Capitan, A. | Search bioRxiv

bioRxiv2025

Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity

BackgroundThe current cattle reference genome, derived from a single Hereford cow, does not capture the full spectrum of genetic diversity present within the species. Moreover, detecting structural variations (SVs [≥] 50 nucleotides long) remains challenging using only standard approaches of either short or long-read sequence approaches against a linear reference genome. Recent advances in long-read sequencing technologies and graph-based assembly now enable the construction of breed-specific pangenomes, revealing previously uncharacterized genomic regions that may contribute to important agricultural traits. ResultsIn this study we constructed a cattle pangenome graph using 16 high-quality haplotype-resolved genome assemblies originating from nine breeds representing the diversity of French cattle populations, and including Yak (Bos grunniens) as a close outgroup species. Using a trio-based strategy combined with complementary sequencing technologies and bioinformatics methods, we identified and characterized 101,219 structural variations. Of these, 33,634 were classified as non-reference unique insertions (NRUIs), adding several megabases of novel genomic sequences absent from the current Hereford reference genome. Analysis of the distribution of these NRUIs revealed significant genome-wide enrichment within QTL regions associated with milk production and morphological traits, suggesting their contribution to the genetic basis of economically relevant phenotypes. Furthermore, their functional annotation highlighted two NRUIs located within the intronic regions of ARMH3 and EPHA5, both specific to the Normande breed and significantly associated with milk production and morphological traits, respectively. ConclusionsOur findings demonstrate the value of pangenome approaches to uncover functionally relevant SVs, particularly NRUIs, that are systematically not in the current reference genome. By linking these variants to economically important traits, our work underscores the need to incorporate breed diversity into future genomic analyses and reference-building efforts in cattle.

genetics↗

bioRxiv2024

A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing mutation in the GNPAT gene

BackgroundGenetic defects that occur naturally in livestock species provide valuable models for investigating the molecular mechanisms underlying rare human diseases. Livestock breeds are subject to the regular emergence of recessive genetic defects, due to their low genetic variability, while their large population sizes provide easy access to case and control individuals, as well as massive amounts of pedigree, genomic and phenotypic information recorded for selection purposes. In this study, we investigated a lethal form of recessive chondrodysplasia observed in 21 stillborn calves of the Aubrac breed of beef cattle. ResultsDetailed clinical examinations revealed proximal limb shortening, epiphyseal calcific deposits and other clinical signs consistent with human rhizomelic chondrodysplasia punctata, a rare peroxisomal disorder caused by recessive mutations in one of five genes (AGPS, FAR1, GNPAT, PEX5 and PEX7). Using homozygosity mapping, whole genome sequencing of two affected individuals, and filtering for variants found in 1,867 control genomes, we reduced the list of candidate variants to a single deep intronic substitution in GNPAT (g.4,039,268G>A on Chromosome 28 of the ARS-UCD1.2 bovine genome assembly). For verification, we performed large-scale genotyping of this variant using a custom SNP array and found a perfect genotype-phenotype correlation in 21 cases and 26 of their parents, and a complete absence of homozygotes in 1,195 Aubrac controls. The g.4,039,268A allele segregated at a frequency of 2.6% in this population and was absent in 375,535 additional individuals from 17 breeds. Then, using in vivo and in vitro analyses, we demonstrated that the derived allele activates cryptic splice sites within intron 11 resulting in abnormal transcripts. Finally, by mining the wealth of records available in the French bovine database, we demonstrated that this deep intronic substitution was responsible not only for stillbirth but also for juvenile mortality in homozygotes and had a moderate but significant negative effect on muscle development in heterozygotes. ConclusionsWe report the first spontaneous large animal model of rhizomelic chondrodysplasia punctata and provide both a diagnostic test to counter-select this defect in cattle and interesting insights into the molecular consequences of complete or partial GNPAT insufficiency in mammals.

genetics↗