Journal of Animal Breeding and Genetics最新文献

{"title":"A Recursive Model Approach to Include Epigenetic Effects in Genetic Evaluations Using Simulated DNA Methylation Effects.","authors":"Adrián López-Catalina, Mohamed Ragab, Antonio Reverter, Oscar González-Recio","doi":"10.1111/jbg.12925","DOIUrl":"https://doi.org/10.1111/jbg.12925","url":null,"abstract":"<p><p>The advancement of epigenetics has highlighted DNA methylation as an intermediate-omic influencing gene regulation and phenotypic expression. With emerging technologies enabling the large-scale and affordable capture of methylation data, there is growing interest in integrating this information into genetic evaluation models for animal breeding. This study used methylome information from six dairy cows to simulate the methylation profile of 13,183 genotyped animals. The liability to methylation was treated as an additive trait, while a trait moderated by methylation effects was also simulated. A multiomic model (GOBLUP) was adapted to incorporate methylation data in genomic and genetic evaluations, using the traditional BLUP method as a benchmark. The GOBLUP accurately recovered heritability estimates for the liability to methylation in all low, medium and high heritability scenarios and was consistent at estimating the heritability for the epigenetics-moderated trait of interest at a low-medium heritability of 0.14. The genetic variance recovered by the BLUP model was influenced by the h² of the liability to methylation, and a part of the methylation variance for the phenotypic trait was captured as additive. The h² of the phenotypic trait partially relies on the h² value for the methylation windows in the traditional model. A newly proposed estimated epigenetic value (EEV) combines the traditional additive genetic information from genotyping arrays with epigenetic information. The correlation between the traditional estimated breeding value (EBV) and EEV was high (0.92-0.99 depending on the scenario), but the correlation of the EEV with the true breeding value was higher than the correlation between the traditional EBV and the TBV (0.85 vs. 0.75, 0.71 vs. 0.66 and 0.61 vs. 0.62 depending on the scenario). This study demonstrates that the GOBLUP multiomic recursive model can effectively separates additive and epigenetic variances, enabling improved breeding decisions by accounting for genetic liability to DNA methylation. This enables more informed breeding decisions, optimising selection for desired traits. Emerging sequencing techniques offer new opportunities for cost-effective simultaneous acquisition of genetic and epigenetic data, further enhancing breeding accuracy.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048854","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":"Graphical Model Selection to Infer the Partial Correlation Network of Allelic Effects in Genomic Prediction With an Application in Dairy Cattle.","authors":"Carlos A Martínez, Kshitij Khare, Syed Rahman, Giovanni M Báez","doi":"10.1111/jbg.12921","DOIUrl":"https://doi.org/10.1111/jbg.12921","url":null,"abstract":"<p><p>We addressed genomic prediction accounting for partial correlation of marker effects, which entails the estimation of the partial correlation network/graph (PCN) and the precision matrix of an unobservable m-dimensional random variable. To this end, we developed a set of statistical models and methods by extending the canonical model selection problem in Gaussian concentration, and directed acyclic graph models. Our frequentist formulations combined existing methods with the EM algorithm and were termed Glasso-EM, Concord-EM and CSCS-EM, whereas our Bayesian formulations corresponded to hierarchical models termed Bayes G-Sel and Bayes DAG-Sel. We implemented our methods in a real bull fertility dataset and then carried out gene annotation of seven markers having the highest degrees in the estimated PCN. Our findings brought biological evidence supporting the usefulness of identifying genomic regions that are highly connected in the inferred PCN. Moreover, a simulation study showed that some of our methods can accurately recover the PCN (accuracy up to 0.98 using Concord-EM), estimate the precision matrix (Concord-EM yielded the best results) and predict breeding values (the best reliability was 0.85 for a trait with heritability of 0.5 using Glasso-EM).</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016713","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":"Analysis of Social Genetic Effects on Pigs Fed With Automatic Feeders Using a Visit-Based Approach.","authors":"P Nuñez, C Casto-Rebollo, S Negro, S Gol, J Reixach, L Varona, J Casellas, N Ibáñez-Escriche","doi":"10.1111/jbg.12924","DOIUrl":"https://doi.org/10.1111/jbg.12924","url":null,"abstract":"<p><p>Social behaviour traits and their impact on feed efficiency are of particular interest in pig farming. The integration of automatic feeders enables the collection of multiple phenotypes for breeding purposes. The additive genetic and social genetic effect can be estimated considering all the visits to the feeder by modelling each visit independently in a 'visit-based approach'. This study aimed to determine the impact of the social genetic effect on individual feed intake and duration per visit in Pietrain pigs and Iberian pigs separately. The dataset comprised 883,906 visits from 1608 Pietrain pigs and 775,054 visits from 856 Iberian pigs. In the Pietrain population, the social genetic effects did not explain a substantial percentage of the phenotypic variance (~1%). In contrast, the Iberian population exhibited more substantial contributions, with social genetic effects accounting for 6.2% of the variance in duration per visit and 5.5% in feed intake per visit. The correlations between additive direct genetic and additive social genetic effects were slightly positive for feed intake across all analyses, and around zero for duration per visit with most of them including the zero in the highest posterior density interval (HPD95%). These weak correlations suggest that both effects could be selected independently. The visit-based approach successfully identified social genetic effects in the studied populations. Models incorporating social genetic effects demonstrated lower residual variance, enhancing the accuracy of additive values and, consequently, the potential for an improved response to selection.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016712","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":"Derivation of Economic Values for Breeding Objective Traits of Chinese Holstein Dairy Cows Using a Bio-Economic Model.","authors":"R Shi, A van der Linden, S Oosting, Y Wang, B Ducro","doi":"10.1111/jbg.12922","DOIUrl":"https://doi.org/10.1111/jbg.12922","url":null,"abstract":"<p><p>Holstein cattle account for the largest proportion of dairy cattle in China. The current China Performance Index (CPI) consists mainly of production traits. To derive economic values (EV) of additional traits for balanced breeding programs, a bio-economic model is necessary. Landless and intensive dairy farms are dominant in China, wherein all feed is purchased, and in-farm technicians and veterinarians are employed. Therefore, in the present study, a tailored bio-economic model was developed using the parameters of a typical dairy farm in North China. The typical farm had 1500 cows and 1400 youngstock, with a replacement rate of 33.5% per year and a productive life of 1090 days. The bio-economic model was on a per cow per year basis and described the revenues and costs from different animal categories. The EVs of 17 traits, including production, calving, fertility, longevity, and health traits, were derived and used to develop a more balanced selection index. Results showed that the bio-economic model can represent the typical dairy farm system in North China. The EVs of production traits were 2.39 Chinese Yuan (CNY), 32.85 CNY, and 89.60 CNY per kg milk yield, fat yield and protein yield, respectively. The EVs of production traits were two to three times higher than those in some European countries, due to the higher prices on milk volume and milk solids in China. The EVs of health traits ranged from -0.45 CNY to -11.95 CNY and were nearly half of those in other countries, due to the lower in-farm veterinarian labour costs. The EVs of most other functional traits were in line with the published values of other countries with similar economic assumptions in the model. Using the calculated EVs, a more balanced selection index was derived by including functional traits. This index had higher relative weight (46.8%) on functional traits than the current CPI (12.5%). With the high milk prices, it is still most profitable to allow for a decline in functional traits, although the decline is considerably smaller with the developed balanced index than with the CPI. Collectively, the bio-economic model and EVs provided the foundations for implementing balanced breeding programs in the Chinese Holstein population.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959094","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":"Single-Step Genome-Wide Association Study of Factors for Evaluated and Linearly Scored Traits in Swedish Warmblood Horses.","authors":"Anahit Nazari-Ghadikolaei, W Freddy Fikse, Åsa Gelinder Viklund, Sofia Mikko, Susanne Eriksson","doi":"10.1111/jbg.12923","DOIUrl":"https://doi.org/10.1111/jbg.12923","url":null,"abstract":"<p><p>Swedish Warmblood horses (SWB) are bred for show jumping and/or dressage with young horse test scores as indicator traits. This study aimed to investigate possible candidate genes and regions of importance for evaluated and linearly scored young horse test traits. A single-step genome-wide association study (ssGWAS) was done using the BLUPF90 suite of programs for factors scores from factor analysis of traits assessed at young horse tests together with height at withers. The ssGWAS included 20,814 SWB with factors scores for four factors for evaluated traits. A total of 6436 of these horses also had factor scores for 13 factors for linearly scored traits. Genotypes from a 670K SNP array were available for 380 of the horses in this study. All genotyped horses had factor scores for evaluated traits, and 379 also had factors scores for linearly scored traits. Significant SNPs associated with three factors related to size were located on ECA3 within or nearby a well-known region, including the genes ligand dependent nuclear receptor corepressor like (LCORL), non-SMC condensin I complex subunit G (NCAPG), DDB1 and CUL4 Associated Factor 16 (DCAF16), and the Family with Sequence Similarity 184 Member B (FAM184B). Significant SNPs were also detected for two factors for evaluated traits representing conformation and jumping, and four factors for linearly scored traits related to body length, neck conformation, walk and trot (hindleg position and activity), respectively. Among nearby genes, calcium/calmodulin-dependent protein kinase type 1D (CAMK1D) for the factor for linearly scored traits related to neck conformation and GLI Family Zinc Finger 2 (GLI2) for the factor for evaluated jumping traits, were most promising. For these, top associated SNPs were detected within the genes, and the known gene functions seems to be related to the phenotypes. In conclusion, ssGWAS is beneficial to detect plausible candidate genes/regions for desired traits in warmblood horses.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928734","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":"Estimation of Genetic Parameters and GWAS on Water Efficiency Traits in the Senepol Cattle.","authors":"Christhian B Souza, Gilberto R O Menezes, Andrea Gondo, Andrea A Egito, Pedro V B Ramos, Rodrigo C Gomes, Marcelo N Ribas, José Antônio Fernandes Júnior, Simone E F Guimarães","doi":"10.1111/jbg.12920","DOIUrl":"https://doi.org/10.1111/jbg.12920","url":null,"abstract":"<p><p>The need for producing in environmentally resilient system drives new research to achieve sustainable beef production. Water footprint of the beef supply chain is a concern that must be addressed, aiming to improve water use within the production chain. One approach is genetic selection of beef cattle for water efficiency. However, it is essential to understand the genetic architecture and mechanisms involved in the expression of this phenotype to choose the best selection criteria. Thus, our study aimed to estimate genetic parameters for water efficiency traits, conduct a genome-wide association study (GWAS) and identify the genetic networks and biological processes involved. A population of 1762 purebred Senepol cattle was phenotyped for the following water efficiency traits: water intake (WI), gross water efficiency (GWE), water conversion ratio (WCR), residual water intake based on average daily gain (RWI_ADG) and residual water intake based on dry matter intake (RWI_DMI). A subset of 1342 animals was genotyped using GGP Bovine 50 K SNP Chip with (734 animals) or 100 K (508 animals), and imputation from 50 K to 100 K was performed with Beagle software. The heritability estimates were 0.36 ± 0.06, 0.26 ± 0.05, 0.22 ± 0.05, 0.24 ± 0.05 and 0.20 ± 0.05 for WI, GWE, WCR, RWI_ADG and RWI_DMI, respectively. Unlike the raw measures of WI, the phenotypic correlations between average daily gain (ADG) and the residuals (RWI_DMI and RWI_ADG) were zero. All water efficiency traits were moderately to highly correlated with each other. GWAS were used to estimate the effect of 79,860 single nucleotide polymorphisms (SNPs), and significant SNPs were only observed for WCR. Enrichment analysis of genes in the significant regions revealed the involvement of different biological processes, such as saliva production, water transport, renal system and immune system. Genetic selection of Senepol cattle for water efficiency traits is feasible and can reduce water requirements for meat production. Water efficiency measures are polygenic traits, and different biological processes act simultaneously on the expression of related phenotypes.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900520","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":"Using Weighted Goal Programming Model to Achieve Genetic Gain in a Beluga Sturgeon Breeding Program.","authors":"Mina Rahbar, Roghieh Safari, Carlos I Perez-Rostro","doi":"10.1111/jbg.12916","DOIUrl":"https://doi.org/10.1111/jbg.12916","url":null,"abstract":"<p><p>We estimated the desired genetic gains for important traits in Beluga sturgeon (Huso huso) using an analytic hierarchy process (AHP) and weighted goal programming (WGP). Two questionnaires were distributed to 122 private Beluga sturgeon farmers in Iran in two stages. The initial stage involved the first questionnaire, which aimed to gather information on the environmental and management aspects of the farms. Additionally, farmers were requested to rate 4 important traits from a list of 12 traits for genetic improvement in the Beluga breeding program. Based on the results, four traits, that is, ovarian fat lobe weight (OFW), total caviar weight (CW), body weight of broodstock (BW) and larval body area at hatching (LBA) were rated highest. In the second stage, the second questionnaire asked farmers to make six pairwise comparisons between the above traits to determine preferences of these traits. The analytical hierarchy process was used to estimate individual preference (Ind-P) values using Super Decisions software. The medians of the Ind-P values were OFW and CW (0.30), BW (0.27) and LBA (0.10). Social group preference (Soc-P) values were estimated for five categories, with 13 social groups using the WGP model in LINGO software. Most disagreements in Soc-P values were found between the commercial products and water temperature categories. Consensus preference values (Con-P) for the above two categories were obtained by the extended WGP model with the range of λ between 0 and 1 in LINGO software. The average best Con-P values were OFW = BW (0.29), LBA (0.21) and CW (0.19). Desired genetic gains (%) were calculated using the percentage genetic improvement (G%) multiplied by the mean of Con-P, yielding values of 2.09, 1.88, 1.44 and 0.62 for BW, CW, LBA and OFW, respectively. The most important achievements of this research are the determination of the economic traits importance and multi-traits selection in the Beluga breeding program.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900521","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":"Bayesian Recursive and Structural Equation Models to Infer Causal Links Among Gait Visual Scores on Campolina Horses.","authors":"Fernando Bussiman, Jennifer Richter, Jorge Hidalgo, Fabyano Fonseca E Silva, Ricardo Vieira Ventura, Rachel Santos Bueno Carvalho, Elisângela Chicaroni Mattos, José Bento Sterman Ferraz, Joanir Pereira Eler, Júlio Cesar de Carvalho Balieiro","doi":"10.1111/jbg.12919","DOIUrl":"https://doi.org/10.1111/jbg.12919","url":null,"abstract":"<p><p>Gait visual scores are widely applied to horse breeding because they are a fast and easy phenotyping strategy, allowing the numeric interpretation of a complex biological process such as gait quality. However, they may suffer from subjectivity or high environmental influence. We aimed to investigate potential causal relationships among six visual gait scores in Campolina horses. The data included 5475 horses with records for at least one of the following traits: Dissociation (Di), Comfort (C), Style (S), Regularity (R), Development (De), and Gait total Scores (GtS). The pedigree comprised three generations with 14,079 horses in the additive relationship matrix. Under a Bayesian framework, (co)variance components were estimated through a multitrait animal model (MTM). Then, the inductive causation algorithm (IC) was applied to the residual (co)variance matrix samples. The resulting undirected graph from IC was directed in 6 possible causal structures, each fitted by a structural equation model. The final causal structure was chosen based on deviance information criteria (DIC). It was found that S significantly impacts the causal network of gait, directly and indirectly affecting C. The indirect causal effect of S on C was through the direct effect of S on De, then the direct effect of De on R, and finally, the direct effect of R on C. Di was caused by S, which is the reason for the genetic correlation between Di and GtS, due to causal effects being added to the model, they absorb the genetic correlation between Di and GtS. Those paths have biological meaning to horse movements and can help breeders and researchers better understand horses' complex causal network of gait.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857033","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":"Multiple Trait Bayesian Analysis of Partitioned Genetic Trends Accounting for Uncertainty in Genetic Parameters. An Example With the Pirenaica and Rubia Gallega Beef Cattle Breeds.","authors":"David López-Carbonell, Andrés Legarra, Juan Altarriba, Carlos Hervás-Rivero, Manuel Sánchez-Díaz, Luis Varona","doi":"10.1111/jbg.12918","DOIUrl":"https://doi.org/10.1111/jbg.12918","url":null,"abstract":"<p><p>Genetic trends are a valuable tool for analysing the efficiency of breeding programs. They are calculated by averaging the predicted breeding values for all individuals born within a specific time period. Moreover, partitioned genetic trends allow dissecting the contributions of several selection paths to overall genetic progress. These trends are based on the linear relationship between breeding values and the Mendelian sampling terms of ancestors, enabling genetic trends to be split into contributions from different categories of individuals. However, (1) the use of predicted breeding values in calculating partitioned genetic trends depends on the variance components used and (2) a multiple trait analysis allows accounting for selection on correlated traits. These points are often not considered. To overcome these limitations, we present a software called \"TM_TRENDS.\" This software performs a Bayesian analysis of partitioned genetic trends in a multiple trait model, accounting for uncertainty in the variance components. To illustrate the capabilities of this tool, we analysed the partitioned genetic trends for five traits (Birth Weight, Weight at 210 days, Cold Carcass Weight, Carcass Conformation, and Fatness Conformation) in two Spanish beef cattle breeds, Pirenaica and Rubia Gallega. The global genetic trends showed an increase in Carcass Conformation and a decrease in Birth Weight, Weight at 210 days, Cold Carcass Weight, and Fatness Conformation. These trends were partitioned into six categories: non-reproductive individuals, dams of females and non-reproductive individuals, dams of sires, sires with fewer than 20 progeny, sires between 20 and 50 progeny, and sires with more than 50 progeny. The results showed that the main source of genetic progress comes from sires with more than 50 progenies, followed by dams of males. Additionally, two additional features of the Bayesian analysis are presented: the calculation of the posterior probability of the global and partitioned genetic response between two time points, and the calculation of the posterior probability of positive (or negative) genetic progress.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857035","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":"Optimal Combination of Different Selection and Mating Strategies on Exploiting Genetic Diversity and Genetic Gain in Small Pig Conservation Populations.","authors":"Qingbo Zhao, Huiming Liu, Qian Zhang, Qamar Raza Qadri, Yuchun Pan, Guosheng Su, Pinghua Li, Ruihua Huang","doi":"10.1111/jbg.12917","DOIUrl":"https://doi.org/10.1111/jbg.12917","url":null,"abstract":"<p><p>Both selection and mating systems are essential tools for breeders to conserve the genetic variance and improve the performance of livestock animals. How to effectively balance the genetic gain and inbreeding has always been an important issue in quantitative genetics research. In this study, a total of 11 selection methods, including random and truncation selection, six conventional selection methods, three different optimal contribution selection (OCS) methods and three mating strategies including random mating, minimum-coancestry mating based on pedigree (MCPed) and genomic information (MCmarker), were performed using stochastic simulations. The long-term effects of different combinations of selection and mating strategies on the genetic gain, the rate of inbreeding and genetic diversity in the small-scale pig conservation populations were investigated. The results showed that different strategies of selection and mating methods had different effects on genetic gain and inbreeding rate. For maintaining additive genetic variance, the optimal strategy was random selection with random mating, followed by SIREhalf-DAMfullRandom selection (which means selecting dams randomly from each full-sib family) and random mating. For mainting the number of common ancestors, the optimal strategy was SIREhalf-DAMfull selection (which means selecting dams with the highest estimated breeding value within each full-sib family) and random mating, followed by SIREhalf-DAMfullRandom selection and random mating, OCS and MCPed mating. For genetic diversity metrics, taking He and Ho as an example, the optimal strategy was GOCS (optimal contribution selection based on genomic information) with MCmarker mating. For genetic gain, the optimal strategy was truncation selection and MCmarker mating, followed by POCS (optimal contribution selection based on pedigree information) and MCmarker mating, truncation selection and MCPed mating. For the rate of inbreeding, the optimal strategy was SIREhalf-DAMfull selection and MCPed mating. Our findings can help breeding managers and farmers choose a more suitable and sustainable strategy for maintaining the genetic diversity and improving the genetic gain of local pig breeds.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848401","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}