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PubMed2025

Genomic prediction and genome-wide association study for liver abscesses in crossbred beef cattle.

Liver abscesses are a concern in feedlot cattle, and little is known about the role of genetics in their development. This study aimed to estimate genetic parameters and to identify single-nucleotide polymorphisms (SNPs) associated with liver abscesses. Crossbred cattle representing 18 breeds in the U.S. Meat Animal Research Center Germplasm Evaluation Program were phenotyped for liver abscesses at slaughter (n = 9,044). Seventeen percent of cattle had liver abscesses. These cattle had genotypes that were imputed to sequence variant genotypes. After filtering and quality control, 340,723 SNPs were used in the analysis. Liver abscess prevalence was modeled with a single-step genomic best linear unbiased prediction (ssGBLUP) threshold model using a Bayesian framework. The model included contemporary group (sex, treatment group, and slaughter date), additive genomic, and residual effects. Genomic heritability was 0.039 (95% highest posterior density = 0.005, 0.081), which was very small. To assess prediction quality, a 5-fold random cross-validation structure was used. Method Linear Regression was used to assess accuracy, bias, and dispersion by comparing estimated breeding values (EBV) from full and reduced analyses. Cross-validation metrics showed EBV based on genotypes had 0.05 reliability (SD < 0.01) with no bias relative to EBV based on genotypes and phenotypes. For the genome-wide association study, SNP effects were back calculated from the EBV solutions from ssGBLUP. No SNPs were associated with liver abscesses at a Benjamini-Hochberg adjusted 0.05 significance level. Although a large dataset was used, this result was because of the low genomic heritability and imprecise EBV used to calculate SNP effects. Based on these results, environmental factors contribute to most of the variation in liver abscesses. Genetic selection to reduce liver abscesses would be slow because of the low genomic heritability, measurement late in life, and inability to measure breeding animals. A faster approach would be finding additional environmental interventions that maintain animal performance.

Animals↗

PubMed2026

Microsatellites Versus Genome-Wide SNPs Data for Pedigree Reconstruction in Twin Simmental Crossbred Cattle.

Accurate pedigree reconstruction is critical for genetic evaluation in admixed cattle populations, yet the relative performance of microsatellite and genome-wide SNP markers in twin-rich herds with incomplete pedigree records remains unclear. We compared 12 ISAG-recommended microsatellite markers with whole-genome SNP data for dam-calf assignment in a Simmental crossbred population (n = 43, 13 dam-calf groups) from southern China. Twin zygosity was determined from SNP identity-by-descent (PI_HAT) values: nine calf pairs were dizygotic, one pair was monozygotic (20A/21A), and one adult pair was composed of dizygotic twin sisters (31A/34A). Admixture analysis at K = 3 revealed ancestry proportions of 50.7% European taurine, 28.9% Chinese indicine and 20.4% East Asian taurine. The SNP-based neighbor-joining tree correctly recovered 12 of 13 groups (92.3%, 95% CI: 64.0-99.8%), whereas the microsatellite-based tree recovered 11 (84.6%, 95% CI: 54.6-98.1%); the difference was not statistically significant (exact McNemar test, p = 1.0). Locus INRA023 was monomorphic (PIC = 0), reducing the effective number of markers to 11. These results indicate that genome-wide SNPs show a favourable trend in accuracy and are less prone to false-positive clustering than a standard microsatellite panel in admixed, twin-rich cattle populations.

SNP↗

PubMed2026

Research note: Genetic background influences the relationship between age at first egg and long-term egg production in layers.

Age at first egg (AFE) is a key selection criterion in layers breeding. With the laying cycle being extended to 100 weeks, the relationship between AFE and long-term productivity and egg quality should be evaluated to ensure that selection for AFE aligns with current breeding objectives. In this study, Beijing-You chickens and White Leghorns were used to generate purebreds and crossbreds. Egg-laying performance was recorded including AFE, egg number and cumulative egg number at different stages from onset till 100 weeks, and egg quality traits at 32, 54, 72, 86, and 100 weeks. Genetic correlations were estimated, both in the combined population of purebreds and crossbreds and within each genetic group. In the combined population, a positive genetic correlation was observed between AFE and cumulative egg number till 100 weeks. Age-dependent genetic correlations between egg number at different stages and AFE further revealed that extremely early-maturing hens showed initial production advantages, but these advantages diminished at later stages. Importantly, the genetic and phenotypic correlations between AFE and egg quality traits were weak, with correlation coefficients ranging from -0.18 to 0.35. Within each genetic group, the relationships between AFE and egg production also showed consistent age-dependent patterns. For the long-term production targets, optimal AFE seems to differ by genetic backgrounds. White Leghorns showed higher egg production with earlier maturity, whereas in Beijing-You chickens, maintaining AFE at approximately 140-189 days appeared to be more favorable. Overall, these findings demonstrated that earlier AFE does not ensure higher egg production at extended laying cycles and has negligible influence on egg quality, highlighting the importance of optimizing AFE according to genetic background.

Age at first egg↗

PubMed2026

Multi-omics identification of ZFPM2 and CD44 as key candidates for testicular size in sheep.

Testicular size is a key determinant of ram fertility, yet its genetic architecture in sheep remains poorly understood. Crossbred sheep exhibit substantial testicular developmental variation and serve as ideal models for screening fertility-related genes. Here, we performed whole-genome sequencing (WGS)-based genome-wide association study (GWAS) on 115 rams, including seven crossbred populations (each derived from a distinct sire breed crossed with Hu sheep) and a purebred Hu sheep population. We identified two variants within ZFPM2, including an intronic single nucleotide polymorphism (SNP) rs421073404 and a missense SNP rs1086332841, both significantly correlated with testis weight, length, and width. Importantly, these variants exerted testis-specific effects, consistent with their weak correlation with body weight (r < 0.2). Genomic selection scans (FST and π-ratio) between rams with large (>150 g/side) and small (<75 g/side) testes revealed multiple divergent genomic regions, with prominent haplotype differentiation at the CD44 locus on chromosome 15. Notably, two linked missense variants (rs160734053 and rs414318703) in CD44 exerted opposing effects on testicular size, suggesting allelic heterogeneity at this locus. Integrative RNA-seq and ATAC-seq across 0-12 months further uncovered prepubertal stage-specific expression and chromatin accessibility patterns of ZFPM2 and CD44, providing mechanistic insights into their regulatory roles. Collectively, this study provides candidate SNPs for sheep marker-assisted selection and multi-omic evidence for dissecting the genetic basis of testicular development in ovine breeding.

Animals↗

PubMed2026

Generation of a New Immunodeficient Rat Model of Retinal Degeneration With LSL TdTomato Reporter and TdTomato-Pcp2 Expression.

PURPOSE: The purpose of this study was to develop a fluorescently labeled immunodeficient retinal degenerate (RD) rat model for studying photoreceptor degeneration and transplant-host connectivity using the Cre-lox system. METHODS: We developed gene constructs for CAG-LSL-TdTomato (expressing floxed TdTomato) and Pcp2-Cre (marker for ON-bipolar cells) that were injected into rat embryos. The LSL TdTomato reporter strain, created on immunodeficient RhoS334ter-3 rats (RRRC #539), was bred to homozygosity (strain SD-Foxn1rnuTg((Rho-S334X)3,CAG-TdTomato)1010Mjsuc, RRRC #1055, "RNT"). The gene construct Pcp2-Cre was injected into Long-Evans (LE) rat embryos, resulting in two Pcp2-cre founders (strain PCP2 Cre-1105 RKI, "Pcp2"), with targeted and targeted/random insertion of the transgene. F1 offspring were bred to homozygosity and immunodeficiency. To test whether TdTomato expression can be induced in "RNT" rats expressing floxed TdTomato, retinal explants of P9 "RNT" rats were exposed to AAV-PHP.eB-hSyn-myc-Cre (AAV-Syn-Cre) virus. Homozygous rats of both strains ("RNT" and Pcp2-Cre) were crossbred to generate RD TdTomato-Pcp2 ("RTP") rats. Retinas were stained for various retinal markers. GFP-expressing rat retinas were transplanted to 6-week-old "RTP" rats and analyzed after 37 and 77 days. RESULTS: AAV-Syn-Cre induced TdTomato expression in "RNT" retinas. TdTomato-Pcp2 RD rats developed RD similar to the original Rho S334ter-3 rats. Retinas with targeted Pcp2-Cre insertion showed TdTomato in retinal interneurons, overlapping with Pcp2-staining ON bipolar cells, and cones. Retinas with random Pcp2-Cre insertion exhibited additional TdTomato in many other cells. Pcp2-TdTomato expression defined transplant-host boundaries. CONCLUSIONS: We created a unique RD rat model for studying retinal transplant connectivity which can also be used to generate RD rats with other cell-specific labels. TRANSLATIONAL RELEVANCE: This newly created rat is useful for cell therapy and retinal degeneration studies.

Animals↗

PubMed2026

Systematic Approach for Compound Angus Populations Revealing Positional Candidate Genes and Improving Prediction Accuracy in Carcass Traits.

Carcass traits, which reflect growth performance and muscle development, are economically important in beef cattle, yet their genetic determinants remain poorly characterized. Both single-population Genome-wide association studies (GWAS) methods, such as BLINK, and cross-population meta-analysis approaches are widely used to identify genetic variants, yet their comparative performance in genomic prediction for complex traits in structured populations remains underexplored. Few studies have directly compared these methods in genomic prediction. To address this gap, this study aims to (i) identify positional candidate genes associated with carcass traits and (ii) evaluate the context-dependent advantages of Covariate Adjustment (CA) and meta in genomic prediction. In this study, we analyzed carcass weight (CW), live weight (LW), and dressing percentage (DP) in 279 crossbred Angus cattle genotyped with the PHR0105_Bt140K_v1.0 SNP chip. GWAS was performed on the full population using BLINK, and results from three subpopulations were combined via meta-analysis, with significance thresholds for both approaches determined by a shuffle-based method. Candidate genes located within ±10 kb of significant SNPs were associated with different carcass traits, including STRIT1, SEL1L3, NOC4L and ANK1 for DP; SNCA and DNAH5 for CW; and GYPC, GPR158, and GUCY1A1 for LW. Prediction accuracy under MAS and MABLUP showed meta slightly outperformed BLINK in MAS, while BLINK was better with covariate adjustment; after incorporating kinship in MABLUP, meta achieved higher accuracy and population partitioning was negligible. Overall, MABLUP yielded the highest accuracy (0.52-0.79) versus MAS (0.37-0.54) in all traits. These findings provide a methodological basis for selecting appropriate GWAS strategies in structured populations and highlight candidate genes.

GS↗

PubMed2026

Effect of founder breeds on genotype imputation accuracy in Canchim cattle.

UNLABELLED: Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP – single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson’s correlation between observed and imputed genotypes (R2). PERC values ranged from 66.52% to 97.39% and R² from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13353-026-01060-z.

Animal breeding↗