Journal of Animal Breeding and Genetics最新文献

{"title":"Genetic Parameters and Genome-Wide Association Analysis of Reproductive Traits in Egyptian Buffalo.","authors":"Amin M S Amin, Ayman G El Nagar, Maher H Khalil, Hamdy Abdel-Shafy, Mohammed M Hegazy, Ayman F Ashour, Mohamed M I Salem","doi":"10.1111/jbg.70085","DOIUrl":"https://doi.org/10.1111/jbg.70085","url":null,"abstract":"<p><p>Reproductive efficiency is a crucial factor in the sustainability and profitability of buffalo production systems. However, genetic improvement of reproductive traits is challenging due to low heritability, environmental sensitivity, limited recording, and shrinking reference populations caused by crossbreeding. This study aimed to estimate genetic parameters and detect the genomic architecture of key reproductive traits in Egyptian buffalo using pedigree-based analyses and genome-wide association studies (GWAS). Over a 44-year period (1980-2024), reproductive records from five Egyptian experimental herds were analysed. The dataset comprised 2843 buffalo cows, sired by 140 bulls and out of 1328 dams. In total, 2359 records were available for age at first calving (AFC), 10,478 for gestation length (GL), 7966 for calving interval (CI), 6705 for days open (DO), and 12,909 for calving ease (CE) and stillbirth (SB). For genome-wide association analysis, 275 Egyptian buffaloes were genotyped using the Affymetrix Buffalo 90 K array, and 66,295 high-quality SNPs were retained after quality control. De-regressed proofs derived from pedigree-based genetic evaluations were used as response variables in a mixed linear model implemented in the rMVP package. Genome-wide association analysis identified putative genomic regions associated with GL, CI, CE, and SB, whereas no genome-wide significant associations were detected for AFC and DO. Functional annotation and QTL enrichment analyses were subsequently used to provide exploratory biological context for the identified genomic regions. Heritability estimates were generally low: 0.16 for AFC, 0.06 for GL, 0.02 for CI, 0.02 for DO, 0.18 for CE, and 0.06 for SB. Manhattan plots revealed that 15 genomic regions containing significant SNPs were identified on chromosomes 2, 4, 10, 12, 13, 15, 19, 20, and 25 for the reproductive traits of GL, CI, CE, and SB. These findings provide preliminary evidence of genomic regions potentially contributing to variation in reproductive traits in Egyptian buffalo, although the relatively small number of genotyped animals limits the power to detect and validate small effect loci. Seven significant genomic regions on chromosomes 10, 13, 15, 20, and 25 were associated with the GL trait. Additionally, three suggestive SNPs mapped to chromosomes 2 and 19 were associated with the CE trait, and three suggestive SNPs mapped on chromosome 12 were significantly associated with the SB trait. The results of KEGG enrichment analyses and QTL classification analyses for reproductive traits in Egyptian buffalo suggest that candidate genes within known QTL may be involved in complex biological networks involving immune competence, cellular homeostasis, and systemic physiological resilience. Among the enriched pathways, Fc gamma R-mediated phagocytosis, protein export, viral myocarditis, and arrhythmogenic right ventricular cardiomyopathy (ARVC) were highlighted. Most annotated genomic region","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149277261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Association Studies for Anogenital Distance and Linear Type Traits in Gir Cattle.","authors":"Renata de Fátima Bretanha Rocha, Andréia Ferreira Machado, Fabrício Pilonetto, Marcos Vinícius Barbosa da Silva, Domingos Lollobrigida de Souza Netto, José Domingos Guimarães, Fábio Luiz Buranelo Toral, Victor E Gomez Leon, Simone Eliza Facioni Guimarães","doi":"10.1111/jbg.70083","DOIUrl":"https://doi.org/10.1111/jbg.70083","url":null,"abstract":"<p><p>Although linear type traits have been under selection in the Dairy Gir cattle for the past three decades, there are few studies exploring genetic architecture for these traits. The aim of this study was to identify candidate genes for anogenital distance and linear type traits in the Gir breed. For this study, the body measures of rump length (cm, RL), ilium width (cm, ILW), hip height (cm, HH), body length (cm, BL), thoracic perimeter (cm, TP) and rump area (cm², RA) along with anogenital distance (cm, AGD) were collected from 604 Gir dairy cows, around 5.69 years old. The pedigree file included 2206 animals, of which 742 were genotyped with different SNP panels and imputed to Illumina BovineHD BeadChip (777 K). Genome-wide association studies were carried out using the blupf90+ program for all traits and for a phenotypic index created to assist selecting candidate genes. The top 5 windows for the traits and top 10 windows for the index explaining the highest percentage of additive genetic variance were selected for gene search. Biological processes and transcription factors were searched from the genes found. In total, 90 genes were identified for all seven traits, of which 17 were pleiotropic, that is, they were common results for pairs or trios of traits. From that, the candidate genes (chromosome) identified from the phenotypic index were CXCL13 (6), CNOT6L (6), MRPL1 (6), CCSER1 (6), CDH26 (13), DOCK8 (8), ZNG1 (8) and PGM5 (8). For those eight genes, 11 transcription factors and 59 biological processes were identified. In conclusion, BTA6 seems to have a deeper role in linear type traits in the Gir breed. Even though there are few studies confirming the action of those genes on body conformation, all eight candidate genes are recommended for future studies to validate their action on muscle and skeletal development or fat deposition due to their biological process functions, which could be pleiotropically affecting linear traits in cattle.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Transformation From Methane Concentration From Sniffers to Methane Production for Implementation in Breeding Programs and Comparison With Tier 2 Equation.","authors":"O González-Recio, E Teran, J A Jiménez-Montero, C I V Manzanilla-Pech, B Gredler-Grandl","doi":"10.1111/jbg.70080","DOIUrl":"https://doi.org/10.1111/jbg.70080","url":null,"abstract":"<p><p>Reducing methane emissions from dairy cattle has gained considerable attention due to its dual benefits of improving feed efficiency and mitigating climate change. Consequently, phenotyping methane emissions in dairy populations has become increasingly important to enable direct genomic selection for lower methane emissions in breeding programs. Sniffer devices are receiving growing attention and are currently being deployed on commercial farms. However, these devices do not measure airflow and therefore provide methane concentration measurements rather than direct estimates of methane production. In this study, a new method is proposed to estimate individual cow methane production from sniffer device data that does not rely on regression on production traits and can therefore be classified as a Tier 3 approach. This novel methane production trait was derived using sniffer measurements collected in two dairy cattle populations: Spain (n = 1576) and The Netherlands (n = 2470). The proposed trait was compared with two alternative methane production estimates derived from production traits, representing a Tier 2 and an existing Tier 3 method. Phenotypic correlations between the Tier 3 traits were high (R > 0.90), whereas correlations between the Tier 2 and Tier 3 methods were substantially lower, ranging from 0.04 to 0.44. Strong agreement was observed between herd-level averages of the Tier 3 traits, while discrepancies between Tier 2 and Tier 3 estimates were more pronounced. Overall, the Tier 2 equation yielded higher methane production estimates than those obtained from sniffer-based Tier 3 traits. Heritability estimates for the Tier 3 traits ranged from 0.06 to 0.13, whereas a higher heritability (0.18-0.22) was observed for the Tier 2 trait, with standard errors between 0.02 and 0.03. Repeatability estimates were greater for the Tier 3 traits, with values ranging from 0.54 to 0.58 in Spain and from 0.25 to 0.29 in The Netherlands. The Tier 2 trait also exhibited a high repeatability (0.55-0.80). We propose this new sniffer-based Tier 3 trait as an alternative methane production phenotype that is not derived from individual production traits, thereby reducing the risk of spurious associations between methane emissions and yield-related traits. The proposed phenotype showed strong agreement with previously used Tier 3 traits and exhibited comparable heritability estimates. Nevertheless, several limitations must be acknowledged. In particular, this trait provides an estimate of methane production rather than a direct measurement, as current sniffer devices cannot capture the complete expiration or eructation plume. Despite these limitations, the trait enables the estimation of genetic trends and the prediction of breeding values expressed in biologically meaningful units. As such, it represents a valuable tool for supporting mitigation strategies and informing breeding policies aimed at reducing methane emissions from dairy cattle.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Selection for High Growth on Resilience of Giant Freshwater Prawn Macrobrachium rosenbergii.","authors":"Tran Thi Mai Huong, Tran Huu Phuc, Nguyen Thanh Vu, Pham Dang Khoa, Nguyen Hong Nguyen","doi":"10.1111/jbg.70084","DOIUrl":"https://doi.org/10.1111/jbg.70084","url":null,"abstract":"<p><p>Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its pre-disturbance state. To the best of our knowledge, no previous study has investigated resilience in the giant freshwater prawn (GFP, Macrobrachium rosenbergii). In this study, we aimed to estimate the genetic parameters of resilience indicators, the correlations between resilience and growth and survival traits, and the correlated genetic responses to selection for high growth in the present GFP line. A resilience indicator based on standardised body weight (BW) deviation was analysed in 39,134 individuals (offspring of 810 females and 515 males), specifically the logarithm-transformed variance (LnVar). The heritability estimate for the resilience indicator (LnVar) was low (0.09 ± 0.03) but statistically significant. The genetic correlations between LnVar and body weight (BW) and total length (TL) were moderate and positive (0.33 ± 0.04 and 0.18 ± 0.01, respectively), whereas those between LnVar and body and carapace widths were negative (-0.28 to -0.32). The correlated response of the resilience indicator (LnVar) to selection for high growth was low but favourable, averaging 0.77%-2.89% over eight generations, or only 0.002 and 0.006 phenotypic and genetic standard deviation units, respectively. In conclusion, this study demonstrates the presence of heritable genetic variation in the resilience indicator derived from BW deviations in the giant freshwater prawn. Selection for high body weight has slightly improved resilience in this species, highlighting the potential to enhance resilience through selective breeding, albeit at a slow rate.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149139169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimates of Genetic Parameters for Ewe Longevity and Lifetime Reproductive Performance Traits in South African Merino Sheep.","authors":"Luis Fernando Batista Pinto, Carina Visser, Artur O Rocha, Jackeline Santos Alves, Luiz F Brito","doi":"10.1111/jbg.70082","DOIUrl":"https://doi.org/10.1111/jbg.70082","url":null,"abstract":"<p><p>Ewe's functional longevity impacts flock profitability by reducing annual ewe replacement costs and increasing ewe outputs over the production cycle. In this context, the main objective of this study was to estimate variance components and genetic parameters of five ewe longevity indicators in South African Merino sheep. The traits evaluated included age at the last lambing (ALL), length of productive life (PL, measured as the number of days between the first and last lambing records), total number of litters (TNL), total number of lambs born (TLB) and total number of lambs weaned (TLW). These traits were recorded on a population of 39,011 ewes. Ewe's own birth type (singletons, twins, or triplets), the concatenated effect of birth flock-year and age at first lambing (3 classes: < 710, 710-743, 744-1095 days) were the fixed effects fitted in the animal models, while the animal and contemporary group (birth flock-year-season) were fitted as random effects. Variance components were estimated based on the Restricted Maximum Likelihood method implemented in the BLUPF90+ family of programmes. The sample size and mean (standard deviation) were 38,929 ewes and 1452.1 (559.3) days for ALL; 30,714 ewes and 918.9 (456.5) days for PL; 38,795 ewes and 2.98 (1.51) litters for TNL; 38,842 ewes and 4.26 (2.49) lambs born for TNB; and 19,322 ewes and 3.87 (2.39) lambs weaned for TNW. The heritability estimates were: 0.061 ± 0.0074 (ALL), 0.051 ± 0.0082 (PL), 0.061 ± 0.0073 (TNL), 0.059 ± 0.0072 (TNB) and 0.058 ± 0.0098 (TNW). The genetic correlation estimates ranged from 0.73 ± 0.056 (PL × TNW) to 0.99 ± 0.0023 (ALL × PL), while phenotypic correlation ranged from 0.82 ± 0.0019 (PL × TNB) to 0.99 ± 0.0001 (ALL × PL). Parents of ewes with phenotypic records had estimated breeding value average accuracy above 0.30 for all traits. Positive genetic trends were found for all traits, suggesting genetic gains per year of 0.34 days in ALL, 0.27 days in PL, 0.0082 litters in TNL, 0.0022 lambs born in TNB and 0.002 lambs weaned in TNW. Given similar heritability estimates and high genetic correlation among the traits, TNW is recommended as a selection criterion to improve Merino longevity, as this trait could improve both ewe longevity and reproductive performance.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149149111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Correlations Between Fleece Shedding and Production Traits Indicate Minimal Trade-Offs When Breeding for Maternal Shedding Sheep.","authors":"Erin G Smith, John R Keiller, Matt P Kelly, Daniel J Brown, Samuel F Walkom","doi":"10.1111/jbg.70081","DOIUrl":"https://doi.org/10.1111/jbg.70081","url":null,"abstract":"<p><p>Fleece shedding is becoming an increasingly important trait in sheep production systems focused on meat and dairy, where wool has limited economic value and reducing shearing costs is desirable. For inclusion in breeding programmes, a trait must exhibit genetic variation, sufficient heritability, and have well-defined relationships with other economically important traits, as well as economic or desired value. The aim of this study was to estimate the genetic and phenotypic correlations between fleece shedding, recorded in both lambs and adult ewes, and key production traits currently included in the Australian national genetic evaluation for maternal sheep. Using these relationships, the implications of incorporating fleece shedding into a within-flock maternal sheep breeding objective were also examined through desired gains indexes. Genetic correlations between shedding and body weight, carcase, and most visual traits were generally low, indicating limited biological constraints to simultaneous improvement. In contrast, favourable genetic relationships were observed between shedding and parasite resistance, fleece traits such as greasy fleece weight, fibre diameter, and staple strength. Reproductive traits were associated with weak but significant antagonistic genetic correlations with shedding, with phenotypic correlations also indicating that highly productive ewes tended to shed less. Under the base index (regular index with no emphasis on shedding), genetic progress in shedding was minimal, indicating that explicit inclusion of direct emphasis on shedding is required to achieve meaningful improvement. Within-flock selection index simulations demonstrated that low to moderate (desired improvement of 0.33 to 0.66 of a shedding score in 10 years) inclusion of shedding could be achieved with minimal impact on gains in production traits over a 10-year horizon. However, higher levels of emphasis (> 1 shedding score improvement) on shedding resulted in reduced responses in reproductive traits and increased mature weight, alongside diminishing economic returns. These results demonstrate that fleece shedding can be incorporated into multi-trait breeding programmes with limited trade-offs at moderate levels of selection pressure. However, higher levels of emphasis introduced important biological and economic trade-offs. The findings highlight the importance of balanced breeding objectives to ensure that improvements in fleece shedding do not compromise overall productivity.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149139262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing Runs of Homozygosity and Inbreeding in American Mink Using SNP Data and Pedigree Information.","authors":"Persia Carol Thapa, Duy Ngoc Do, Pourya Davoudi, Ghader Manafiazar, Younes Miar","doi":"10.1111/jbg.70079","DOIUrl":"https://doi.org/10.1111/jbg.70079","url":null,"abstract":"<p><p>Inbreeding increases the likelihood of deleterious recessive alleles becoming homozygous and consequently affecting economically important traits. Runs of homozygosity (ROH), the continuous homozygous segments of the genome and the higher than expected homozygosity (HOM) are genomic indicators of inbreeding, quantified as F_ROH and F_HOM, respectively. Previous ROH analyses in American mink (Neogale vison) were restricted to scaffold-level references and could not resolve long autozygous segments. In this study, we characterized ROH in 1413 mink genotyped with the Affymetrix Mink 70K panel (50,902 autosomal SNPs after quality control) on the chromosome-level genome assembly and compared F_ROH with F_HOM and with pedigree-based inbreeding (F_PED) derived from 24,633 pedigree records. ROH were detected in all individuals, with a mean of 149.61 ± 13.82 segments per individual. Segments longer than 8 Mb, not detectable in earlier studies of this population, represented 12.86% of all ROH and accounted for 0.10 of the mean F_ROH of 0.28. Mean F_HOM and F_PED were -0.03 and 0.02, respectively. ROH were unevenly distributed across chromosomes and chromosomes 1, 2, 3, 4, 6 and 11 harboured 78.59% of all segments. The Pearson correlation coefficient was highest (0.72) between F_ROH and F_HOM and moderate (0.34) between genomic inbreeding and F_PED, increasing with ROH length to 0.35 for segments longer than 16 Mb. Because the density of the marker panel limits the resolution of short segments, quantitative inference was restricted to ROH longer than 4 Mb. Our results indicate that recent autozygosity in this closed population is concentrated in a small number of long genomic segments, providing an opportunity to inform mating decisions.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149139155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Control of Canalization for Twinning Rates in Polypay and Rambouillet Sheep Using Threshold or Double Hierarchical Generalized Linear Models","authors":"Carrie S. Wilson,&nbsp;J. Bret Taylor,&nbsp;Luiz F. Brito","doi":"10.1111/jbg.70060","DOIUrl":"10.1111/jbg.70060","url":null,"abstract":"&lt;p&gt;In most sheep production systems, the ideal scenario is for every ewe to lamb and successfully raise twins. However, selection for increased number of lambs born (NLB) is often accompanied by a higher incidence of triplet and higher-order births, which increases management challenges and producer reluctance to intensify selection for this trait. Therefore, there is a need to identify animals who not only exhibit a high twinning rate, but also canalized reproductive performance, characterized by consistent expression of twin births and reduced variability toward extreme litter sizes. In this context, the double hierarchical generalized linear model (DHGLM) provides a mechanism to evaluate both the mean and the dispersion components of a trait, enabling the evaluation of the heteroskedastic residual variance for each animal, and thereby select animals with lower residual variances. Therefore, the main objectives of this study were to estimate (co)variance components and genetic parameters for the mean and dispersion traits related to number of lambs born and twinning rate and to develop a strategy to identify rams whose daughters consistently produce twins. Data from the US Sheep Experiment Station (USSES; Dubois, ID, USA) Polypay flock recorded from 1999 to 2025 included 8061 litters (3115 dams; 293 sires) and the Rambouillet flock included 5948 litters (2333 dams; 228 sires) recorded from 2005 to 2025. The proportion of twin litters have significantly decreased in the Polypay flock while remaining unchanged (&lt;i&gt;p&lt;/i&gt; = 0.13) in the Rambouillet flock. For both breeds, the proportion of single lamb litters have decreased while triplets have increased. For sires with a minimum of 15 daughter litters, the average litter size was 1.53 ± 0.55 for 1-year-old ewes and 2.29 ± 0.75 for mature ewes for the Polypay and 1.24 ± 0.43 for 1-year-old ewes and 1.93 ± 0.64 for mature ewes for the Rambouillet. A DHGLM was used to estimate both the mean and dispersion of the NLB3 considering 3 classes (1, 2 or 3+) and NLB for all classes (1 to 5 for Polypay and 1 to 4 for Rambouillet) traits using the DHGLMF90 package. A bivariate animal model was fitted each for NLB3 and NLB, and their associated dispersions (vNLB3 and vNLB) with contemporary group as a concatenation of ewe age category and birth year fitted as a categorical fixed effect and animal (ewe), permanent environment, and the residual as random effects for a model including data from all ewes (ALL) and excluding phenotypic records from 1-year-old ewes (MATURE). The same mean traits and twinning (TWIN; 1 for non-twins and 2 for twins) were evaluated using a threshold model with the THRGIBBSF90 package. Heritability estimates ranged from 0.024 ± 0.012 for vNLB3 analysed using the DHGLM model to 0.110 ± 0.020 for NLB3 analysed using the threshold model for the ALL Polypay dataset and from 0.016 ± 0.014 for vNLB3 analysed using the DHGLM model to 0.094 ± 0.022 for NLB3 analysed using the threshold model for","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 6","pages":"807-820"},"PeriodicalIF":1.9,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.70060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Evaluation of Growth Rate and Kleiber's Ratio Traits in Deccani Sheep Using Bayesian Inference","authors":"Yogesh B. Kandalkar,&nbsp;Nitin Eknath Gade,&nbsp;Ravindra G. Nimase","doi":"10.1111/jbg.70057","DOIUrl":"10.1111/jbg.70057","url":null,"abstract":"<div>\u0000 \u0000 <p>The present study aimed to estimate the contributions of direct additive and maternal genetic effects on growth rate and Kleiber's ratio traits in Deccani sheep. Data from 2590 lambs born between 2011 and 2020 at the ICAR–Network Project on Sheep (Deccani) Improvement, Maharashtra, India, were utilised. Growth traits were assessed as average daily gain from birth to weaning (ADG1), weaning to 6 months (ADG2), and 6 to 12 months of age (ADG3), along with the corresponding Kleiber's ratios (KR1, KR2, and KR3). Bayesian inference was employed to estimate (co)variance components and genetic parameters by fitting animal models that included direct additive and maternal genetic effects, as well as significant fixed effects, using BLUPF90 programs. Estimates of direct heritability for ADG1, ADG2, ADG3, KR1, KR2, and KR3 were 0.07 ± 0.04, 0.05 ± 0.03, 0.08 ± 0.07, 0.03 ± 0.01, 0.04 ± 0.01, and 0.12 ± 0.06, respectively. Maternal genetic and permanent environmental effects accounted for up to 9% and 4% of the total phenotypic variance in the studied traits. A negative genetic correlation between direct additive and maternal genetic effects indicated an antagonistic relationship, whereas positive genetic correlations were observed among the growth and Kleiber's ratio traits. The study results suggested that although additive genetic variation for these traits is low, incorporating maternal effects in selection strategies could enhance growth performance in Deccani sheep populations.</p>\u0000 </div>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 6","pages":"737-745"},"PeriodicalIF":1.9,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148207068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of Estimating Genetic Variance in the Target Group on Reliability Metrics of the Linear Regression Validation Method Under Selection","authors":"Alan M. Pardo,&nbsp;Daniel O. Maizón,&nbsp;Sebastián Munilla,&nbsp;Andrés Legarra","doi":"10.1111/jbg.70059","DOIUrl":"10.1111/jbg.70059","url":null,"abstract":"<div>\u0000 \u0000 <p>The Linear Regression (LR) method is a validation approach based on comparing predictions from partial and whole data for a predefined target group (or focal group, in the LR sense). Reliability metrics derived from this comparison depend critically on the additive genetic variance of that group. However, this variance often differs from the base population because of selection, drift, and changes in relatedness, raising practical questions about how its estimation affects LR-based reliability metrics. We simulated a beef cattle population under two contrasting selection schemes (phenotypic and EBV-based), defined two focal groups with contrasting selection status (selected sires and unselected females), and evaluated three strategies for estimating focal-group variance: (i) an empirical MCMC estimator (VarEst-eMCMC), (ii) a closed-form estimator (VarEst-CF), and (iii) an inbreeding-adjusted base variance (VarF). Both VarEst-eMCMC and VarEst-CF recovered the true focal-group additive genetic variance in both focal groups, with estimates close to simulated values in sires (phenotypic: 0.202; EBV: 0.157–0.158 vs. 0.153) and small deviations in unselected females (0.262 vs. 0.256 under phenotypic selection; 0.247 vs. 0.237 under EBV-based selection). In selected sires, VarF consistently overestimated the focal-group genetic variance, by about 40% under phenotypic selection (0.289 vs. 0.202) and more than 80% under EBV-based selection (0.282 vs. 0.153). In unselected females, the overestimation was more moderate (20%). These findings directly relate to LR metrics. In sires under EBV-based selection, LR reliabilities computed using VarEst-CF and VarEst-eMCMC remained close to simulated values for selected and unselected individuals (0.079 vs. 0.091; 0.508 vs. 0.538), whereas VarF-based estimates were markedly underestimated (0.044 and 0.084, respectively). A similar pattern was observed under phenotypic selection. In females, LR reliabilities calculated with VarEst-CF and VarEst-eMCMC also remained close to the simulated values, whereas those calculated with VarF were slightly underestimated. Overall, these findings confirm that properly estimating focal-group additive genetic variance under selection is essential for meaningful LR metrics. We also provided the first implementation of the closed-form estimator as a practical alternative for routine LR-based validation.</p>\u0000 </div>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 6","pages":"762-773"},"PeriodicalIF":1.9,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148280099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}