Wiley: Animal Genetics: Table of Contents

Integrative Multi‐Omics Analysis Identifies Novel Enhancer Variants on SSC2 Associated With Backfat Thickness in Landrace Pigs

Tue, 09 Jun 2026 16:59:49 -0700

ABSTRACT

Backfat thickness is an economically important trait in pig production, yet the functional regulatory variants underlying it remain poorly characterized. Here, we performed a genome-wide association study (GWAS) for backfat thickness at 100 kg (BF100) in a large Landrace population (n = 5923) using 13.46 million imputed SNPs. We identified two significant quantitative trait loci (QTLs) on SSC2 (1.21–3.69 Mb; explaining 2.3% of phenotypic variance) and SSC12 (51.70–52.88 Mb; explaining 0.8% of phenotypic variance). While nonsynonymous SNPs were limited (16 variants), we prioritized functional non-coding variants by integrating high-resolution Hi-C interaction maps, epigenomic marks, and previously published enhancer and promoter annotation results from public backfat datasets. This multi-omics strategy revealed that the SSC2 QTL functions as an active three-dimensional regulatory hub, with over 20 enhancer–promoter loops physically engaging the promoters of IGF2, CTSD, TSPAN32, and TSSC4. Similarly, the SSC12 QTL formed more than 10 long-range interactions with the promoters of ASGR1, YBX2, GPS2, MDPU1, and TP53. Focusing on SSC2, we prioritized two tightly linked SNPs (2-1280617 and 2-1280654) located within a putative enhancer, representing two major haplotypes. Dual-luciferase reporter assays in PK15 and 3T3-L1 cells confirmed that the GG haplotype drives significantly higher transcriptional activity than the AT haplotype (p < 0.001). Consistently, pigs carrying the GG haplotype exhibited significantly lower backfat thickness. By integrating multi-omics and functional assays, this study not only decodes the regulatory architecture of two backfat QTLs but also provides new molecular markers for genetic improvement in Landrace breeding.

Fecal DNA Identifies a Disjunct Population of an Endemic Deer (Mazama jucunda) From the Atlantic Forest, Brazil

Fri, 05 Jun 2026 21:44:16 -0700

ABSTRACT

Limited knowledge of brocket deer distribution persists due to their elusive behavior and the morphological similarities among species. A population of red brocket deer (genus Mazama) was recently discovered in the Rio Doce State Park (PERD), a protected area within the Brazilian Atlantic Forest; however, species-level identification was lacking. Given that two endemic and threatened red brocket species inhabit this biome, we aimed to identify the species present in PERD using fecal DNA analyses. We sequenced six mitochondrial DNA regions (1450 bp) from fecal samples collected in PERD and other Atlantic Forest sites, analyzing them against reference specimens. We conducted phylogenetic analyses and employed coalescent-based molecular species delimitation methods (GMYC and bPTP) to define molecular operational taxonomic units (MOTUs). Additionally, we constructed a haplotype network and a genetic distance matrix. Our analyses linked the PERD samples to Mazama jucunda (small red brocket) but revealed a reciprocally monophyletic topology, identifying two distinct MOTUs. PERD harbors unique haplotypes, and its genetic distance to M. jucunda is comparable to that between M. jucunda and M. nana (Brazilian dwarf brocket). We propose that PERD hosts an evolutionarily significant unit (ESU) of M. jucunda, located 700 km from its known range. The observed genetic structure and PERD's isolation support the hypothesis of a potentially new red brocket species, warranting further cytogenetic investigation. This study represents a significant advancement in understanding the distribution and genetic structure of a threatened Neotropical forest deer and has immediate conservation implications in one of the world's most degraded biodiversity hotspots.

Stage‐Dependent Transcriptional Reprogramming of B‐Cell Receptor Signaling and Antigen Presentation During Bovine Leukemia Virus–Driven Lymphomagenesis

Fri, 05 Jun 2026 07:50:52 -0700

ABSTRACT

Bovine leukemia virus (BLV), an oncogenic deltaretrovirus, establishes lifelong infection in cattle and induces enzootic bovine leukosis in a subset of animals following prolonged latency. Despite extensive evidence of immune dysregulation, stage-specific transcriptional reprogramming of B cells, the primary viral reservoir remains incompletely understood. In this study, we performed a targeted RNA-sequencing analysis to characterize B-cell–associated transcriptional profiles across three clinical stages: uninfected controls (CT), asymptomatic BLV-infected cattle (AC), and persistent lymphocytosis (PL). Differential gene expression analysis revealed a dynamic, stage-dependent remodeling of B-cell immune functions. Asymptomatic infection was characterized by significant upregulation of key B-cell receptor (BCR) signaling components, including CD79B and SYK, alongside increased expression of major histocompatibility complex class II genes (BoLA-DRA, BoLA-DRB3) and immunoglobulin assembly gene JCHAIN, indicating enhanced antigen responsiveness and partial activation of antibody-related pathways. However, transcriptional regulators of terminal plasma cell differentiation (PRDM1 and XBP1) remained unchanged, suggesting incomplete maturation. In contrast, progression to persistent lymphocytosis was associated with attenuation of canonical BCR signaling and reduced expression of antigen presentation and immunoglobulin assembly genes relative to the asymptomatic stage. Notably, germinal center–associated transcription factors (BCL6, AICDA, RGS13, MEF2B) remained largely unchanged across all comparisons, indicating that BLV-driven lymphomagenesis does not resemble a classical germinal center–derived process. Collectively, these findings support a biphasic model of BLV-induced B-cell modulation, characterized by early immune activation followed by functional reprogramming and immune attenuation during disease progression. This stage-dependent remodeling provides new mechanistic insights into BLV pathogenesis and B-cell transformation.

ASIP Variants in Livestock: It's Not Black and White

Isabella M. Brown, Kylie A. Munyard — Thu, 04 Jun 2026 00:26:47 -0700

ABSTRACT

Fur and feather pigmentation play an important role in the survival and reproduction of many species, as well as in selective breeding and agriculture. The synthesis of pigment molecules, eumelanin and pheomelanin, is partially regulated by the agouti signalling protein (ASIP) encoded by the ASIP gene. Although ASIP has been widely studied, variants and associated phenotypes are often studied within individual species. This review synthesises current knowledge across mammalian and avian livestock, classifying ASIP variants by type and genomic location and linking them to characteristic pigmentation outcomes. Regulatory and structural variants primarily affect spatial and temporal expression, producing region-specific pigmentation or whole-body pheomelanic phenotypes, whereas coding variants are consistently associated with eumelanic phenotypes through loss of ASIP function. Comparative analysis highlights conserved relationships between variant classes and phenotypic outcomes across livestock species and emphasises the central role of regulatory architecture, including promoter usage, copy-number variation and fusion transcripts. This demonstrates the value of cross-species approaches for interpreting ASIP functional variants and provides a framework for understanding pigmentation diversity in livestock.

Correction to “Genetic Dissection of Production Traits in Commercial Pigs: Comparative Effects of Terminal Sire Lines and Genome‐Wide Associations”

Wed, 03 Jun 2026 18:57:57 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

WWOX Exon 4 Copy Number Gain in Dogs With Testicular or Ovotesticular XX (SRY‐Negative) Disorder of Sex Development

M. Sobczak, Z. Sawicz, I. Szczerbal, M. Switonski, J. Nowacka‐Woszuk — Wed, 03 Jun 2026 01:27:08 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

Unraveling the Genetic Basis of an Abnormal Gold Feather Phenotype in Auto‐Sexing Chickens

Li Rong, Xueying Wu, Md. Ahsanul Kabir, Jiao Li, Yanping Feng, Shijun Li — Tue, 02 Jun 2026 19:00:45 -0700

ABSTRACT

The silver-gold (S/s) sex-linked locus is critically employed in chicken breeding for the auto-sexing of day-old layer chicks. However, the emergence of an abnormal gold feather phenotype, where females lack the characteristic dorsal stripes, leads to frequent misidentification and substantial economic loss. The genetic basis of this abnormality was unknown. To address this, we conducted a genome-wide association study (GWAS) using 9 445 763 high-quality SNPs obtained from whole genome resequencing of 103 female chicks (53 abnormal, 50 normal). Our analysis identified a single sharp peak on chromosome 2 (−log₁₀(P) = 34.7; 236 significant SNPs), which was refined to a 390-kb interval (102.62–103.01 Mb) by FST analysis. The top Absolute allele frequency difference (absAFD) variant, NC_006089.5:g.102638974T>C, located in intron 2 of the GATA6 gene, showed an allele frequency difference of 0.567 (p = 1.35 × 10⁻¹²). This study identifies chromosome 2 as the major genomic region responsible for the abnormal gold feather phenotype, with a noncoding variant in GATA6 as the primary candidate causal mutation. This is the first study of the abnormal gold feather phenotype, and it provides a molecular target for developing a diagnostic assay to preserve auto-sexing accuracy in commercial layer breeding.

Investigation of the Relationship Between Ovine Selection Signature DIS3 Like 3′‐5′ Exoribonuclease 2 (DIS3L2) Gene and Weaning Weight and Average Daily Gain Until Weaning in Lambs

Tue, 02 Jun 2026 16:49:53 -0700

ABSTRACT

The growing demand for animal products, combined with declining livestock production due to urbanization and climate change, underscores the need for sustainable breeding strategies. In sheep production, liveweight and weight gain until weaning are key economic traits. Selection signature analyses have previously identified the DIS3L2 gene, located on OAR2 (~233 Mbp), as a candidate under positive selection for body weight and morphology in sheep. However, its direct association with growth traits remained uninvestigated. This study explored the association between a splice region variant in the DIS3L2 gene (rs421664828) and pre-weaning growth traits in four indigenous sheep breeds in Türkiye: Central Anatolian Merino, Karayaka, Akkaraman, and Morkaraman. A total of 1862 lambs from 10 herds were genotyped using a custom TaqMan Genotyping assay. Body weights were recorded at birth and on Days 30, 60, and 90, with average daily gain (ADG) calculated until weaning. The AG genotype was the most prevalent (92.1%), and all breeds deviated from Hardy–Weinberg equilibrium. Association analysis revealed significant effects of rs421664828 on weight at Days 60 and 90 and on ADG-90. The AG genotype was consistently associated with higher growth performance. These findings support the use of DIS3L2-rs421664828 in marker-assisted selection to enhance growth traits in sheep.

Correction to “Identifying Candidate Genes for Late‐Feathering Subtypes of the Shouguang Chicken by Genome‐Wide Association Study and Differential Expression Analysis”

Tue, 02 Jun 2026 16:19:42 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

Neurobehavioural Genes Associated With Growth in Dusky Kob (Argyrosomus japonicus)

J. E. Sampson, C. Rhode — Wed, 27 May 2026 23:59:59 -0700

ABSTRACT

Growth is a complex trait, influenced by numerous genes and environmental factors that transect various physiological pathways. This study sought to characterise the relationship between neurobehavioural development genes and growth in dusky kob juveniles. Five candidate neurobehavioural genes were identified from the literature and assessed for gene sequence variants. Thirteen SNPs in two genes, Brain-derived neurotrophic factor (bdnf) and Early growth response 1 (egr1), were identified. Case–control association analyses were conducted applying two methods of correcting for family structure: (1) categorical, based on family identity; and (2) quantitative, based on co-ordinate analysis eigenvalues. The eigenvalue-corrected association analysis outperformed the categorical analysis in both model adherence and estimates of effect sizes. Six significantly associated SNPs were identified, three in each gene. Linkage disequilibrium was significant within both genes, with the formation of haplotype -GA- in egr1 associated with increased growth and haplotype -CG- in bdnf associated with decreased growth. A non-synonymous mutation (Serine > Proline) was identified in bdnf, and protein modelling suggests significant disruption of protein structure in small individuals that likely explains the functional mechanism of action. This study has identified novel SNPs and haplotypes in neurobehavioural development genes, which highlight the impact of neurological and behavioural pathways on growth in dusky kob.

Conservation Status of Two Italian Local Poultry Breeds: Faraona Camosciata and Oca Padovana

Tue, 26 May 2026 03:35:41 -0700

ABSTRACT

The present study aimed to assess the conservation status and characterize the phenotypic and genomic diversity of two endangered Italian poultry genetic resources to guide their conservation plans. Blood samples and morphometric data were collected on 50 Faraona Camosciata (FAC, Numida meleagris) and 50 Oca Padovana (OPD, Anser anser) adult animals. Genomes were profiled by low coverage whole genome sequencing. Observed and expected heterozygosity, genomic inbreeding, population structure, runs of homozygosity (ROH), ROH islands, and Gene Ontology enrichment were evaluated. Morphometric measures revealed significant sexual dimorphism within both breeds. FAC females exceeded males for several traits, and OPD males exceeded females for most features. Both breeds had very low heterozygosity and high inbreeding, consistent with their small effective sizes. The ROH length spectra indicated distinct histories: FAC was enriched in numerous short tracts under 2 Mb, compatible with older, diffuse autozygosity, and OPD carried a higher burden of long tracts between 4 and 16 Mb, consistent with more recent common ancestry. Recurrent ROH islands were detected in both breeds. In FAC, islands were enriched for hydrolase and catabolic functions, and organelle related components, including genes such as RAD54L, SEC63, and POMGNT1. In OPD, islands emphasized kinase regulation, ion channel and contractile complexes, and endocrine metabolism, featuring IGF2, INS, TH, and GJA1 genes. Results provide a baseline for genetic management that prioritizes avoidance of matings among relatives, rotation of animals across centers, balanced contributions, and monitoring through genetic methods, while underscoring the importance of improved genome annotation for these non-model species.

Unraveling Sexual Size Dimorphism in Growth Traits of Dairy Goats: A Genetic Evaluation That Accounts for Dominance Effects

Jamshid Ehsaninia, Alireza Bagheripour — Tue, 26 May 2026 03:25:06 -0700

ABSTRACT

Sexual size dimorphism (SSD) is a major determinant of growth and productivity in domestic animals, yet dominance genetic effects have rarely been incorporated into its evaluation in goats. This work presents an extensive analysis of SSD in Murciano-Granadina (MG) goats for pre-weaning growth traits, birth weight (BWT), weaning weight (WWT), average daily gain (ADG), Kleiber ratio (KR), and growth efficiency (GE) through genetic models including additive, dominance, and maternal components. Data from 17 404 kids of 337 sires and 3966 dams indicated pronounced SSD as males were 9% heavier at birth, 4% heavier at weaning, and 6%–11% higher for ADG, KR, and GE. Models including dominance effects provided better fit, with dominance heritabilities (hd2$$ {h}_{\mathrm{d}}^2 $$ = 0.12–0.54) exceeding additive ones (ha2$$ {h}_{\mathrm{a}}^2 $$ = 0.03–0.14), highlighting significance of nonadditive genetic variance. Maternal effects were trait- and sex-specific (hm2$$ {h}_{\mathrm{m}}^2 $$ = 0.04–0.18). Cross-sex additive genetic correlations (ram,f$$ {r}_{\mathrm{a}}\left(\mathrm{m},\mathrm{f}\right) $$) were usually high (0.73–1.00), whereas dominance correlations were moderate to high (0.44–0.92), indicating partial sex-specific nonadditive effect. Traits that were lower in ram,f$$ {r}_{\mathrm{a}}\left(\mathrm{m},\mathrm{f}\right) $$ like BWT and WWT revealed higher potential of divergence under sex-specific selection. Comparisons of sex-joint and sex-specific evaluations indicated substantial re-ranking of top sires for WWT and BWT, moderate re-ranking for ADG and minimal changes for KR and GE. Overall, while sex-joint models are suitable for standard evaluation work, integrating dominance effects and sex-specific models improves selection accuracy of SSD traits, offering a practical framework to refine genetic evaluations and optimize breeding programs in dairy goats.

TG Nonsense Variant in Dwarf Rottweiler Dogs

Fri, 22 May 2026 18:15:24 -0700

ABSTRACT

We identified a dwarfism syndrome in six Rottweiler dogs characterized by reduced height and body weight; limb deformities, shortening of the tail and abnormally thick skin in puppies; developmental delays, pain and non-goitrous hypothyroidism. Histological examination of the thyroid gland revealed severe chronic diffuse bilateral atrophy with loss of thyroid follicles and lack of colloid. Pedigree analysis suggested an autosomal recessive transmission. Whole genome sequencing of an affected dog and filtering for private variants against 1539 control genomes identified a homozygous nonsense variant in the TG gene encoding thyroglobulin, NM_001048104.1:c.3694C>T. The variant was predicted to introduce a premature stop codon truncating 55% of the wild-type open reading frame, NP_001041569.1:p.(Arg1232*). The TG glycoprotein is the precursor to the thyroid hormones triiodothyronine (T3) and tetraiodothyronine (T4). TG deficiency leads to comparable phenotypes in human patients, cattle and goats. Genotyping six affected and 87 control Rottweiler dogs confirmed the expected genotype–phenotype association, with all affected dogs being homozygous for the mutant allele and control dogs being either heterozygous or homozygous wild-type. All four obligate carriers were heterozygous and among the 74 unrelated control dogs without known relationships to cases we found a 5.4% carrier frequency. Correct co-segregation in the available families was also observed. Taken together, this study provides an initial clinical and pathological characterization of an inherited dwarfism syndrome in Rottweilers and identifies a TG variant as a causal genetic defect. The results enable genetic testing to avoid unintentional risk matings.

Detection of Parental Reciprocal Translocations via Inter‐Chromosomal Linkage Disequilibrium in Offspring Genotypes

Anne Boshove, Aniek C. Bouwman, Torsten Pook, Martijn F. L. Derks — Tue, 19 May 2026 07:35:48 -0700

ABSTRACT

Reciprocal translocations (RTs) are among the most common structural chromosomal abnormalities observed in both humans and livestock, characterized by the exchange of DNA segments between two non-homologous chromosomes and associated with reduced fertility in carriers. Live-born offspring of RT-carriers have an approximately 50% chance of inheriting a balanced translocation, increasing the linkage disequilibrium (LD) between the affected chromosomes. In this study, we explored the potential for detecting RTs in pigs by identifying abnormal LD patterns in offspring populations. We performed extensive LD analyses on progeny groups from seven RT-positive boars and compared the results to a reference dataset comprising 1000 RT-negative boars. Additionally, we evaluated the impact of RTs on fertility using phenotypes from 15 RT-positive boars. Our findings demonstrate that RTs can be reliably detected when genotype data from at least 30 offspring are available, with a false positive rate of 0.1%. Fertility analysis revealed that RT carriers have significantly reduced litter sizes, on average 35% lower than their respective breed averages, emphasizing the relevance of RT identification in breeding programs. Overall, this study confirms that LD patterns offer a practical and cost-efficient method for RT screening in pigs without the use of cytogenetic testing, provided offspring genotype data is available.

Integrated Transcriptomic and Metabolomic Analysis Reveals Gut Microbiota–Mediated Regulation of Muscle Fiber Composition and Metabolism in Germ‐Free Pigs

Tue, 19 May 2026 01:09:24 -0700

ABSTRACT

The gut microbiota is a key regulator of host metabolism and skeletal muscle physiology, yet its role in muscle fiber-type transformation in pigs remains unclear. Here, we used germ-free (GF) and specific pathogen-free (SPF) Rongcheng piglets to explore how microbial absence influences muscle development. GF piglets showed significantly reduced body weight and an increased proportion of fast-twitch fibers compared with SPF controls. Transcriptome sequencing identified 1332 differentially expressed genes (DEGs), notably those involved in cGMP-PKG, Thyroid hormone, HIF-1, VEGF, and Butanoate metabolism signaling pathways, which are essential for myofiber specification. Non-targeted metabolomic profiling revealed 320 differentially expressed metabolites (DEMs), with major alterations in Bile secretion. Integrated transcriptomic and metabolomic uncovered 10 KEGG pathways co-enriched with DEGs and metabolites, including Bile secretion, Ferroptosis, Inflammatory mediator regulation of TRP channels, and HIF-1 signaling pathway. Correlation analysis revealed that strong positive correlations were observed between fast-twitch fiber genes (e.g., PRKCA, MYOZ3, NFATC1) and fatty acid-related metabolites (e.g., Dodecanoic acid, Valproic Acid, and Decanoic acid), whereas negative correlations were detected between these genes and bile acid-related metabolites (e.g., Cholic acid and 7-Ketolithocholic acid), suggesting microbial metabolites is associated with muscle fiber phenotype via metabolic and signaling crosstalk. Collectively, our findings demonstrate that gut microbial absence in pigs disrupts bile acid metabolism and fatty acid metabolism, which in turn drives the shift of skeletal muscle fiber composition toward fast-twitch glycolytic fibers. These metabolites are identified as key microbial mediators linking the gut microbiota to the transcriptional regulatory function of porcine muscle fiber type specialization, providing new insights into the gut–muscle axis and highlighting the important role of microbiota-derived metabolites in maintaining porcine muscle fiber composition and metabolic balance.

Genetic Diversity of the Beta‐Casein Gene in Brown Swiss and Creole Cattle From the Peruvian Highlands

Mon, 18 May 2026 23:54:53 -0700

ABSTRACT

Cattle's milk and derivatives are essential for human nutrition. However, up to 90% of people experience gastrointestinal discomfort after consumption. Milk digestibility depends on its protein composition. Casein, about 80% of milk proteins, includes beta-casein (CSN2) with two variants: A1 and A2. The A1 variant is linked to gastrointestinal issues, while A2 is easier to digest. Therefore, some dairy farms now market A2 milk from cattle homozygous for the A2 allele. This study aimed to evaluate the genetic diversity of the CSN2 gene in Brown Swiss and Creole cattle in the Andes of Peru (Junín, Huánuco, Pasco, Ayacucho and Puno). Blood from 445 Brown Swiss and 190 Creole was collected, DNA extracted with a commercial kit, and genotyped using the Axiom Bovine v3 SNP array. The distribution of A1 and A2 alleles and genotypes showed variation across breeds and regions, likely influenced by local breeding practices and selection programs. In Brown Swiss, the average A2 allele frequency was 0.66 (0.60 to 0.73) and the genotypic frequencies of A2A2 was 0.43 (0.35 to 0.52) and the A1A2 frequency was 0.45 (ranged from 0.41 to 0.50). In Creole, the A2 allele frequency was 0.60 (0.55 to 0.66), and the A1A2 genotypic frequency was 0.53 (0.49 to 0.56), being the most common. In conclusion, the frequency of the A2 allele was high in Creole but intermediate in Brown Swiss. These results suggest that the Brown Swiss and Creole have a favorable genetic potential for A2 milk production in the Highlands of Peru.

Correction to “Additional Evidence Fails to Associate Variation in KCNE4 With Equine Anhidrosis”

Fri, 15 May 2026 01:51:31 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

Discovery of Novel Viruses and Common Contaminants From Unmapped DNA and RNA in Pigs and Chickens Under Different Housing Conditions

Martijn F. L. Derks, Bert Dibbits, Richard P. M. A. Crooijmans, Kim Lensing — Wed, 13 May 2026 07:02:37 -0700

ABSTRACT

Unmapped sequencing reads in livestock often contain valuable information about pathogens but are typically discarded. We analyzed blood-derived DNA and RNA from chickens and pigs kept under high- and low-biosecurity conditions, focusing on unmapped reads. In chickens, low-biosecurity farms harbored substantially more viral sequences, primarily plant viruses, indicating environmental contamination. In pigs, Mycoplasmoides pneumoniae and several pig-specific viruses were detected. Our bioinformatics pipeline, involving host read removal, assembly, BLAST, and taxonomic filtering, efficiently identified candidate pathogens and contaminants. This approach demonstrates the potential of sequencing-based environmental DNA monitoring to track microbial and viral presence, assess farm biosecurity, and support animal health surveillance.

Genetic Dissection of Production Traits in Commercial Pigs: Comparative Effects of Terminal Sire Lines and Genome‐Wide Associations

Zihao Zhao, Qianjin Xue, Simin Feng, Tingting Ma, Yan Fu, Xuewen Xu — Wed, 13 May 2026 02:47:27 -0700

ABSTRACT

The genetic antagonism between lean meat yield and meat quality dictates the need for precise selection in pigs. This study evaluated the impact of terminal sire lines (Duroc [D], Pietrain [P], and their F1 cross [PD]) on production traits and performed a genome-wide association study (GWAS) in a 1295 commercial population. Results revealed a clear genetic trade-off: D-sired progeny showed superior intramuscular fat (IMF) and meat color (p < 0.05), while P-sired progeny excelled in loin muscle area and leanness. PD-sired pigs generally showed intermediate performance and did not outperform the purebred terminal-sire groups for the major traits evaluated. GWAS replicated major known QTLs, including the VRTN locus for rib count (SSC7:97575068_A_G, p = 2.30e-39) and the BMP2 locus for carcass length (SSC17:15820953_G_A, p = 1.59e-09). Rib count was positively correlated with adjusted carcass straight length (r = 0.393, p = 5.80e-31), and combined genotype analysis of the VRTN and BMP2 loci revealed a joint effect on axial skeleton traits. Novel QTLs were discovered for drip loss (SSC13, SSC14) and myofiber perimeter (SSC1), with TUSC1 identified as a candidate gene. Our findings demonstrate that the PD cross does not mitigate the leanness-quality trade-off and highlight the VRTN and BMP2 loci, together with novel trait-associated markers, as potential targets for crossbred breeding programs.

Identifying Candidate Genes for Late‐Feathering Subtypes of the Shouguang Chicken by Genome‐Wide Association Study and Differential Expression Analysis

Xiayi Liu, Junying Li, Haigang Bao — Mon, 11 May 2026 03:31:35 -0700

ABSTRACT

Late-feathering phenotype can be classified into subtypes based on the difference in length between primary and primary-covert feathers of 1-day-old chicks. In this study, a chick with its primary feathers shorter than its primary-covert feathers is identified as Subtype 1 (T1), and a chick with its primary feathers as long as its primary-covert feathers is identified as Subtype 2 (T2). The objective of this study was to obtain candidate genes for late-feathering subtypes in Shouguang chickens. Fifty-three Shouguang chickens were genotyped using a 600 K SNP chip, and two genomic regions on Chromosome 3 and 10 were identified as being associated with late-feathering subtypes by Genome-wide association study (GWAS). Twelve hair follicle samples of flight feathers from 12 1-day-old Shouguang chicks, including 6 of each subtype, were collected. RNA sequencing analysis was performed, and no overlapping genes were found between differentially expressed genes (DEGs) identified by differential expression analysis and candidate genes by GWAS. In order to find the relationship between the two sets of genes, a protein–protein interaction (PPI) network was constructed using all protein-coding genes in the two sets, and the result showed that four genes (CDC40, EFL1, AK9, and ZBTB24) from GWAS and 21 DEGs were enriched in the largest subnetwork associated with muscle function. Considering the spatiotemporal characteristics of gene differential expression and the fact that the two most significant SNP loci in GWAS were located on EFL1 and CDC40, we propose that the two genes are more suitable as candidate genes for late-feathering subtypes.

Genetic Evidence of a Recent Decline and Crossbreed Distribution of TRPV4 c.1024G>T Variant in Domestic Cats

Sun, 10 May 2026 19:49:51 -0700

ABSTRACT

The folded ear phenotype of Scottish Fold cats is associated with an autosomal dominant TRPV4 variant (c.1024G>T) linked to osteochondrodysplasia. Although genetic testing has been implemented to guide breeding, empirical evidence of its impact on allele frequency remains limited, and crossbreed investigations are lacking. Here, we evaluated longitudinal changes in TRPV4 c.1024G>T allele frequencies in Scottish Folds and surveyed the variant in 8610 cats from 14 breeds in Japan. Overall, between 2017 and 2024, the proportion of homozygous cats significantly declined (from 14.2% to 1.9%, p < 0.001), whereas the frequency of heterozygous cats remained stable (39.3% vs. 51.5%, p > 0.74). The variant was identified primarily in Scottish Folds but was also detected in American Curls, Norwegian Forest Cats, Munchkins, and Minuets. Taken together, our results highlight that integrating TRPV4 c.1024G>T genotyping into breeding programs can effectively reduce the prevalence of this hereditary disorder, and they warrant the expansion of genetic testing to additional breeds.

Meta‐Analysis of Transcriptomic Datasets Reveals Key Immune Gene Profiles and Signaling Pathways in Bos taurus

Sun, 10 May 2026 19:30:40 -0700

ABSTRACT

Improving disease resistance in cattle relies on informed breeding and vaccine development, both depend on our understanding of immune mechanisms in cattle. However, transcriptomic studies of bovine immune responses often show considerable variability due to differences in tissue type, pathogen, time point, and experimental design, limiting the generalizability. Meta-analysis integrates multiple transcriptomic studies to identify consistent gene expression patterns and enhance statistical power. We integrated bovine RNA-seq datasets using immune-response specific keywords, species constraints, and high-throughput sequencing filters to prioritize biologically comparable and meta-analysis-ready studies. Specifically, in this study, we performed a meta-analysis of four bovine transcriptomic datasets to identify immune-related differentially expressed genes (DEGs) in Bos taurus. These datasets showed consistent results across analyses and represent immune responses related to mycobacterial infections (Mycobacterium bovis and Mycobacterium avium subsp. paratuberculosis), making them suitable for combined analysis. Our pipeline included FastQC, Trimmomatic, Bowtie2, SAMtools, FeatureCounts, DESeq2, and MetaRNASeq, identifying 28 DEGs (12 upregulated and 16 downregulated). We identified key immune-related genes (IL1A, RGS2, RCAN1, ZBP1, TIMD4, PPARG, TLR10, and ACP5) with known regulatory roles in immunity. KEGG enrichment analysis revealed involvement in necroptosis, osteoclast differentiation, oxytocin signaling, and cGMP–PKG signaling pathways, associated with inflammatory cell death, cytokine signaling, and immune cell differentiation. Using reproducible transcriptomic signals across systematically selected bovine immune datasets rather than relying on single-experiment analyses, we provide a robust meta-analytic framework. This meta-analysis enhances our understanding of conserved immune signaling mechanisms in cattle for identifying conserved immune mechanisms with broader biological and translational relevance.

A New TYR Splice Donor Variant Causing Oculocutaneous Albinism Type I in Angus Cattle

Fri, 08 May 2026 06:26:07 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

Straightened Small Pinnae in TRPV4 c.1024G>T Heterozygous Cats

Wed, 06 May 2026 01:41:00 -0700

ABSTRACT

The folded-ear phenotype of Scottish Fold cats results from a dominant variant of the TRPV4 gene (c.1024G>T). Producing homozygous individuals is discouraged due to severe osteochondrodysplasia and identifying heterozygous carriers is critical for breeding. Although carriers are generally expected to have folded ears, straight-eared individuals have also been suspected among them. Here, we investigated the relationship between ear phenotype and TRPV4 genotype using longitudinal photographic data and TRPV4 genotyping in 114 cats. We identified seven individuals that transitioned from folded to straight ear phenotype during maturation. Genotyping confirmed all were heterozygous carriers, with 12.7% found among heterozygous cats. Morphometric analysis of 14 cats with high-quality photographs demonstrated these “straightened” cats had smaller pinnae than genetically wild-type straight-eared cats (p < 0.05), suggesting cartilage anomalies. These findings confirm “cryptic folds”—phenotypically straight but genetically heterozygous cats. Consequently, visual inspection for breeding selection is insufficient, highlighting the necessity of TRPV4 genotyping to prevent unintentional production of homozygous offspring with severe osteochondrodysplasia.

Revisiting Genetic Relationships of the Endangered Austrian Turopolje With Balkan and Commercial Pig Breeds Using Genome‐Wide SNP Data

Tue, 05 May 2026 06:26:39 -0700

ABSTRACT

The endangered Austrian Turopolje (AT) pig population, which originated from six Croatian Turopolje founders imported during the early 1990s, is nowadays preserved through a national conservation project. This study aims to identify genetic relations, genetic distances and migration events between the AT population, four Austrian commercial breeds, and seven local Balkan breeds, as well as their inbreeding levels by using medium-density single nucleotide polymorphism (SNP) arrays. The AT population was well separated from the other breeds (multi-dimensional scaling and Admixture analyses), although displaying a relative genetic proximity to Croatian Turopolje, Hungarian Mangalitsa, and Swallow bellied Mangalitsa. AT did not show any sign of possible gene flow deriving from the other breeds, except for the Banija Spotted (Treemix analysis). The AT genetic variability did not appear negatively influenced by its recent demographic history (inbreeding based on runs of homozygosity, F _ROHav = 0.17 ± 0.05). Its inbreeding trend, although increasing, does not appear to be alarming compared to Croatian Turopolje. In conclusion, the results of this study possibly highlight how an efficient management of an originally very narrow genetic stock may have contributed to shape the current genetic make-up of this recently established population. The observed differentiation between AT and its ancestral counterpart (Croatian Turopolje) may not only reflect the consequence of the initial founder effect but also derive from different management practices over the last three decades. This study represents a first step towards awareness raising about the originality of a local pig population traditionally characterised by the intimate connection with its rural breeding area.

Genotype and Allele Frequencies of Canine Degenerative Myelopathy‐Associated SOD1 Gene Variant in Irish Wolfhound Dogs

Yoshihiko Yu, Margret L. Casal — Tue, 05 May 2026 00:29:18 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

Influence of MC1R Gene Variants on Coat Color of Indicine Cattle Breeds

Sat, 02 May 2026 00:56:27 -0700

ABSTRACT

Indicine cattle display a broad range of coat colors, representing a relevant and breed-defining trait required for registration in breeder association. Among the genes involved in pigmentation, MC1R stands out for modulating the synthesis of melanin-related proteins and remains poorly explored in indicine cattle breeds. Therefore, we aimed to perform fine mapping of the MC1R gene and to evaluate the association between its polymorphisms and coat color as well as skin pigmentation in seven zebu cattle breeds. A total of 295 individuals belonging to Gir, Nelore, Sindi, Indubrasil, Tabapuã, Guzerá, and Brahman cattle breeds were genotyped through PCR-sequencing, followed by estimates of genotypic and allelic frequencies, linkage disequilibrium, and association with phenotypes using the Kruskal–Wallis test. We identified nine polymorphisms: six non-synonymous SNPs, one coding indel, one synonymous SNP, and one 3′ downstream SNP. We report, for the first time, the SNP c.274G>A (p.Val92Met), here designated E ^Z1, and SNP c.871G>A (p.Ala291Thr) associated with the dark skin phenotype in Gir cattle, here designated E ^Z2. Additionally, the indel c.310del was associated with depigmentation in Sindi, Guzerá, and Gir cattle breeds. The variants described herein represent potential molecular markers to support selection strategies targeting desired coat and pigmentation phenotypes.

A Longitudinal Genome‐Wide Association Study Identifies New Candidate Genes for Abdominal Fat Thickness in White Feather Broilers

Wed, 29 Apr 2026 16:24:37 -0700

ABSTRACT

Abdominal fat thickness (AFT) is a crucial indicator for assessing fat deposition in White Feather broilers. Previous genome-wide association studies (GWAS) have primarily focused on single-point measurements of abdominal fat, with limited attention given to longitudinal phenotype records. Compared to traditional GWAS models, the longitudinal data-based GWAS (LONG-GWAS) model accounts for temporal phase effects, thereby more effectively controlling the false positive rate. This study conducted a genome-wide association analysis on 1654 White Feather broilers at four distinct ages during the laying period of broiler breeders (25, 27, 35, and 43 weeks). Three SNP loci associated with fat were identified (rs16341267, rs740644432, and rs15049519), which were annotated to three candidate genes: FDFT1, HTR2C, and ALDH3A2. These genes are involved in regulating lipid metabolism, energy balance, and fat deposition. This study provides new insights into the genetic basis of abdominal fat thickness in White Feather broilers and offers stage-specific marker information that can accelerate precision breeding for abdominal fat control in white feathered broilers.

Integrating GWAS and RNA‐Seq Reveals QTLs and Candidate Genes for Fat Deposition in Large White × Tongcheng Crossbred Pigs

Tue, 28 Apr 2026 23:15:14 -0700

ABSTRACT

Fat deposition traits are crucial economic characteristics that directly influence production efficiency in pigs. To better understand the genetic mechanisms underlying fat deposition, four traits including backfat thickness (BF), caul fat rate (CFR), leaf fat rate (LFR), and internal fat rate (IFR) were measured in 421 Large White × Tongcheng crossbred pigs. A GWAS analysis identified 666, 15, 22, and 61 SNPs significantly associated with BF, LFR, CFR, and IFR, respectively. Bayesian fine-mapping revealed a major QTL on SSC7 (29.62–30.62 Mb) that influences all four fatness traits and harbors the candidate gene HMGA1 and NUDT3. Additionally, a QTL on SSC5 (28.67–30.52 Mb) was associated with BF and contains the candidate gene TBK1, while a QTL on SSC18 (8.01–9.88 Mb) associated with CFR includes AGK and TBXAS1. Integration of transcriptome, 3D genomic, and epigenomic data identified rs703100168 on SSC7 as a candidate functional SNP to control HMGA1 expression and regulate fat deposition in pigs. These findings provide valuable candidate genes and genetic variants for improving fatness traits in pig breeding programs.

Association of the Disheveled 2 (DVL2) Gene c.2044delC Variant with Increased Risk of Canine Cleft Palate

Mon, 27 Apr 2026 01:27:19 -0700

ABSTRACT

Canine congenital cleft palate is one of the most common craniofacial anomalies in dogs, characterized by a failure of the palatal shelves to fuse properly during fetal development, leading to abnormal communication between the oral and nasopharyngeal cavities. Patients with cleft palate can experience significant challenges including feeding difficulties, aspiration pneumonia, and respiratory distress, all of which can profoundly impact quality of life and, in severe cases, survival. The clinical management of cleft palate in dogs involves a combination of medical and surgical interventions. The aim of this study was to identify common genomic variants associated with cleft palate. A GWAS with 266 cases ascertained from a general population of more than 1 million dogs attending primary care veterinary clinics in the United States was used to identify an association in the region of the disheveled 2 (DVL2) gene variant c.2044delC, previously linked to Robinow-like syndrome and the screw tail phenotype in Bulldogs and related breeds. The association was confirmed through genotyping of the DVL2 variant. In summary, this study identifies the DVL2 variant that is fixed and breed defining in several breeds as a risk factor for cleft palate in dogs.

A Familial X‐Linked Disorder of Sexual Development in Thoroughbred Horses Associated With a Novel Androgen Receptor Splice‐Site Variant

Anna Letko, Vidhya Jagannathan, Cord Drögemüller, Gesine Lühken — Sun, 26 Apr 2026 21:09:06 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.

Additional Evidence Fails to Associate Variation in KCNE4 With Equine Anhidrosis

Jessica L. Petersen, Carrie J. Finno — Sun, 26 Apr 2026 15:28:21 -0700

ABSTRACT

A prior genome-wide association (GWA; N = 200) including Thoroughbreds and stock horses implicated chromosome 6 (NC_009149.3) in owner-reported equine anhidrosis. A missense variant in KCNE4 (NC_009149.3:g.11813731A>G) was proposed as a risk allele, although its association with anhidrosis was not reported. Variant annotation and protein modelling in the original study suggested the G allele conferred risk. We reported no association of the G allele with anhidrosis in 50 horses phenotyped by an intradermal terbutaline sweat test (ITST); all horses produced sweat regardless of genotype. It later appeared the A allele was instead suggested to confer disease risk. To reassess this, we genotyped 20 ITST-tested Thoroughbreds including 9 with partial or complete anhidrosis. The KCNE4 A allele was not associated with phenotype when analyzed as a binary trait (p = 0.16) or when classifying affected horses as having either partial or complete anhidrosis (p = 0.21). The locus was also uninformative in four clinical cases (AA = 1, AG = 1, GG = 2). Reasoning that a true risk allele should be in linkage disequilibrium (LD) with the associated GWA SNV (AX-103822151; rs68656009), we evaluated whole-genome sequence (N = 2) from the initial publication. Both case and control were homozygous AA at the putative risk locus; the case was heterozygous at the GWA SNV. In public data (N = 897), LD between loci was low (r² = 0.19). In 369 Thoroughbreds, LD was 0.58. Restricting to Thoroughbreds in the original GWA (N = 85), we found no association of chromosome 6 with anhidrosis. Collectively, these data do not support a role of the KCNE4 variant or the GWA SNV in equine anhidrosis.

Mucopolysaccharidosis IIID and Beta‐Mannosidosis in Brazilian Anglo‐Nubian Goats: Molecular and Genealogical Insights for the Development and Implementation of a Genetic Disease Eradication Program

Wed, 22 Apr 2026 03:40:09 -0700

ABSTRACT

Beta mannosidosis and Mucopolysaccharidosis IIID are two autosomal recessive lysosomal storage diseases identified in Anglo-Nubian goats. Even though they are well characterized from the clinical and molecular point of view, there is a gap in studies aiming to understand distribution and dissemination risk in goat populations throughout the world. Considering this, we developed probe-based qPCR tests and combined it with pedigree analysis to deepen the knowledge related to the distribution of both mutations in Brazilian Anglo-Nubian population. This study revealed, for the first time, that the mutation associated with Mucopolysaccharidosis IIID is segregating in our country, expanding the knowledge of the worldwide distribution of this disease-associated allele. Additionally, the combination of genotyping and pedigree analysis enabled the estimation of additional high-confidence putative genotypes, contributing to the reduction of genotyping costs and highlighting a putative pathway associated with the introduction/dissemination of the Mucopolysaccharidosis IIID-associated allele in Brazil. These results can be considered as an initial basis for the proposition of a program to control/eradicate mutations associated with genetic diseases in Brazilian goat populations.

Issue Information

Wed, 22 Apr 2026 02:56:28 -0700

Animal Genetics, Volume 57, Issue 3, June 2026.