Analysis of pedigree data and whole‐genome sequences in 12 cattle breeds reveals extremely low within‐breed Y‐chromosome diversity

Abstract

Summary In this article, we analyzed pedigree information on males from 12 bovine breeds born in France between 2015 and 2019. We report an overall small number of paternal lineages with, for example, a minimal number of ancestors accounting for 95% of the Y‐chromosome pool of their breed ranging from only 2 to 15 individuals. Then, we mined whole‐genome sequence data from 811 sires (2 ≤ n ≤ 510 per breed) and built a median‐joining network using 1411 SNPs. Most branches were breed‐specific and in agreement with the geographic and genetic relatedness of these populations. The within‐breed haplotype diversity was lower than expected based on genealogical information, which supports the existence of major male founder effects predating pedigree recording. In addition, we observed de novo mutation events among the descendants of the same ancestors, which are of interest to define paternal sub‐lineages. Our results pave the way to future studies on the estimation of the effects of Y‐chromosome haplotypes on male reproductive performances and on the conservation of Y‐chromosome diversity.

A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing mutation in theGNPATgene

“…Cattle breeds are genetically small populations created 150 years ago from a limited number of founders, whose genetic variability has been further reduced over the last 50 years by the overuse of influential sires through AI [42,43]. Typically, cattle breeds have effective population sizes (Ne) ranging from 12 to 150, and a minimum number of ancestors contributing to 50% of the breed's gene pool ranging from 5 to 71, as reported in a recent study of 26 cattle breeds reared in France (https://idele.fr/detail-dossier/varume-resultats-2023; accessed 2024/03/28).…”

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies

“…In domestics, the most pronounced MSY signals are male bottlenecks during the domestication process, the distribution of domestic lineages, admixture between wild and domestic populations, and the massive decline of MSY diversity due to amplification of few selected males in recent intensive breeding regimes. This has been shown in horses (Remer et al., 2022; Wallner et al., 2017), sheep (Deng et al., 2020), goats (Nijman et al., 2022; Xiao et al., 2021), pigs (Ai et al., 2021; Guirao‐Rico et al., 2018), cattle (Chen, Cai, et al., 2018; Chen, Zhou, et al., 2018; Escouflaire & Capitan, 2021; Ganguly et al., 2020), and dogs (Oetjens et al., 2018; Smeds et al., 2019).…”

Massive detection of cryptic recessive genetic defects in cattle mining millions of life histories

“…We considered 55.5 million inseminations performed during the period 2013-2022, of which 2.0 million involved females and males that were both genotyped. To estimate the number of homozygous calves (NH), we took into account the total number of inseminations (NAI), the proportion of at-risk mating observed within genotyped couples (PR), the Mendelian probability (0.25), the average conception rate in each breed (CR), and finally the proportion of females bred by AI (%AI): NH = NAI*PR *CR*0.25/ %AI (Supplementary Table 6; Escouflaire and Capitan 2021.…”