Journal of Animal Breeding and Genetics最新文献

{"title":"Unravelling the Genetic Mechanisms of Litter Traits in a Maternal Line of Pigs","authors":"Guilherme Oselame,&nbsp;Suelen Fernandes Padilha,&nbsp;Maurício Egídio Cantão,&nbsp;Jane de Oliveira Peixoto,&nbsp;Aline Zampar,&nbsp;Adriana Mércia Guaratini Ibelli,&nbsp;Luis Orlando Duitama Carreño,&nbsp;Jader Silva Lopes,&nbsp;Pedro Henrique Ferreira Freitas,&nbsp;Marcelo Silva Freitas,&nbsp;Mônica Corrêa Ledur","doi":"10.1111/jbg.70042","DOIUrl":"10.1111/jbg.70042","url":null,"abstract":"<p>Reproductive traits related to litter size are the main indicators of reproductive efficiency in pig production and are continuously evaluated for the selection of maternal lines. Several environmental and genetic factors are involved with the development of these traits. Genome-wide association studies (GWAS) allow a better understanding of the genetic control of complex traits, especially those with low heritability (<i>h</i>²). Therefore, this study aims to estimate the genetic parameters and to identify genomic regions and candidate genes associated with total number born (TNB), number born alive (NBA), and viable piglets at Day 5 (PV5) in a Large White female line. For this, 17,011 phenotypic records, 190,000 pedigree records, and 4366 animals genotyped with the Illumina 50 K and 80 K panels were used. Estimates of <i>h</i>², genetic (<i>r</i>_<i>g</i>) and phenotypic (<i>r</i>_<i>p</i>) correlations, and GWAS were performed with the BLUPF90 family programs. Positional candidate genes, their main biological processes, and networks were investigated using the Ensembl database and the BioMart, PANTHERdb, and STRING tools. The studied traits presented low <i>h</i>² estimates, but with high and positive <i>r</i>_<i>g</i> and <i>r</i>_<i>p</i>. In the GWAS, 14 significant genomic windows were identified for TNB, 10 for NBA, and 15 for PV5. These regions include 157 genes for TNB, 101 for NBA, and 140 for PV5, mapped across 10 different chromosomes. Among the genes located in those regions, the <i>ESR1, THRB, SLIT2</i>, and <i>ZBTB2</i> were common to the three traits and are involved in processes of hormonal regulation, embryogenesis, immunity, and homeostasis. Moreover, 12 of those genes were new positional candidates for TNB, NBA, or PV5. Among them, we highlight the <i>FSTL4</i>, <i>PAPPA</i>, and <i>TCF7</i> genes associated with PV5, which are involved with hormonal regulation, growth factors, and immunity, respectively. The <i>SLIT2</i>, <i>MTHFD1L</i>, <i>OVOL2</i>, <i>SHB</i>, and <i>EXOSC3</i> genes, involved with embryogenesis and neurogenesis, were associated with TNB and NBA. Furthermore, uncharacterized genes, such as <i>ENSSSCG00000058091</i>, related to mitochondrial homeostasis, were associated with TNB, while <i>ENSSSCG00000040472</i>, related to protein synthesis, was identified for PV5. These new findings reveal common and exclusive genetic mechanisms that may influence important litter traits in pigs, helping the development of breeding strategies to optimise reproductive efficiency.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 4","pages":"560-580"},"PeriodicalIF":1.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.70042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146167574","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":"Estimation of Genetic Parameters for Reproductive Traits in Murciano–Granadina Dairy Goats","authors":"Jamshid Ehsaninia,&nbsp;Mohammad Bagher Zandi,&nbsp;Moein Taned,&nbsp;Alireza Bagheripour","doi":"10.1111/jbg.70041","DOIUrl":"10.1111/jbg.70041","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;The primary objective of this study was to estimate the variance and covariance components, genetic parameters, and genetic trends for key reproductive traits in Murciano–Granadina (MG) dairy goats reared under Iranian breeding conditions. Data were collected over 6 years (2016–2021) from a commercial dairy goat farm located in the Chahshahi region of Kerman Province, southern Iran. The analysed reproductive traits included age at first service (AFS), age at first kidding (AFK), kidding interval (KI), gestation length (GL), service period (SP) and dry period (DP). The dataset comprised 7573 animals with detailed pedigree information involving 337 sires and 3772 dams. The flock was reared under standardised nutritional and management conditions within an intensive breeding system, ensuring optimal conditions for reliable genetic parameter estimation. Variance component and genetic parameters were estimated by Bayesian inference fitting a univariate animal model using the GIBBS1F90 program. Direct heritability estimates (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;h&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) ranged from low to moderate, with GL showing the highest &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;h&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; (0.23 ± 0.03), followed by DP (0.12 ± 0.05), AFK and AFS (both 0.12 ± 0.03). KI had a low &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;h&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; of 0.10 ± 0.02, while SP showed the lowest estimate (0.007 ± 0.001), suggesting stronger environmental and management influences on this trait. Repeatability was moderate for GL (0.45 ± 0.06) and DP (0.19 ± 0.04), but low for SP (0.04 ± 0.01), reflecting variable trait consistency across parities. Genetic and phenotypic trend analyses revealed minimal, statistically non-significant (&lt;i&gt;p&lt;/i&gt; &gt; 0.05) fluctuations in all reproductive traits. The study demonstrates that reproductive traits in Murciano–Granadina goats under Iranian breeding conditions exhibit low to moderate &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msubsup&gt;\u0000 &lt;mi&gt;h&lt;/mi&gt;\u0000 &lt;mi&gt;a&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msubsup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, yet maintain sufficient additive genetic variance to allow for potential genetic improvement through selection.","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 4","pages":"581-594"},"PeriodicalIF":1.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146196112","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":"Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed","authors":"N. Mejuto-Vázquez,&nbsp;C. Hervás-Rivero,&nbsp;R. Rodríguez-Bermúdez,&nbsp;D. López-Carbonell,&nbsp;M. Hermida,&nbsp;P. Martínez,&nbsp;L. Varona","doi":"10.1111/jbg.70034","DOIUrl":"10.1111/jbg.70034","url":null,"abstract":"<p>In autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using ~63,000 SNPs to assess inbreeding depression in four key traits: age at first calving (AFC) with 3503 records, calving interval (CI) with 3315 records, birth weight (BW) with 4878 records and weight at 210 days (W210) with 3285 records. Runs of homozygosity were sorted by length ([1,2], (2,4], (4,8], (8,16], &gt; 16 Mb), and the corresponding inbreeding coefficients (<i>F</i>_ROH&gt;1, <i>F</i>_ROH&gt;2, <i>F</i>_ROH&gt;4, <i>F</i>_ROH&gt;8, <i>F</i>_ROH&gt;16) were calculated using the <i>consecutiveRUNs</i> R package. A Genomic BLUP (GBLUP) was conducted for each <i>F</i>_ROH estimate using the <i>BLUPF90+</i> programs. The results revealed significant inbreeding depression for AFC and CI, whereas W210 and BW exhibited similar inbreeding trends, but the effects of inbreeding on these traits were not statistically significant. To further explore the genetic basis of inbreeding depression, SNPs located within ROHs were tested, though a <i>t</i>-test, for their association with phenotypic traits. Genes located in significant regions (−log(<i>p</i>-value) &gt; 3 from <i>t</i>-test) were annotated using Ensembl BioMart within a ± 0.5 Mb window. Recent inbreeding (ROH &gt; 8 Mb) showed significant negative effects on reproductive traits, and key genomic regions—particularly on chromosome 2 involving <i>MSTN</i>, <i>NAB1</i>, and <i>COL5A2</i>—were linked to increased AFC and reduced BW and W210; ROH-based inbreeding estimates proved effective in detecting inbreeding depression in this native breed. Overall, ROH-based analyses revealed genomic regions and candidate genes, notably <i>MSTN</i>, contributing to inbreeding depression and key production traits in Rubia Galega cattle.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 4","pages":"508-523"},"PeriodicalIF":1.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.70034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145764036","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":"Is There a Genetic Link Between Resting Infrared Thermography in Young Horses and Longevity in Jumping Competition?","authors":"Anne Ricard,&nbsp;Séverine Deretz,&nbsp;Cathy Menard,&nbsp;Bernard Dumont Saint Priest","doi":"10.1111/jbg.70038","DOIUrl":"10.1111/jbg.70038","url":null,"abstract":"<p>The objective was to evaluate the genetic relationship between the surface temperature of regions of interest, measured using infrared images of young horses and functional longevity in jumping. This relationship was assessed by comparing the temperatures measured in the offspring of two groups of sires, one favourable and one unfavourable, to longevity. The study used a specific data collection protocol on a sample of 921 young progeny, before they began competing, of 141 extreme stallions, comprising 61 favourable and 80 unfavourable sires. These stallions had been selected based on estimated breeding values for functional longevity derived from official competition data of 202,320 horses. Infrared imaging provided 49 temperature variables, including average and maximum values for regions of interest such as temperature differences from the body for eyes, hocks, fetlocks, feet, carpi and back. It also included differentials between these regions, asymmetry between right and left sides and variability within each area. Heritability was estimated using a mixed model with fixed effects, of age, sex, coat colour, weight and visit, along with random genetic effects (considering a pedigree of 8002 horses). The effect of temperature on the group of sires was assessed using multivariate partial least squares logistic regression, adjusting temperature for fixed effects. Results indicated high heritability for the temperature of regions of interest: body (0.53 ± 0.14), carpi (0.55 ± 0.19), fetlocks (0.47 ± 0.12), feet (0.46 ± 0.12 and 0.38 ± 0.12). Lower heritability was observed for differences between regions (around 0.20) and even lower for asymmetry and variability. Lower average and maximum eye temperatures, lateral asymmetry in hind feet temperature and temperature variability in the back were associated with a higher probability of belonging to the favourable group of sires for functional longevity. Infrared imaging may be a tool for identifying easily measurable selection criteria associated with longevity. Given the limited number of horses, the limited number of significant variables associated with the group of sires and the specificity of the protocol, verification and validation studies are necessary before its use.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 4","pages":"481-495"},"PeriodicalIF":1.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.70038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145710252","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 Parameters of Methane Emission, Feed Efficiency, Feeding Behaviour, and Growth Traits in Beef Cattle","authors":"J. A. Silva,&nbsp;J. P. S. Valente,&nbsp;L. F. M. Mota,&nbsp;G. R. D. Rodrigues,&nbsp;T. L. S. Soares,&nbsp;J. O. S. Marcatto,&nbsp;A. M. Pelaez,&nbsp;F. M. Monteiro,&nbsp;R. C. Canesin,&nbsp;L. G. Albuquerque,&nbsp;M. E. Z. Mercadante","doi":"10.1111/jbg.70037","DOIUrl":"10.1111/jbg.70037","url":null,"abstract":"<p>Climate change has intensified the need to reduce greenhouse gas emissions, particularly methane (CH₄) from enteric fermentation. Genetic selection has emerged as a promising mitigation strategy; however, studies on <i>Bos taurus indicus</i>, especially Nellore cattle, remain limited. This study aimed to estimate heritabilities and genetic correlations for CH₄ emission traits and their relationships with feeding behaviour, feed efficiency, and performance, as well as to evaluate the direct and correlated responses to selection for lower CH₄ emissions. Data were from 2418 Nellore cattle evaluated in feed efficiency trials. Traits included dry matter intake (DMI), feeding time per day (FTd), feed events per day (FEd), and feeding rate (FR), residual feed intake (RFI), average daily gain (ADG), and mid-test body weight (MBW). Methane emissions were measured in 1153 animals using the SF₆ tracer technique, providing daily CH₄ emission (g/day), CH₄ per unit of DMI (CH₄DMI, g/day), and residual CH₄ (CH₄res). Variance components were estimated using the single-step genomic BLUP (ssGBLUP) method through Bayesian inference. Heritability estimates were moderate for CH₄ (0.25), CH₄DMI (0.14), CH₄res (0.14), and performance traits such as DMI (0.35), ADG (0.36), and MBW (0.40). Higher estimates were observed for feeding behaviour traits FTd (0.49) and FR (0.42). Genetic correlations between CH₄ and production traits were high, particularly with DMI (0.79), ADG (0.90), and MBW (0.91), indicating that selection for reduced CH₄ emissions may affect growth. Direct selection for CH₄ led to a modest annual reduction in emissions but also a correlated decline in MBW. These results demonstrate that while CH₄ emissions are heritable, their strong genetic association with productivity traits indicates that isolated selection for reduced emissions may lead to undesirable outcomes in feed intake and performance. Therefore, strategies aiming to reduce CH₄ emissions should consider the genetic relationships with growth and efficiency traits to avoid compromising animal productivity.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 4","pages":"496-507"},"PeriodicalIF":1.9,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.70037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745838","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":"Impact of Model Parameterisation and Variance Component Estimates on Genomic Predictions of Carcass Traits in Montana Composite Cattle","authors":"Caroline Assis Almeida,&nbsp;Felipe Eguti de Carvalho,&nbsp;Flávia Cristina Bis,&nbsp;Rachel Santos Bueno Carvalho,&nbsp;Elisângela Chicaroni de Mattos,&nbsp;Rafael Espigolan,&nbsp;Joanir Pereira Eler,&nbsp;Luís Telo da Gama,&nbsp;Fernando Baldi,&nbsp;José Bento Sterman Ferraz","doi":"10.1111/jbg.70032","DOIUrl":"10.1111/jbg.70032","url":null,"abstract":"<p>This study evaluated the influence of variance component (VC) estimates, obtained from different models and two relationship matrices, pedigree-based (BLUP) and genomic information-based (ssGBLUP), on genomic predictions of carcass traits in Montana composite cattle. Phenotypic records from 14,422 animals were analysed for ribeye area, rump fat thickness, backfat thickness and marbling, along with pedigree information from 193,129 animals and genomic data from 3911 animals genotyped with 49,457 SNPs. Variance components and heritability estimates were calculated using restricted maximum likelihood under single-trait linear models. Across five models (M1–M5), fixed effects included contemporary group, embryo transfer, age at ultrasound and cow age at calving, while random effects included direct genetic effect and residual. From model M2 onwards, biological type, heterosis and both combined and specific recombination effects were also considered. The Akaike information criterion (AIC) was used to identify the best-fitting model. Different VC estimates were applied in ssGBLUP predictions to evaluate predictive ability based on accuracy, bias and dispersion. Variance component and heritability estimates were similar between methods, although ssGBLUP yielded higher direct additive genetic variances and heritabilities. More parameterised models using ssGBLUP provided a better fit according to AIC. However, less parameterised models showed superior predictive ability, regardless of whether VCs were estimated by BLUP or ssGBLUP. When comparing predictive ability across sources, pedigree-based VC estimates resulted in more accurate predictions. Thus, the choice of model complexity should be guided by the analysis objective and the available data structure.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 3","pages":"431-442"},"PeriodicalIF":1.9,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13054125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589584","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 Beef Sires Using a Beef-on-Dairy Crossbred Reference Population","authors":"Julius Mugambe,&nbsp;Christin Schmidtmann,&nbsp;Jorge Hidalgo,&nbsp;Rana Ahmed,&nbsp;Georg Thaller","doi":"10.1111/jbg.70030","DOIUrl":"10.1111/jbg.70030","url":null,"abstract":"<p>In recent years, Beef-on-Dairy (BoD) crossbreeding programs have gained momentum to enhance dairy cattle's economic and genetic merits while meeting the demand for high-quality beef. However, bulls with superior growth potential can lead to calving problems; thus, Holstein dairy farmers must decide which semen to use to avoid calving problems while producing heavier BoD calves. In this study, our objective was to genetically evaluate beef sires using a BoD crossbred reference population for three major economic traits, i.e., gestation length (GL), birth weight (BW), and calving ease (CE). A population comprising 4420 BoD calves sired by bulls from Angus (ANG), Limousin (LIM), Wagyu (WAG), and White-Belgian Blue (WBB) was used to perform a joint genetic evaluation of the sire for traits. Univariate and bivariate (linear-linear or threshold-linear) models were applied to estimate variance components and genomic breeding values using single-step methods. Estimates from CE models were transformed from the liability to the observable scale for more straightforward interpretation. Direct heritabilities for GL, BW, and CE (after transformations) ranged from 0.33 to 0.35, 0.33 to 0.37, and 0.02 to 0.14, respectively, while maternal heritabilities ranged from 0.11 to 0.17 for all traits. Generally, male BoD calves had higher probabilities for calving difficulty, with calvings being more difficult if sired by LIM (13%) as compared to ANG (7%) and WBB (9%) when considering male calves. The bivariate models outperformed the univariate models. For CE, the accuracy of predictions was up by 95% with a reduction in bias and dispersion. WBB sires were preferred when crossing with higher parity cows compared to ANG sires. These findings demonstrate that a well-structured BoD reference population enables accurate genomic evaluation of beef sires, facilitating the selection of sires that produce economically viable calves with reduced calving difficulties.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 3","pages":"390-402"},"PeriodicalIF":1.9,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13054129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145524760","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":"Application of Genomic Random Regression Models for Genetic Parameter Estimations of Female Fertility Traits in Different Parities in German Holsteins","authors":"Sina Sakhaei-far,&nbsp;Tong Yin,&nbsp;Sven König","doi":"10.1111/jbg.70027","DOIUrl":"10.1111/jbg.70027","url":null,"abstract":"&lt;p&gt;The aim of the present study was to infer genetic (co) variance components and to estimate parity-specific breeding values for the female fertility traits non-return rate after 56 days, the interval from calving to first service and days open by applying random regression models on a time-dependent parity scale. In this regard, we considered a female fertility dataset comprising 592,829 records on 190,269 German Holstein cows and heifers kept in 45 large-scale dairy contract herds. From a subset of 21,316 cattle with phenotypic records, (imputed) 50 K genotypes were available. The applied genomic random regression model considered Legendre polynomials of order 2 for the additive-genetic effects along the parity scale, and combined pedigree and genomic relationships through the &lt;b&gt;H&lt;/b&gt;-matrix. Results were compared with genetic parameter estimates from a multiple-trait model, considering the same fertility trait in different parities as different traits. From both modelling approaches, we observed the trend of increasing genetic variances and heritabilities with increasing parity. Especially for the non-return rate, the genetic variance in heifers was substantially smaller than in all parities of cows. With regard to the random regression model, genetic correlations between the same fertility traits from adjacent parities were close to 1, but gradually declined with increasing parity distances. Small genetic correlations were also estimated between non-return rates in heifers with non-return rates in all cow parities, i.e., 0.50 with parity 1, 0.44 with parity 2, 0.41 with parity 3, 0.35 with parity 4, 0.33 with parity 5, and 0.25 with parity 6. A similar pattern for genetic correlations in the same traits across parities was confirmed from the multiple-trait model application. Estimated breeding values for all fertility traits in different parities of sires with at least 10 phenotyped daughters per trait (estimates from the random regression model) were correlated with their official breeding indexes from the national genetic evaluation. In this regard, moderate differences were observed when comparing breeding value correlations for non-return rates in heifers with respective correlations in all cow parities. From a practical breeding perspective, the most important results were the rather small genetic correlations for the same traits in different parities (e.g., 0.24 between calving to first service in parities 1 and 6), and differing breeding value correlations with other breeding indexes in different parities. These findings suggest the implementation of specific genetic evaluations for specific cow parities, as an extension to the existing separation between heifer and cow fertility traits. Parity-specific breeding value correlations from the random regression and the multiple-trait model considering the sires with at least 10 daughters were larger than 0.85, suggesting only minor re-rankings of sires from the two different modeling app","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 3","pages":"377-389"},"PeriodicalIF":1.9,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13054121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145514535","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 Parameter Estimation for Plasma Biomarkers Associated With Energy Reserves During Critical Physiological Stages in Sheep","authors":"Agnes Nyamiel,&nbsp;Andres Legarra,&nbsp;Didier Marcon,&nbsp;Christian Durand,&nbsp;Sébastien Douls,&nbsp;Gaetan Bonnafe,&nbsp;Anne Tesnière,&nbsp;Eliel González-García,&nbsp;Dominique Hazard","doi":"10.1111/jbg.70028","DOIUrl":"10.1111/jbg.70028","url":null,"abstract":"<p>The ability of ruminants to mobilise and restore body reserves (BR) over time, referred to as BR dynamics, is currently considered an interesting biological component to be included in breeding programs targeting enhanced BR resilience. However, genetic studies of proxies for BR levels and BRD remain scarce, particularly in small ruminants. The aim of this study was to estimate the genetic parameters for key plasma biomarker concentrations in sheep at critical physiological stages (PhySt i.e., mating; mid-pregnancy, before-lambing, after-lambing, and weaning), and their changes over time. Non-esterified fatty acids (NEFA), β-hydroxybutyrate (BHB), triiodothyronine (T3) and insulin (INS) were monitored at those PhySt in successive production cycles. A total of 659 productive Romane ewes were phenotyped for one (<i>n</i> = 252, multiparous) or two (<i>n</i> = 407, primiparous and multiparous) cycles. BR mobilisation was observed from the second half of pregnancy and during suckling while BR accretion was more evident from weaning until the next mid-pregnancy. Considering biomarkers concentrations as repeated measurements through the whole production cycle, heritability estimates were 0.07, 0.09, 0.15, and 0.10 for NEFA, BHB, T3, and INS, respectively. Heritability estimates for plasma biomarkers at key PhySt ranged from 0.08 to 0.16 for NEFA, 0.07 to 0.12 for BHB, 0.09 to 0.18 for T3, and 0.04 to 0.15 for INS. Heritability estimates for biomarker changes over time ranged from 0.01 to 0.23. Genetic correlation estimates between different PhySt were positive for each plasma biomarker and ranged from 0.19 to 0.87 for NEFA, from 0.50 to 0.89 for BHB, from 0.54 to 0.95 for T3 and from 0.34 to 0.90 for INS. Most genetic correlation estimates between biomarkers at a given PhySt were generally low to moderate (<i>r</i>_<i>g</i> = −0.52 to 0.59), with few showing strong negative or positive values beyond 0.60 in magnitude. Considering changes over time, correlations were similarly low to moderate (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>r</mi>\u0000 <mi>g</mi>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> = −0.59 to 0.53), with only a few estimates reaching high values (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>r</mi>\u0000 <mi>g</mi>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> = −0.60 to −0.97 and 0.67 to 0.97). This study demonstrates that blood biomarkers related to energy BR have genetic variation, indicating their potential for implementation in sheep breeding programs aimed at improving BR use and build-up.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 3","pages":"443-456"},"PeriodicalIF":1.9,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13054124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145643179","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":"The Changes in Genetic Parameters and Genomic Selection of Lambing Rate in Hu Sheep Following Marker-Assisted Selection","authors":"Yuan Zhao,&nbsp;XiaoXue Zhang,&nbsp;FaDi Li,&nbsp;Huibin Tian,&nbsp;DeYin Zhang,&nbsp;Xiaolong Li,&nbsp;YuKun Zhang,&nbsp;JiangBo Cheng,&nbsp;ZongWu Ma,&nbsp;ChangChun Lin,&nbsp;XiWen Zeng,&nbsp;LiMing Zhao,&nbsp;WeiMin Wang","doi":"10.1111/jbg.70036","DOIUrl":"10.1111/jbg.70036","url":null,"abstract":"<div>\u0000 \u0000 <p>The identification of quantitative trait locus (QTL) or genes responsible for key agronomic traits has significantly enhanced genetic improvement through marker-assisted selection (MAS). However, the impacts of MAS on genetic parameters and subsequent selection processes have not been thoroughly characterised. Here, through genome-wide selective sweep analysis, we identified a diverse set of genes involved in oocyte meiosis, including <i>PPP3CA</i>, <i>AR</i>, <i>PPP1CB</i>, <i>SPDYA</i>, <i>MAD1L1</i>, and <i>BMPR1B</i>. The genome-wide association study (GWAS) further identified three genes <i>UNC5C</i>, <i>BMPR1B</i>, and <i>PDLIM5</i> as being associated with lambing rate in Hu sheep. From these analyses, the <i>FecB</i> loci emerged as a potential molecular marker for lambing rate. with an increase of 0.5 lambs per G allele. The heritability of the lambing rate was estimated to be 0.19 (±0.02). Moreover, based on 10-fold cross-validation, the accuracy of genomic selection (GS) was found to be 0.30. Simulated MAS resulted in a reduction of the additive genetic variance components, with estimated heritability dropping to 0.14 (±0.02) and GS accuracy decreasing to 0.18—representing a decline of 26.42% and 34.81%, respectively. To address the reduced GS accuracy, we performed GWAS on the reference set to identify weighted single nucleotide polymorphisms (SNPs). This method has the potential to increase accuracy by 13.8%. Our study found that MAS has a negative impact on GS. To address this issue, we integrated prior information on SNPs from GWAS, which exhibit pleiotropic genetic architecture. This integration enables us to utilise genetic markers for complex traits more effectively, thereby improving the accuracy and efficiency of GS.</p>\u0000 </div>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"143 3","pages":"465-478"},"PeriodicalIF":1.9,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145702895","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}