The rate and spectrum of germline mutations in chicken from a commercial pedigree line
Abstract
BackgroundPedigree-based studies of germline mutations provide a direct understanding of the origin and consequences of genetic variation, and allow quantification of how mutations affect functional variation. Here, we use whole-genome sequencing data from 194 chicken (Gallus gallus) trios from a commercial pedigree line to estimate the germline mutation rate and spectrum, and to characterize patterns of mutational variation across the genome and genes, aiming to rank protein coding genes by their expected contributions to mutational variance (Vm).ResultsWe estimated a mutation 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 (λ = 6.22). A read-based phasing approach revealed a strong sex bias, with males contributing approximately twice as many mutations as females. Microchromosomes showed a point estimate of mutation rate approximately 8% higher than macrochromosomes, likely owing to their higher GC content and a mutation spectrum dominated by C→T transitions. From this spectrum, we built a codon transition matrix and show that genes vary widely in their propensity to mutation based on codon composition, likely reflecting large differences in their contributions to Vm. Specifically, we found that genes involved in immunity and development rank among those most prone to non-silent mutations.ConclusionsOur results reveal predictable patterns of gene-level mutational variation and provide a framework for anticipating how new mutations generate functional variation. By bridging quantitative genetics and molecular biology, we provide a mechanistic basis for variation in Vm across the genome, showing that heterogeneity in Vm can arise from gene-specific features, particularly codon composition and mutational target size. These metrics offer a way to rank genes and prioritize genetic variants by their expected contributions to biological functions as a consequence of de novo mutation. This provides a new basis for informed management of genetic variation in breeding populations and for understanding the evolutionary dynamics of functionally important genes.
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BibTeX
@article{lopezcortegano2026rate,
title = {{The rate and spectrum of germline mutations in chicken from a commercial pedigree line}},
author = {Eugenio López-Cortegano and Bolívar Samuel Sosa-Madrid and Andreas Kranis},
journal = {Genetics Selection Evolution},
year = {2026},
month = sep,
doi = {10.1186/s12711-026-01085-2},
url = {https://hal.science/hal-05766448v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - The rate and spectrum of germline mutations in chicken from a commercial pedigree line
AU - Eugenio López-Cortegano
AU - Bolívar Samuel Sosa-Madrid
AU - Andreas Kranis
PY - 2026
DA - 2026/09/28
JO - Genetics Selection Evolution
DO - 10.1186/s12711-026-01085-2
UR - https://hal.science/hal-05766448v1
AB - BackgroundPedigree-based studies of germline mutations provide a direct understanding of the origin and consequences of genetic variation, and allow quantification of how mutations affect functional variation. Here, we use whole-genome sequencing data from 194 chicken (Gallus gallus) trios from a commercial pedigree line to estimate the germline mutation rate and spectrum, and to characterize patterns of mutational variation across the genome and genes, aiming to rank protein coding genes by their expected contributions to mutational variance (Vm).ResultsWe estimated a mutation 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 (λ = 6.22). A read-based phasing approach revealed a strong sex bias, with males contributing approximately twice as many mutations as females. Microchromosomes showed a point estimate of mutation rate approximately 8% higher than macrochromosomes, likely owing to their higher GC content and a mutation spectrum dominated by C→T transitions. From this spectrum, we built a codon transition matrix and show that genes vary widely in their propensity to mutation based on codon composition, likely reflecting large differences in their contributions to Vm. Specifically, we found that genes involved in immunity and development rank among those most prone to non-silent mutations.ConclusionsOur results reveal predictable patterns of gene-level mutational variation and provide a framework for anticipating how new mutations generate functional variation. By bridging quantitative genetics and molecular biology, we provide a mechanistic basis for variation in Vm across the genome, showing that heterogeneity in Vm can arise from gene-specific features, particularly codon composition and mutational target size. These metrics offer a way to rank genes and prioritize genetic variants by their expected contributions to biological functions as a consequence of de novo mutation. This provides a new basis for informed management of genetic variation in breeding populations and for understanding the evolutionary dynamics of functionally important genes.
SN - 0999-193X
SN - 1297-9686
ER -