Animal genetics最新文献

Early genetic studies have suggested that body size in rabbits can be considered a quantitative trait. Several rabbit breeds can be distinguished based on body size, including a few dwarf breeds differentiated by other morphological characteristics. While a large deletion in the HMGA2 gene is a major locus associated with dwarfism in Netherland Dwarf rabbits, it may not fully explain the reduced body size in this breed or other dwarf breeds. In this study, we compared the genomes of two dwarf rabbit breeds (Dwarf Lop and Netherland Dwarf) with those of non-dwarf rabbits by analysing whole-genome sequencing data obtained using a DNA-pool sequencing approach. We applied the fixation index (F_ST) and pooled heterozygosity (H_P) statistics to identify signatures of selection related to small body size by contrasting dwarf with non-dwarf breeds and comparing dwarf breeds. We identified several genomic regions that contain genes previously linked to body dimensions in various species, including LCORL-NCAPG, COL2A1, GHRHR and CENPE. Functional enrichment analysis of genes within the top differentiated regions revealed biological terms related to skeletal development, further supporting the biological relevance of these loci. Additionally, the use of the latest version of the reference rabbit genome enabled the identification of a genomic region containing FGFR3, a gene linked to achondroplasia. Some genomic regions showed differentiation between the two dwarf breeds, suggesting that their small body size may, in part, arise through different genetic mechanisms. Overall, these findings support a polygenic architecture underlying small size in rabbits, influenced by a few major loci.

Fragile foal syndrome (FFS) is a disease caused by a recessive lethal missense mutation in the PLOD1 gene located on ECA2. Despite its harmful effect, a relatively high frequency of FFS carriers was observed in Warmblood breeds spanning from 7.4% in a random sample of Swedish Warmblood breed to 17% in the Hanoverian and Danish Warmblood, indicating potential heterozygous advantage. Balancing selection can be further studied based on haplotype blocks and via detection of heterozygosity-rich region (ROHet) around the target of selection. In this study we evaluated the presence of haplotype blocks and ROHet on ECA2 in 380 Swedish Warmblood horses. We compared the results of ROHet with the rest of the genome. On average, 11.7 heterozygosity rich regions were identified per horse on ECA2, with no significant difference in numbers and length compared to what was found in other chromosomes. A unique haplotype block containing 28 markers was found in the FFS haplotype, while there were several haplotype blocks in the non-carrier haplotype. This unique haplotype block mostly spanned the region upstream of the PLOD1 gene and included the MFN2 gene. The presence of this extended haplotype, shared by multiple individuals and including both the FFS variant and the MFN2 gene, suggests that this region may be under selection. While we did not find a clear heterozygosity-rich region around the FFS variant, the extended haplotype may reflect either a signature of balancing selection or linkage disequilibrium with a positively selected variant in MFN2, PLOD1, or nearby loci.

This study aimed to conduct a genome-wide association study to identify genomic regions associated with profitability traits in Nelore beef cattle. The dataset included 3614 phenotypic records of accumulated feedlot profitability (AFP) and profit per 15 kg of liveweight gain (PFT) from animals born between 2020 and 2022, participating in the Nelore Brazilian breeding program from the National Association of Breeders and Researchers. From this total, 2127 animals were genotyped with the Clarifide® Nelore 3.0 SNP panel. After quality control, 2127 genotyped animals and 35 658 SNPs remained in the dataset for analysis. The weighted single-step approach for genome-wide association methodology was used to identify genomic regions associated with AFP and PFT. A single-trait animal model was applied to predict genetic values, and SNP effect solutions were obtained from these values. Genomic windows of 10-SNP sliding windows that explained >0.5% of the additive genetic variance of each trait were selected to investigate potential candidate genes. A total of 83 genes within 21 windows and 268 genes within 52 windows associated with the AFP and PFT were identified, respectively. Several genes related to fertility, feed efficiency, carcass traits, muscle and adipose tissue development and metabolism, and lipid and carbohydrate metabolism were identified, along with genes associated with animal behavior. The results revealed that identifying genomic regions and their respective candidate genes contributes substantially to a better understanding of the genetic mechanisms regarding these novel profitability-related phenotypes in Nelore beef cattle.

Quantitative and functional defects of von Willebrand Factor (VWF) cause the hereditary bleeding disorder von Willebrand disease (VWD). Three types of VWD exist; type 3 is the most severe and rare, characterized by an almost complete absence of VWF protein. In this study, we investigated the cause of type 3 VWD in a family of purebred Havanese dogs. Pedigree analysis suggested an autosomal recessive mode of inheritance. We performed whole genome sequencing of the parents and relatives of two affected siblings, revealing a novel missense variant in the VWF gene. The variant causes a cysteine to glycine substitution at residue 2571 (NP_001002932.1:p.(Cys2571Gly)) within the VWF C4 domain. This residue is highly conserved across vertebrates and plays a critical role in maintaining the structural integrity of VWF through disulfide bonds. This change probably disrupts the conformation of the C4 domain, leading to VWF concentrations undetectable by enzyme-linked immunosorbent assay in affected dogs. Genotyping confirmed an autosomal recessive mode of inheritance, and the variant was found exclusively within the family. Our findings provide new insights into the genetic basis of VWD and highlight the importance of conserved cysteine residues for VWF stability.

Feline minimal white spotting associated with blue eyes, a trait called DBE by breeders for dominant blue eyes, was selected recently to create various lineages of cats and the Celestial breed. Previously, we identified three Paired Box 3 (PAX3) gene variants that account for some of the DBE phenotypes in cats, confirming different founding effects. Using a candidate gene approach, we identified a fourth PAX3 variant in a purebred Maine Coon lineage segregating for DBE and lacking a previously identified genomic variant. Segregation of the variant was consistent with the dominant inheritance pattern observed in this DBE lineage called the “Agostino line” by breeders. This PAX3:c.160del frameshift variant, located in PAX3 exon 2, was predicted to produce a truncated PAX3 protein: PAX3:p.(His54ThrTer108) that would lack 78% of the amino acids of the wildtype protein. All 13 DBE Maine Coon cats from the line were heterozygous for the variant, that was absent in all non-DBE Maine Coon cats from the line and in all control cat genomes (n > 300). We propose that this PAX3:c.160del variant represents the DBE^AGO (Agostino Dominant Blue Eyes) allele in the domestic cat. In addition, we improved the phenotypic description of DBE in Maine Coon cats, highlighting the need to reassess the prevalence of deafness and revealing the existence of latent cats in the previously described DBE^RE (Rociri Elvis Dominant Blue Eyes) Maine Coon lineage.

We propose an approach to species identification of four species of the Canidae family, the red fox (Vulpes vulpes), the arctic fox (Vulpes lagopus), the raccoon dog (Nyctereutes procyonoides), and the wolf including the gray wolf (Canis lupus lupus) and the domestic dog (Canis lupus familiaris), based on characteristics of manifestation of microsatellite loci during cross-species amplification. Additionally, we present an approach to DNA identification of the subspecies of Canis lupus, the gray wolf and the domestic dog, based on variations in the copy number of the amylase gene. This comprehensive study of canids living in Belarus makes it possible to reliably differentiate forensic samples by species and subspecies before genetic identification of individuals.

One hundred years ago, the first book with the phrase “Animal Genetics” in its title was published. It was written by F.A.E. Crew, then Lecturer in Genetics and foundation Director of the Department of Research in Animal Breeding at the University of Edinburgh. The 352 pages of text provide a most interesting summary of the knowledge of animal genetics at that time. It is impressive to see the extent to which the understanding of genetics had developed in just a couple of decades since the rediscovery of Mendelism. There was, for example, recognition that genes are borne on chromosomes; that XX/XY sex determination provides a very satisfactory explanation for most of the relevant evidence; that sex-linked inheritance has a practical application; that variation in quantitative traits is determined by the combined action of many genes and many non-genetic factors; that inbreeding results in substantial decreases in fecundity and fertility due to homozygosity for undesirable alleles; that crossing between lines or breeds gives rise to hybrid vigour (heterosis); and that many disorders are inherited in a Mendelian fashion, and hence can be controlled by informed breeding. There is, however, no mention of Fisher's 1918 paper nor of Wright's recently published inbreeding coefficient and coefficient of relationship. Crew's book inspired the next generation of geneticists, such as Fred Hutt, who travelled from Canada to Edinburgh to do a PhD with Crew, and who later published his own very influential book with the same title, which was dedicated to Crew.

The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province in southern China and boasts a rich history. The goats exhibit exceptional traits, including heat and insect resistance, strong reproductive capabilities and superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole-genome resequencing on 21 Zhashi Brown goats. Additionally, we performed a joint analysis using published whole-genome data from 119 goats, including Chengdu Brown goat, Matou goat, Wuxue goat, Xiangdong Black goat, Qaidam Cashmere goat, Ujumqin Cashmere goat and Shanbei Cashmere goat. The results revealed that the Zhashi Brown goat is genetically more pure than other Southern Chinese goat breeds. Furthermore, the genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity and inbreeding coefficient) of the Zhashi Brown goat's genome is at a low level among the eight breeds, indicating the need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide diversity, integrated haplotype score, the fixation index and cross-population extended haplotype homozygosity, we systematically scanned selective signals within the genomic landscape of Zhashi Brown goat. The outcomes underscore strong selection signals associated with genes implicated in immune response, heat tolerance, reproductive performance and meat quality. These findings make a significant contribution to our understanding of the genetics framework associated with adaptive traits in Zhashi Brown goat. Furthermore, this study explores the genetic diversity of the Zhashi Brown goat, which may contribute to the theoretical framework for conserving its genetic resources, while the identified trait-associated variations could inform future strategies to optimize selective breeding programs.

The Fuzhou cattle breed, native to northeast China, is widely recognized for its adaptability, disease resistance, and docility. Despite being known for these qualities, its population has declined recently, and there is a significant lack of genomic studies on this species. We sequenced 21 samples from a primary breeding farm to determine the genetic structure, diversity, and selection signature to address this. Additionally, we combined 100 published genomic datasets from diverse geographical regions to characterize the genomic variation of Fuzhou cattle. There were 53 752 978 bi-allelic SNPs retained for downstream analysis. In population structure analysis, Fuzhou cattle show a predominantly East Asian taurine ancestry, with strong genetic affinities to Hanwoo and Yanbian cattle. Despite high nucleotide diversity within the Bos taurine lineage, genetic diversity analysis also revealed significant levels of inbreeding in Fuzhou cattle populations, indicating the need for conservation. Utilizing various methods such as θπ, iHS, F_ST, π-ratio, and XP-EHH, we identified genes associated with traits like growth, meat quality, energy metabolism, and immunity. Several genes related to cold adaptation were identified, including PLIN5, PLB1, and CPT2. These findings provide a basis for conservation strategies to safeguard the genetic resources of Fuzhou cattle.

Identifying genomic regions under selection is crucial for comprehending the evolutionary history of the domestic chicken. Arabian Peninsula (AP) indigenous chickens are mostly found outdoors, being reared alongside other livestock for production purposes. These birds show high resilience to extreme temperatures (hot and cold), typical of the desert environment. The selection pressures responsible for unique local adaptations in these birds remain largely unidentified. Here, we aimed to investigate the genome diversity and structure of 15 indigenous chicken populations including 13 populations from the AP (n = 5), Ethiopia (n = 6), and the People's Republic of China (n = 2). We also included two commercial chicken populations, Fayoumi (selected for heat tolerance) and Chantecler (known for its cold tolerance). Principal component (PC) analysis separated all the populations based on their geographic areas of origin. PC1 separates the Ethiopian populations from the Chinese and AP populations, while PC2 separates the AP populations from the Chantecler, and the Ethiopian populations from the Dulong and Chantecler. The genome-wide signatures of analyses identified many candidate regions under positive selection. They include genes that may be associated with thermotolerance. These are involved in energy balance and metabolism (SUGCT, HECW1, MMADHC), cells apoptosis (APP, SRBD1, NTN1, PUF60, SLC26A8, DAP, SUGCT), angiogenesis (RYR2, LDB2, SOX5), skin protection to solar radiation (FZD10, BCO2, WNT5B, COL6A2, SIRT1) as well as growth (NELL1). Our findings suggest that Arabian chicken populations have a distinct gene pool polymorphism in relation to their adaptation to the harsh climatic environments of the AP.