Animal genetics最新文献

Sheep provide both meat and valuable non-meat products, including lambskin. Global production of raw sheep skin and lambskins increased from 1.78 million t in 2014 to 2.19 million t in 2023 (23% increase), reflecting growing industrial demand. This review summarizes factors influencing lambskin traits. Non-genetic factors influencing lambskin traits include nutrition, age and lambing seasons. Wool curvature is strongly associated with lambskin traits. Heritability estimates for most lambskin traits are moderate to high (h² = 0.28–0.82). BMP7, Wnt/β-catenin and TGF-β signaling pathways play critical roles in determining lambskin traits. Genes, including KRT25, KRT71 and BMP7, play key roles in lambskin. Other genes with minor effects were also reported regarding the polygenic nature of lambskin-related traits. Understanding the determining factors offers new opportunities to develop efficient breeding programs, enhance market value, and promote sustainable production. In this review, we highlight the need for targeted research, incorporating advanced genomic and epigenomic technologies such as whole-genome sequencing, genome-wide association studies, DNA methylation mapping and ncRNA sequencing, to fill knowledge gaps and facilitate the implementation of a precise breeding program for superior lambskin quality.

Gangliosidoses are inherited lysosomal storage disorders characterised by neuronal accumulation of gangliosides. While GM1 gangliosidosis has been reported in cattle, GM2 gangliosidosis has yet to be. We investigated a herd of Angus cattle with progressive neurological signs, including blindness, ataxia and lethargy. Histopathology revealed widespread neuronal vacuolation, and electron microscopy identified laminated cytoplasmic bodies consistent with ganglioside accumulation. Whole-genome sequencing of an affected calf identified a homozygous frameshift variant in the HEXA gene (NC_037337.1:g.19269480_19269481delinsGGAGT, NM_001075164.2: c.(834_835delinsACTCC)), absent from 18 control genomes and 1842 individuals in the 1000 Bull Genomes Project. The variant was confirmed in homozygous form in all four affected animals by Sanger sequencing and meets multiple criteria for pathogenicity. These findings support a diagnosis of GM2 gangliosidosis type I, representing the first report in cattle and enabling development of a diagnostic test for carrier screening and herd management.

Domestic cattle in Africa can be categorized as either taurine (Bos taurus) or indicine (Bos indicus) based on their domestication histories from the extinct aurochs (Bos primigenius). Close to 150 breeds of indigenous cattle are estimated to exist in Africa and have a complex mixture of B. taurus and B. indicus ancestries. Native cattle in Uganda fall into three broad categories: the Sanga, East African Shorthorn Zebu, and Zenga. There is limited information about the genetics of Ugandan indigenous cattle, despite their representation of nearly 80% of the national herd. In the present study, we describe the genetic diversity and population structure of five native breeds using whole genome sequences of 95 animals. For a comparative context, we included published whole genome sequences of 97 animals in the analysis. Our findings indicate a clear distinction between Zebu, Sanga, and Zenga breeds, with elevated inbreeding and lower genetic diversity levels among the Ugandan breeds. We also observed an introgression of European genetic resources into Ugandan native cattle breeds. Notably, our results suggest existence of two subpopulations within the Nganda breed, a finding that has implications on the conservation efforts of native animal genetic resources. The findings of this study show that indigenous cattle genetic resources in the country are threatened by admixture with imported genetic material and underscore the need for targeted efforts to characterize and conserve them before they are lost to crossbreeding and breed substitution.

Single nucleotide polymorphisms (SNPs) can serve as genetic markers to identify genetic differences between individuals. The primary objective of this study was to use SNP chip data and the concept of Mendelian mismatches to locate genomic regions that contain deletions. The dataset comprises 298 850 Fleckvieh cattle, primarily from Austria and Germany. Animal genotyping was conducted using the Illumina 50K Bead Chip and data from 40 144 autosomal SNPs were utilized. Among the 298 850 animals, sire genotypes were available for 267 393, and dam genotypes were available for 56 546 individuals. Data analysis was performed using plink and SAS. A large number (567 996) of Mendelian mismatches caused by deletions were detected, and the inheritance of the deletions could be traced back to a few ancestors. This study has shown that the detection of hemizygous deletions based on Mendelian mismatches in parent–offspring pairs is a promising approach due to the low cost and wide availability of SNP chip data for cattle. The exact positions and sizes of the deletions may be explored with whole-genome sequence data of animals carrying these deletions.

Primary hyperparathyroidism (PHPT) is an inherited disorder that leads to inappropriate secretion of parathyroid hormone by neoplastic parathyroid cells. Dogs of the Keeshond breed are predisposed to adenomas or hyperplasia of the parathyroid that lead to PHPT. The disorder is inherited in a dominant Mendelian fashion with a high age-related penetrance. The age of onset in PHPT-affected Keeshonden is typically later than 8 years. Genome-wide association studies with 27 affected and 42 unaffected Keeshonden genotyped with 30 896 markers identified a region of strong association with the PHPT phenotype on canine chromosome 20. The most significant array marker was NC_049241.1.g.55977819 C>G. The strength of association of this region with the case phenotype was unique in the genome and concordant with the hypothesis of dominant inheritance (i.e. all case animals in the genome-wide association studies were heterozygous for the most associated variant). Fine-scale variant analysis in the region of association revealed a mutation that creates both a missense and a possible splice-site variant within exon 2 of the gene SIRT6 (NC_049241.1g.55817330A>G; XM_038567756.1.c.193A>G; XP_038423684.1.p.65R>G). The variant appears uniquely within affected dogs when compared with 1987 other genotyped samples in the public domain. Strong concordance was observed between genotypes for the variant in SIRT6 and a promoter variant in eukaryotic elongation factor 2 (NC_049241.1.g. 55973578_55973593dupinsN[180]) used for disorder testing in the USA since 2008. Based on the absence of the SIRT6 variant in any healthy dog and modelled functional behaviour of the variant we conclude that the SIRT6 variant is probably pathogenic for PHPT.

Three colors of Dexter cattle are currently recognized: black, red, and dun. In Dexters, dun is determined by a recessive genotype of TYRP1 (b/b) that dilutes an otherwise black animal (MC1R genotype ED/−); this variant does not impact red cattle. A subset of Dexters with dilute coat colors described as dark dun/chocolate (CD) or light dun/cream (CL) were identified. Although phenotypically similar to dun, they did not have the expected TYRP1 b/b genotype. Given relationships among the reported individuals, we hypothesized that a novel recessive genotype is causative of CD on a black background and CL on a red background. Whole-genome sequence was generated from four dilute Dexters (three CD and one CL), and one black calf of a CD dam. None of the cattle sequenced had the TYRP1 b/b genotype. The comparison of variants in the five Dexter cattle to those from 226 non-Dexter control cattle resulted in the identification of a missense variant in SLC45A2 (NC_037347.1: g.39790189A>C; XM_002696386.6: c.398A>C) that fit the proposed hypothesis. Sanger sequencing of additional Dexter cattle (n = 227) demonstrated complete segregation of the recessive genotype with the CD and CL phenotypes. The mutation, predicted to result in a substitution of glutamine with proline (XP_002696432.2: p.Gln133Pro) in a transmembrane helix was classified as deleterious by SIFT. Further supporting its implication, SLC45A2 is responsible for coat color dilutions and oculocutaneous albinism type IV in multiple species. Testing for the SLC45A2 variant can be a valuable resource for Dexter breeders interested in coat color.

In Friesian horses, withers height is an important trait as a minimum has been set to be eligible to the studbook. Several loci for withers height have been identified in horses. However, withers height has not been studied in the Friesian horse. Therefore, our aim was to identify loci associated with withers height in the Friesian horse population. We performed a genome-wide association study using 70 K SNP data of 2192 Friesian horses. We found ECA1 and ECA9 to be significantly associated with withers height, explaining 19.6% and 3.5% of the phenotypic variance, respectively. In other horse breeds, the LCORL/NCPAG locus on ECA3 showed the strongest association with withers height, but here we found that the best-associated SNP for that locus is nearly fixed in Friesian horses for the allele associated with small size. Moreover, we observed a clear decline followed by a marked increase in average withers height of the Friesian horse over time, probably owing to shifts in its primary use over the course of the years. Additionally, the frequency of the best-associated SNP on ECA1 has increased over time. Together, our study showed that ECA1 and ECA9 are associated with withers height in Friesian horses. Further studies should be performed to confirm candidate causal mutations.

Omani Jabal Akhdar goats are highly valued for their resilience, superior growth rate and twinning rate compared with other Omani goat breeds. Therefore, understanding their genetic diversity and population structure is essential for sustainable breeding efforts and conservation of the breed. This study aimed to assess the genetic diversity and population structure of Jabal Akhdar goats with single nucleotide polymorphisms generated with the Illumina 50K Goat Chip. Multidimensional scaling analysis and Admixture analysis revealed that Jabal Akhdar goats possess a distinct genetic ancestry representing a mixture of the Asian and African goat lineages which highlights the historic maritime trading and interactions of the Omanis with both continents. The multidimensional scaling analysis and the Reynolds unweighted distances both indicated that Jabal Akhdar goats share a close genetic relationship with West Asian breeds such as Iranian Bezoar, the Australian Cashmere, and Turkish breeds such as the Kil goats, all of which are adapted to cold climates and high elevations. Notably, the breed exhibited a moderate genomic inbreeding level (FPlink = 0.219 and FROH = 0.047), comparable with other West Asian breeds, indicating adequate levels of genetic diversity. This study represents the first genome-wide characterization of the Jabal Akhdar goat breed. Despite its moderate inbreeding levels, attention should be focused on conservation efforts to safeguard the distinctive genetic diversity of Jabal Akhdar goats to prevent the erosion of its genetic diversity or admixture with exotic commercial breeds.

Gene editing and genome manipulation offer great promise for treating diseases in both humans and animals. There is a danger, however, that this technology could be used for other purposes such as performance enhancement. To detect such ‘gene doping’ events, we evaluated a targeted enrichment panel and next-generation sequencing to assess its reproducibility, sensitivity, and capability of variant detection on a wide variety of samples and biological matrices. The panel was verified against existing data for the myostatin gene, a PCR-based SNP panel, and whole genome sequencing in a subset of samples. As successful detection of seamless edits will rely on a detailed understanding of the natural population, we also screened over 170 Thoroughbreds and catalogued numerous novel variants. These included several resulting in coding alterations, and a structural variant. Samples spiked with transgenic cDNA-based material to simulate gene doping events were detected down to 3.2% mosaicism, giving confidence that mosaic mutations resulting from embryonic introduction of gene editing reagents can be detected using these methods. The ability of software packages to detect gene doping events was also assessed, including multiple genome alignment tools, variant callers, and structural variant callers. Freebayes performed strongest at SNP-based editing detection, and Delly and Manta had complementary advantages depending on the mutation type. For routine testing, a multi-faceted approach to calling should be taken to maximise the detection capabilities.