Animal genetics最新文献

The beak bean, found only in waterfowl and Galliformes, aids in foraging, self-defense and pecking hard objects. Its rich coloration results from prolonged evolutionary adaptation. This study analyzed beak bean phenotypes of duck at 10, 20, 30 and 40 days of age, revealing that the most common type is the black beak bean, characterized by melanin deposition on the beak surface. This study performed single nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) to investigate the genetic basis of beak bean color, identifying signals on chromosome 1. The copy number variation region-based GWAS revealed a consistent candidate region overlapping with the SNP-based GWAS signals, further supporting the importance of this genomic region. Locus zoom analysis further refined the candidate regions to 48.5–50.5 and 50.8–52.8 Mb. Functional enrichment analysis highlighted six candidate genes within these regions: KITLG, DUSP6, GALNT4, MGAT4C, ATP2B1 and NTS. Notably, KITLG and DUSP6, which are linked to melanin production, were identified as key candidate genes for beak bean color. Our finding revealed the genetic basis of the bean color traits for the first time in ducks, providing a theoretical foundation and technological framework for enhancing duck beak coloration.

The aim of this study was an in-depth genomic analysis for tail length (TL), tail characteristics and body measurements in the Merinoland sheep breed considering whole-genome sequence data. Genomic analyses included the estimation of genetic parameters and dominance effects, genome-wide associations for the additive and dominance component, and the annotation of potential candidate genes. We implemented a unified selection and mating experiment to create extreme lamb groups based on breeding values for TL. The 254 lambs from the mating experiment were phenotyped at birth for TL, tail circumference, and body length (all in cm), for body weight, and X-rayed to count the number of vertebrae and to identify tail abnormalities for tail fractures, axis deviations, block vertebrae, and wedged vertebrae. Heritabilities using the variant-based relationship matrix were large for the morphological measurements TL (0.85), body length (0.93), and body weight (0.85), moderate for tail circumference (0.21), and number of vertebrae (0.29), but close to zero for tail abnormalities. Dominance variance for TL explained 14.95% of the phenotypic variation, but was close to zero for the remaining tail traits. The positive breeding value correlations indicate longer and thicker tails for taller and heavier lambs. Breeding value correlations were negative between TL with block vertebrae and wedged vertebrae. Genome-wide associations for additive-genetic and dominance effects revealed 726 significant variants, which are located close to potential candidate genes. These candidate genes have known functions on skeletal growth, and regulate the development of bone structures and of vertebrae characteristics.

New Zealand (NZ) Huntaway and Heading dogs are working breeds that play active roles on farms across NZ. While these breeds are common in NZ, they are not well-known elsewhere, and little is understood about their genetic make-up. Here, we used whole genome sequencing to provide a comprehensive genomic view of 249 working dogs. As first use of this resource, we report the allele frequencies of provisionally functional variants aggregated from the Online Mendelian Inheritance in Animals (OMIA) database. Of 435 “probably causal” variants, 27 segregated in our sample. Notable examples of disease variants potentially actionable for selection include those in the CUBN, CLN8, SGSH, SOD1, VWF, and VPS13B genes. These findings will enable genetic testing and selection opportunities to help improve the health and performance of future generations of these unique breeds.

This study used double-digest restriction site-associated DNA sequencing to investigate the genetic diversity and population structure of eight populations of Myanmar indigenous chickens (MICs). We conducted genetic diversity and population structure analyses of indigenous chickens from Myanmar and other Asian countries and commercial chickens. A total of 20 261 autosomal SNPs were used. The expected heterozygosity of the eight populations of MICs ranged from 0.259 ± 0.175 (MYN_FCN) to 0.282 ± 0.152 (MYN_YGN), and the observed heterozygosity ranged from 0.245 ± 0.187 (MYN_FCN) to 0.265 ± 0.164 (MYN_YGN). The population structure analyses suggested that MICs possessed a genetic cluster that is limited in many chicken populations in this study. In addition, three distinct groups were found among Myanmar and Asian populations. We then identified differentially selected regions (DSRs) among these groups to understand their differences: 48 DSRs between Myanmar fighting chickens and MICs, 54 DSRs between Myanmar fighting chickens and a group of Myanmar and Asian indigenous chickens, and 48 DSRs between MICs and a group of Myanmar and Asian indigenous chickens. Gene Ontology enrichment analysis revealed certain significant genes in those group-pairs. The results revealed genetic differences between Myanmar and other Asian chickens.

With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identified positions that were indels or multiallelic in the WGS. To assess the effectiveness of the 670 K SNP array vs. WGS in trait association studies, we mapped the chestnut coat color. Both technologies showed a clear peak at the expected locus, although neither association had loci reaching Bonferroni-corrected statistical significance, which was not statistically possible in this small group of horses. The findings of this study provide valuable insights for making informed decisions when selecting between SNP arrays and WGS at varying sequencing depths for equine genomic research applications.

The bovine leukocyte antigen DRB3 (BoLA-DRB3) gene, a crucial component of major histocompatibility complex class (MHC) II, influences disease susceptibility and production traits in cattle. Conventional PCR – (Sanger)-sequence-based typing (PCR-SBT) – has limitations, including time-intensive processing and phase ambiguity issues. We developed a nanopore-sequencing-based method for BoLA-DRB3 genotyping. The full-length gene (10.9 kbp) was amplified from blood samples of 109 Japanese Black cattle and sequenced using Oxford Nanopore Technologies’ nanopore MinION. The method achieved high-quality metrics, with a mean coverage of 99.97%, an average sequencing depth of 2599× and a mean Q-score of 20.5. Perfect reference sequence alignment was obtained in 92.7% (101/109) of samples. Alleles of all samples showed complete concordance with the set of PCR-SBT typing results for exon 2. The entire process was completed within 3 days (6 h of hands-on time), substantially reducing the time and cost requirements compared with other methods. This nanopore sequencing method provides accurate BoLA-DRB3 genotyping while resolving phase ambiguity through full-length molecule analysis, presenting a potential new standard for bovine MHC genotyping.

Pigs have been altered throughout the decades to increase the meat content in their carcasses. However, this has led to a reduction in fat levels in subcutaneous, visceral, and intramuscular fats, where intramuscular fat is crucial for flavor. The current study used combined RNA-assay for transposase-accessible chromatin (ATAC) sequencing analysis to identify key transcription factors (TFs) that might regulate important molecular mechanisms associated with fat deposition in the livers of pigs. In this study, two native Złotnicka White pig groups were used that significantly differed in terms of their fat content. RNA-seq identified 272 genes as being differentially expressed (showing >1.2 fold change) and ATAC-seq identified 6333 significant peaks (differentially accessible regions [DARs]) in the transcription start site (TSS) flanking region. Ninety-eight genes overlapped between the RNA and ATAC seq results, and these differentially expressed genes–DARs were included in a subsequent motif analysis. The TRRUST and MEME tools were used to identify crucial TFs, which predicted possible binding TF motifs based on TSS ATAC peaks. The candidate TFs suggested in the present study for fat deposition in pigs are SREBP1, ATF4, KLF11, RORA, and MYC, whose DNA-binding motif sequence was enriched in DAR overlapping TSS. Moreover, for MYC, ATF4, and KLF11 TFs, DARs were identified within the TSS flanking regions. The present study aimed to pinpoint the key liver TFs that are indirectly related to fat deposition in pigs.

Genomic imprinting causes parent-of-origin dependent gene expression, primarily driven by a subset of germline differentially methylated regions that function as imprinting control regions at promoter-associated CpG islands. While these mechanisms have been investigated in depth in mice and humans, our understanding of the molecular basis of genomic imprinting in pigs remains limited, particularly at a non-orthologous porcine locus. This study aimed to investigate a pig locus displaying a canonical DNA methylation-dependent imprinting pattern and explore its potential involvement in transcription-coupled imprinting mechanisms. By comparing parthenogenetic and control porcine day-21 embryos, we identified a maternally methylated differentially methylated region in a previously uncharacterized pig locus, LOC100520903 (ZNF300-like), which may serve as an imprinting control region. This was accompanied by a significantly higher paternal mRNA expression of LOC100520903 in control embryos compared to parthenogenetic embryos (p < 0.05), as detected by RNA-seq. At this locus, a previously unannotated transcript with an alternative first exon located far upstream was predominantly expressed in oocytes (supported by >10 RNA-seq junction reads), alongside a promoter marked by H3K4me3 and an adjacent long terminal repeat element (E-value = 5.8e-62). This transcript was no longer detected from embryogenesis onward (0 reads), at which point the annotated LOC100520903 transcripts became expressed. Concurrently, oocyte-specific DNA methylation was observed at the CpG island of the LOC100520903 gene promoter, indicative of maternal methylation. Moreover, in the pig liver and brain, paternal monoallelic expression was consistently observed based on haplotype-tagged RNA-seq reads. Our findings provide mechanistic insights into genomic imprinting at the porcine LOC100520903 locus.