Animal genetics最新文献

The size of the reference population and sufficient phenotypic records are crucial for the accuracy of genomic selection. However, for small-to-medium-sized pig farms or breeds with limited population sizes, conducting genomic breeding programs presents significant challenges. In this study, 2295 Yorkshire pigs were selected from three distinct regions, including 1500 from an American line, 500 from a Canadian line, and 295 from a Danish line. All populations were genotyped using the GeneSeek 50K GGP Porcine HD chip. To enhance genomic selection accuracy, we proposed strategies that combined multiple populations and leveraged multi-omics prior information. Cis-QTL from the PigGTEx database and QTL identified through genome-wide association studies were incorporated into the genomic feature best linear unbiased prediction (GFBLUP) model to predict the ADG100 and the BF100 traits. Results demonstrated that combining multiple populations effectively improved prediction accuracy for small population, accuracy for ADG100 increased by an average of 0.29 and accuracy for BF100 by 0.05. The GFBLUP model, which integrates biological priors, showed some improvements in prediction accuracy for the BF100 trait. Specifically, for the small population, accuracy increased by 0.09 in Scheme 1, where each population size was predicted independently. In Scheme 3, where the large population was used as a reference group to predict the small population, accuracy increased by 0.03. However, the GFBLUP model did not provide additional benefits in predicting the ADG100 trait. These findings offer effective strategies for genetic improvement in developing regions and highlight the potential of multi-omics integration to enhance prediction models.

Domestic dogs exhibit significant diversity in both morphology and personality. Recent studies focusing on large-breed dogs reported the contribution of genetic factors to personality. However, the genetic influence in small-breed dogs remains unexplored. In the present study, we investigated the personality of two small-breed dogs using a questionnaire and genome-wide single-nucleotide polymorphism data obtained from 301 Toy Poodles and 183 Miniature Dachshunds using the Illumina CanineHD 230K SNP BeadChip. The factor analysis conducted on a questionnaire consisting of 39 items identified seven factors. Among the seven personality factors, ‘activeness’ in Toy Poodles and ‘human-directed sociability’ in Miniature Dachshunds had an estimated heritability of 0.425 (SE = 0.311) and 0.514 (SE = 0.355), respectively. In addition, genome-wide association study suggested that two genomic regions possibly affect personality. The dog breeds focused on in this study are most popular in Japan, thus their information is in high demand.

The Bull Terrier (Miniature) and Bull Terrier are two varieties of a dog breed historically divided by size. We identify variety-associated chromosomal regions identified using stratified genome-wide association analysis of 69 Bull Terriers (Miniature) and 33 Bull Terriers. Next, we assess the significance of possible functional variants for body size using height (N = 1458) and weight (N = 1282) of Dog10K individuals with breed-representative metrics available. Variants significant for size across breeds that are consistent with size alleles observed in four Bull Terriers and four Bull Terriers (Miniature) represented in Dog10K are highlighted. From five identified regions, two include genes already known to influence canine body size and a third contains a potential new height gene (ARFGEF3). Near LCORL, the most highly associated variant for height in Bull Terriers was chr3:91734656A>G (p_{Across-breed height} = 2.459 × 10⁻⁹⁹) and for weight it was chr3:91706639G>A (p_{Across-breed weight} = 9.762 × 10⁻⁸⁵). All Bull Terriers (including Miniature) were monomorphic for the derived allele at the known size variant in LCORL (chr3:91872822A>del). In the first exon of IGF2BP2, the derived allele at chr34:18694869-71ins>del significantly reduces both height and weight in Bull Terriers and across breeds (Dog10K breed representative height and weight) (p_{Across-breed height} = 1.65 × 10⁻⁹; p_{Across-breed weight} = 1.79 × 10⁻⁸). The derived allele of the missense variant in ARFGEF3 chr1:30793904G>A, XP_038382065.1 p.V243I significantly reduces breed representative height but not weight (p_{Across-breed height} = 0.01). The effects on the variants assessed are limited to small variants identified in the Dog10K resource using breed-representative sizes.

The 39th International Society for Animal Genetics conference (ISAG) was held for the first time in Africa under the theme ‘Animal genetics for a sustainable future’ in 2023. The conference convened scientists, policy makers, industry professionals, and students from interdisciplinary fields to share and discuss the latest developments in the space of animal genetics. Since its inception as a society, ISAG has sought to provide a platform advocating for a just and equitable future in animal genetics. At the 39th ISAG conference, this commitment towards furthering inclusion in animal genetic science was progressed with two new offerings to attendees. The first session guided discussions on the political, ethical, legal, socioeconomic, and cultural dynamics that present barriers to participating in and benefitting from the genomic and genetic science fraternity. This session also included principles of social justice, specifically equity, diversity, and inclusion, towards enacting fairness in an unfair world, and focused on constraints related to sustainability in animal genetics. The second session used the important tradition of storytelling to transfer knowledge and wisdom from experienced scientists to upcoming researchers. Experienced scientists shared lived experiences on educational and career paths, challenges, and opportunities, providing networking and opportunities for further mentoring. Here, we report on these equity-based actions and their relevance to address the urgent continent-specific and global disparities in animal genetics to move towards a sustainable future.

Body weight is an important trait associated with meat production in the poultry industry. To better understand the genetic basis of body weights in ducks, we estimated genetic parameters and performed a genome-wide association study. The phenotypic values of body weights at ages 0 weeks (bw0) and 8 weeks (bw8) were collected individually from 199 Loumen ducks, and their genotypes were assayed with whole genome re-sequencing. The heritability of bw0 and bw8 are 0.32 and 0.43, respectively, and the genetic correlation of bw0 and bw8 was very low (−7.256e-5). The genome-wide association study results identified eight SNPs significantly associated with bw0 and bw8. The two and nine genes nearest to the significant SNPs were selected as candidate genes: PIK3R5 and MYH10 for bw0, and LOC119717016, RHOJ, PPP2R5E, BRF1, LOC106018961, NUDT14, JAG2, CEP170B, and AKT1 for bw8. Together, the SNPs and candidate genes identified in this study advance understanding of the complex genetic architecture of bw0 and bw8, and provide important clues for future implementation of a genomic selection program in Loumen ducks.

The Beigang pig was recently identified as one of the endangered breeds during a Chinese indigenous pig genetic resource survey. The Beigang breed is notable for its remarkable roughage tolerance and high reproductive capacity according to historical records. Morphologically, the Beigang pig resembles many indigenous pigs in eastern China, especially in its large ears. This makes the Beigang pig a valuable reference for studying the genetic mechanisms on large ear size in pigs. However, there is currently a lack of clear understanding regarding the genetic structure and inbreeding levels of the Beigang pig population. This study used whole-genome sequencing data from Beigang pig (N = 145 pigs) and integrated genetic information from commercial pigs and indigenous pigs in eastern China to conduct a comprehensive analysis of the Beigang pig's genetic structure. Three selection signal detection methods—runs of homozygosity, fixation index, and integrated haplotype score—were employed to explore the differences in genomic selection signatures between Beigang pig and other pig populations. Additionally, we used a public project for regulatory variants discovery and molecular phenotype prediction in farm animal species called FarmGtex to explore the expression of three genes (WIF1, LEMD3, and MSRB3) related to ear size in Beigang pig. This research identified five homozygous variant sites in the WIF1 gene as important candidate loci potentially influencing ear size in Beigang pig. The results indicate that the Beigang pig holds a unique status among Chinese indigenous pigs, characterized by high genetic diversity and low levels of inbreeding. The study also revealed that WIF1 may play a significant role in influencing ear size in this breed. These findings contribute to a deeper understanding of the population structure and genetic characteristics of Beigang pig.

Goats typically have double coats, with the outermost coarse hairs providing protection against mechanical and radiation damage. While much attention has been paid to cashmere due to its status as a high-end textile material, there is limited information available on coarse hair. This study aimed to identify genomic variants, such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels), associated with coarse hair diameter using a genome-wide association study (GWAS). Coarse hairs and blood samples were collected from 263 adult female goats. The diameter of coarse hairs was measured using an inverted microscope, and whole genome sequencing was conducted on the blood samples. After reads mapping, variants calling, and quality control, totals of 11 322 006 SNPs and 863 734 indels were included for SNP-GWAS and indel-GWAS analyses. Eight significant SNPs (p < 8.98e-8) and three significant indels (p < 1.16e-6) were identified. Among those, one SNP was located on Chromosome 4 and near the genes COL28A1 and C1GALT1. Seven significant SNPs were found in the region chr10_96664101–96670958, with the genes CDO1 and TMED7 located upstream and downstream, respectively. Haplotype analysis revealed that the diverse haplotypes of these seven SNPs presented varying values for coarse hair diameter. Notably, the only consistently significant insertion (chr10_96665085, GTA>G) was also located within the region chr10_96664101–96670958, further highlighting the importance of this genomic region in influencing coarse hair diameter. These significant variants and genomic regions provide valuable insights for investigating the genetic mechanisms underlying the variation in fiber diameter.

Bone fractures are a significant problem in Thoroughbred racehorses. The risk of fracture is influenced by both genetic and environmental factors. To determine the biological processes that are affected in genetically susceptible horses, we utilised polygenic risk scoring to establish induced pluripotent stem cells (iPSCs) from horses at high and low genetic risk. RNA-sequencing on iPSC-derived osteoblasts revealed 112 genes that were significantly differentially expressed. Forty-three of these genes have known roles in bone, 27 are not yet annotated in the equine genome and 42 currently have no described role in bone. However, many of the proteins encoded by the known and unknown genes have reported interactions. Functional enrichment analyses revealed that the differentially expressed genes were overrepresented in processes regulating the extracellular matrix and pathways known to be involved in bone remodelling and bone diseases. Gene set enrichment analysis also detected numerous biological processes and pathways involved in glycolysis with the associated genes having a higher expression in the iPSC-osteoblasts from horses with low polygenic risk scores for fracture. Therefore, the differentially expressed genes may be relevant for maintaining bone homeostasis and contribute to fracture risk. A deeper understanding of the consequences of mis-regulation of these genes and the identification of the DNA variants which underpin their differential expression may reveal more about the molecular mechanisms which are involved in equine bone health and fracture risk.

The origin of domestic sheep (Ovis aries) can be traced back to the Asian mouflon (Ovis gmelini), in the Near East around 10 000 years ago. Genetic divergence within mouflon populations can occur due to factors such as geographical isolation, social structures, and environmental pressures, leading to different affinities with domestic sheep. However, few studies have reported the extent to which mouflon sheep contribute to domestic sheep in different regions. Here, we implemented the demographic analyses of sheep populations across the globe based on the whole genome resequencing data of 410 samples, Y chromosome genetic variation of 417 rams, and 396 complete mitogenomes of O. aries. This revealed genetic differentiation within Iranian mouflons and a close genetic affinity between northern Iranian mouflons and worldwide domestic populations. The result illustrates that domestic sheep in our study may have derived from the same mouflon populations. Furthermore, analyses of paternal and maternal genetic diversity showed that five Y chromosome haplogroups and seven mitochondrial haplogroups were identified, of which the lineages mtF and mtG were newly found and defined. A phylogeographic interpretation of our data reveals a cline of north to south Iranian mouflons, which may be largely explained by increasing urial introgression.

Red deer is a species of family Cervidae that is widely distributed in the world and is often raised to provide antlers, as a trophy or traditional medicine materials, and meat. Currently, the whole genomic data for red deer are very limited. Qingyuan Wapiti (QYW), China's first breed of red deer by artificial breeding, is well known for its high yield of antlers and large body size. The phylogenetic tree showed that QYW had a closer genetic relationship with Tarim red deer than European red deer. To explore the genetic diversity and selection signatures, the whole genome of 28 QYW individuals was sequenced, and 19 401 749 biallelic SNPs and 1 849 784 indels were obtained. The value of observed heterozygosity, expected heterozygosity, and nucleotide diversity were 0.258598, 0.268844, and 0.002193, respectively. Based on Tajima's D and integrated haplotype score analyses, the candidate regions containing 187 genes were detected, including PLD1, ANTXR1, PLCL1, CPE, and CTNNA3, which have been reported to be correlated with osteogenesis and mineralization, growth, and body size by previous studies. The results obtained in this study will contribute to elucidating the genetic mechanisms underlying the formation of excellent traits in QYW and provide the whole genome data for future exploration of genomic diversity and adaptation evolution of red deer worldwide.