealed significant overrepresentation of immune response and body developmental processes, positioning these genes as key sources of new functional variation due to their elevated likelihood of amino acid-altering mutations. We conclude that the germline mutation rate is shaped by genomic and biological context, generating predictable patterns of variation that can inform selection strategies and contribute to the long-term sustainability of breeding programs.

Keywords: 2026

How to Cite:

Kranis, A., López-Cortegano, E. & Sosa-Madrid, B., (2026) “Identifying the drivers of new genetic variation in chickens”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283115. doi: https://doi.org/10.31274/wcgalp.23483

Rights: 1