Jiahong Sun, Emil Ibragimov, Peter Karlskov-Mortensen, Merete Fredholm
{"title":"Genetic factors for hematological traits in pigs","authors":"Jiahong Sun, Emil Ibragimov, Peter Karlskov-Mortensen, Merete Fredholm","doi":"10.1111/age.70043","DOIUrl":"10.1111/age.70043","url":null,"abstract":"<p>Complete blood count with differential is a critical diagnostic tool for evaluating the physiological and health status of individuals by analyzing white blood cells, red blood cells, and platelets. While extensively used in human medicine, the application of complete blood count biomarkers in pigs remain limited. This review focuses on the genetic architecture of hematological traits in pigs (Sus scrofa) using data from genetic association studies. By compiling data from multiple porcine studies, we identified 509 SNPs within 53 high-confidence QTL supported by more than one study. Among these, 37 QTL were homologous to human loci, with 19 containing plausible candidate genes likely to be influencing hematological traits. These genes are often linked to cytoskeletal formation, hematopoiesis, and immune function, highlighting conserved biological mechanisms across species. Our findings provide a foundation for further investigations into the genetic regulation of blood cell parameters in pigs and their implications for health, welfare, and production traits, offering potential translational insights for both veterinary and human medicine.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. P. M. A. Crooijmans, R. Gonzalez Prendes, L. Colli, M. Del Corvo, M. Barbato, E. Somenzi, G. Tosser-Klopp, G. Meszaros, P. Ajmone-Marsan, S. Weigend, B. Wallner, M. E. McCue, L. Orlando, D. Bradley, S. J. Hiemstra, D. Schokker, N. Peynot, A. Stella, G. Restoux, M. A. M. Groenen, M. Tixier-Boichard
{"title":"IMAGE001: A new livestock multispecies SNP array to characterize genomic variation in European livestock gene bank collections","authors":"R. P. M. A. Crooijmans, R. Gonzalez Prendes, L. Colli, M. Del Corvo, M. Barbato, E. Somenzi, G. Tosser-Klopp, G. Meszaros, P. Ajmone-Marsan, S. Weigend, B. Wallner, M. E. McCue, L. Orlando, D. Bradley, S. J. Hiemstra, D. Schokker, N. Peynot, A. Stella, G. Restoux, M. A. M. Groenen, M. Tixier-Boichard","doi":"10.1111/age.70039","DOIUrl":"10.1111/age.70039","url":null,"abstract":"<p>Molecular genetic characterization of genetic resources is essential to study biodiversity. Whereas whole genome sequencing is still relatively expensive, low density SNP arrays offer a cost-effective and standardized solution. However, most of the current arrays are species specific. Their high SNP density often exceeds diversity mapping requirements and remains too costly for many genetic resource managers. The IMAGE H2020 project aimed at developing a low-cost multispecies SNP array to facilitate mapping of the genetic diversity in samples stored in gene banks and in vivo (on farm) traditional populations. This farm animal multispecies array contains approximately 10 K SNPs per species. The species included are cattle, sheep, goat, horse, pig, and chicken. We developed and tested this array on many samples from each of the six species. We describe here the SNP coverage and informativity across 253 breeds. We show that the array can be used to cluster local breeds according to history and genetic diversity. We illustrate its use for parentage testing. The array is publicly available at a reasonable price if ordered in multiples of 384 samples, leading to an overall cost of genotyping of approximately 15 euros per sample.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jingjing Qi, Qian Hu, Yang Xi, Zhao Yang, Mengru Xu, Liang Li, Lili Bai, Hehe Liu
{"title":"Genetic variations for bean color of duck beak revealed by genome-wide association study","authors":"Jingjing Qi, Qian Hu, Yang Xi, Zhao Yang, Mengru Xu, Liang Li, Lili Bai, Hehe Liu","doi":"10.1111/age.70040","DOIUrl":"10.1111/age.70040","url":null,"abstract":"<p>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: <i>KITLG</i>, <i>DUSP6</i>, <i>GALNT4</i>, <i>MGAT4C</i>, <i>ATP2B1</i> and <i>NTS</i>. Notably, <i>KITLG</i> and <i>DUSP6</i>, 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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Johanna Mainzer, Tong Yin, Isabella Giambra, Hannah Hümmelchen, Petra Engel, Henrik Wagner, Axel Wehrend, Sven König
{"title":"Genetic parameters, genome-wide associations and potential candidate genes for additive and dominance effects of tail traits in Merinoland sheep based on whole-genome sequence data in a selection experiment","authors":"Johanna Mainzer, Tong Yin, Isabella Giambra, Hannah Hümmelchen, Petra Engel, Henrik Wagner, Axel Wehrend, Sven König","doi":"10.1111/age.70041","DOIUrl":"10.1111/age.70041","url":null,"abstract":"<p>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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Florence Smith, Thomas Lopdell, Melissa Stephen, Millicent Henry, Keren Dittmer, Hayley Hunt, Nick Sneddon, Liam Williams, Jack Rolfe, Dorian Garrick, Mathew D. Littlejohn
{"title":"Survey of functional Mendelian variants in New Zealand Huntaway and Heading dog breeds","authors":"Florence Smith, Thomas Lopdell, Melissa Stephen, Millicent Henry, Keren Dittmer, Hayley Hunt, Nick Sneddon, Liam Williams, Jack Rolfe, Dorian Garrick, Mathew D. Littlejohn","doi":"10.1111/age.70042","DOIUrl":"10.1111/age.70042","url":null,"abstract":"<p>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 <i>CUBN</i>, <i>CLN8</i>, <i>SGSH</i>, <i>SOD1</i>, <i>VWF</i>, and <i>VPS13B</i> genes. These findings will enable genetic testing and selection opportunities to help improve the health and performance of future generations of these unique breeds.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Su Lai Yee Mon, Moe Lwin, Aye Aye Maw, Lat Lat Htun, Saw Bawm, Yukio Nagano, Atsushi J. Nagano, Kotaro Kawabe, Yasuhiko Wada, Shin Okamoto, Takeshi Shimogiri
{"title":"Exploring genetic diversity and population structure of Myanmar indigenous chickens using double digest restriction site-associated DNA sequencing","authors":"Su Lai Yee Mon, Moe Lwin, Aye Aye Maw, Lat Lat Htun, Saw Bawm, Yukio Nagano, Atsushi J. Nagano, Kotaro Kawabe, Yasuhiko Wada, Shin Okamoto, Takeshi Shimogiri","doi":"10.1111/age.70038","DOIUrl":"https://doi.org/10.1111/age.70038","url":null,"abstract":"<p>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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144869856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samantha L. Van Buren, Jessica L. Petersen, C. Titus Brown, Carrie J. Finno
{"title":"Genotype concordance and trait mapping efficacy comparing data from the Equine 670 K SNP array with whole genome sequence in 21 horses","authors":"Samantha L. Van Buren, Jessica L. Petersen, C. Titus Brown, Carrie J. Finno","doi":"10.1111/age.70037","DOIUrl":"https://doi.org/10.1111/age.70037","url":null,"abstract":"<p>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.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A recessive deleterious missense variant in PEX7 causes a lethal form of chondrodysplasia in Bazadaise cattle","authors":"Cécile Grohs, Stéphanie Minéry, Sébastien Fritz, Mekki Boussaha, Aurélien Capitan","doi":"10.1111/age.70035","DOIUrl":"https://doi.org/10.1111/age.70035","url":null,"abstract":"<p>The term ‘bulldog calves’ colloquially refers to a heterogeneous group of skeletal malformations, typically characterized by severe craniofacial deformities reminiscent of the brachycephalic appearance of Bulldog dogs. These conditions include type II achondrogenesis, spondyloepimetaphyseal dysplasia, and rhizomelic chondrodysplasia punctata (RCDP) caused by mutations of <i>COL2A1</i>, <i>ACAN</i>, and <i>GNPAT</i>, respectively (Boulling et al., <span>2025</span>; Bourneuf et al., <span>2017</span>; Cavanagh et al., <span>2007</span>; Daetwyler et al., <span>2014</span>).</p><p>Since 2020, four ‘bulldog calves’ (two males, two females) have been reported to the French National Observatory for Bovine Abnormalities by the breeding society of the local Bazadaise breed. All were stillborn and exhibited disproportionate dwarfism, characterized by craniofacial dysmorphism, shortened limbs with hypermobile joints, and low birth weight despite a normal gestation length (~20–25 kg vs. 40 kg; Figure 1a,b). Ear biopsies were obtained from three cases, but no specimens were available for comprehensive pathological examination due to rapid carcass disposal.</p><p>Pedigree analysis using the PEDIG software package (Boichard, <span>2002</span>) identified a single common ancestor four to seven generations back across all lineages, supporting a recessive mode of inheritance (Figure 1c).</p><p>Homozygosity mapping using the Illumina EuroGMD SNP array (Boichard et al., <span>2018</span>) and established methods (Boulling et al., <span>2025</span>; Mesbah-Uddin et al., <span>2019</span>) revealed a significant peak on chromosome 9, defined by a 74-marker haplotype homozygous in all cases and none of 223 controls (Bonferroni-adjusted <i>p</i> < 0.01; Figure 1d).</p><p>The whole genome of an affected calf was sequenced as described by Boulling et al. (<span>2025</span>). After excluding variants present in a control panel of 1869 cattle from over 70 non-Bazadaise breeds (dataset described in Besnard et al., <span>2024</span>), 16 candidate variants remained within the associated interval (NC_037336.1:73 454 255–79 825 274 bp; ARS-UCD1.2 genome assembly; Table S1). Among them, only the NC_037336.1:g.74831677G>T substitution in the gene encoding peroxisomal biogenesis factor 7 (PEX7), leading to a p.Asp205Tyr amino acid change, was predicted to be deleterious (SIFT score = 0.01). Interestingly, mutations in <i>PEX7</i> and four other genes involved in peroxisomal protein import or ether phospholipid synthesis (<i>PEX5</i>, <i>AGPS</i>, <i>FAR1</i>, and <i>GNPAT</i>) have been implicated in human RCDP (de Vet et al., <span>1998</span>; Devi et al., <span>2021</span>; Dodt et al., <span>1995</span>; Motley et al., <span>1997</span>; Ofman et al., <span>1998</span>; Purdue et al., <span>1997</span>).</p><p>Furthermore, as outlined in the introduction, our team identified a recessive <i>GNPAT</i> variant as the cause of the RCDP subtype of bulldog calves in Aubra","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"56 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/age.70035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}