Journal of Animal Breeding and Genetics最新文献

{"title":"Evaluation of breeding strategies to reduce the inbreeding rate in the Friesian horse population: Looking back and moving forward","authors":"Marije J. Steensma,&nbsp;Harmen P. Doekes,&nbsp;Torsten Pook,&nbsp;Martijn F. L. Derks,&nbsp;Nynke Bakker,&nbsp;Bart J. Ducro","doi":"10.1111/jbg.12872","DOIUrl":"10.1111/jbg.12872","url":null,"abstract":"<p>In the past, small population sizes and unequal ancestor contributions have resulted in high inbreeding rates (Δ<i>F</i>) in the Friesian horse. Two decades ago, the studbook implemented a mating quota and started publishing individual kinships and reduced Δ<i>F</i> below 1% per generation. However, since then, the breeding population size has decreased and this raises the question whether current breeding strategies are sufficient to keep Δ<i>F</i> below desired rates. The aim of this study was to (1) reflect on past inbreeding trends and their main determinants, using pedigree analysis and (2) evaluate the effectiveness of the current and additional breeding strategies using stochastic simulations. We estimated the current Δ<i>F</i> (2013–2022) at 0.72% per generation. While the total contribution of the top 10 sires to the number of offspring per year has decreased from 75% in 1980 to 35% in 2022, this was mainly due to an increased number of approved studbook sires, and not due to more equalized contributions among sires. Of the simulated breeding strategies, selecting only breeding stallions with a below average mean kinship (i.e., “mean kinship selection”) was most effective to decrease Δ<i>F</i> (from 0.66% to 0.33%). Increasing the number of breeding sires only had an effect when also a mating quota was applied. However, its effect remained limited. For example, a ~1.5 fold increase, combined with a mating quota of 80 offspring per sire per year, reduced Δ<i>F</i> from 0.55% to 0.51%. When increasing the number of breeding mares, a practically unfeasible large increase was needed for a meaningful reduction in Δ<i>F</i> (e.g. twice as many mares were needed to reduce Δ<i>F</i> from 0.66% to 0.56%). Stratified mating quotas, a novel approach in which we assigned each sire a mating quota (of 60, 80, 100 or 120 offspring per year) based on its mean kinship to recently born foals, resulted in a lower Δ<i>F</i> (0.43%) than a general mating quota of 90 offspring per sire per year (0.55%). Overall, while the current Δ<i>F</i> is below 1%, we recommend to implement additional strategies to further reduce Δ<i>F</i> below 0.5% in the Friesian horse population. For this breed and similar populations, we recommend to focus on breeding strategies based on kinship levels to effectively reduce Δ<i>F</i>.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"668-684"},"PeriodicalIF":1.9,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12872","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923819","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":"Plateau-linear reaction norm model analysis of number born alive in purebred Landrace pigs using meteorological data in Japan","authors":"Shinichiro Ogawa,&nbsp;Toshihiro Okamura,&nbsp;Yo Fukuzawa,&nbsp;Motohide Nishio,&nbsp;Kazuo Ishii,&nbsp;Makoto Kimata,&nbsp;Masamitsu Tomiyama,&nbsp;Masahiro Satoh","doi":"10.1111/jbg.12871","DOIUrl":"10.1111/jbg.12871","url":null,"abstract":"<p>We performed a plateau-linear reaction norm model (RNM) analysis of number born alive (NBA) in purebred Landrace pigs, where breeding value changes according to maximum temperature at mating day, using public meteorological observation data in Japan. We analysed 52,668 NBA records obtained from 10,320 Landrace sows. Pedigree data contained 99,201 animals. Off-farm daily temperature data at the nearest weather station from each of the farms were downloaded from the Japan Meteorological Agency website. A plateau-linear RNM analysis based on daily maximum temperature on mating day (threshold temperature of 16.6°C) was performed. The percentage of the records with daily maximum temperatures at mating days of ≤16.6, ≥25.0, ≥30.0 and ≥35.0°C were 34.3%, 33.6%, 14.0% and 0.8%, respectively. The value of Akaike's information criterion for the plateau-linear RNM was lower than that for a simple repeatability model (RM). With the plateau-linear RNM, estimated value of heritability ranged from 0.14 to 0.15, while that from the RM analysis was 0.15. Additive genetic correlation between intercept and slope terms was estimated to be −0.52 from the plateau-linear RNM analysis. Estimated additive genetic correlations were &gt;0.9 between NBA at different temperatures ranging from 16.6 to 37.6°C. For the 10,320 sows, average values of prediction reliability of the intercept and slope terms for breeding values in the plateau-linear RNM were 0.47 and 0.16, respectively. Increasing weight for slope term in linear selection index could bring positive genetic gain in the slope part, but prediction accuracy would decrease. Our results imply that genetically improving heat tolerance in sows reared in Japan focusing on NBA using RNM is possible, while RNM is more complex to implement and interpret. Therefore, further study should be encouraged to make genetic improvement for heat tolerance in sows more efficient.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"656-667"},"PeriodicalIF":1.9,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140913392","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 for maintenance energy requirements and residual feed intake in Nellore cattle","authors":"Roberto D. Sainz,&nbsp;Fernando Baldi,&nbsp;Larissa Bordin Temp,&nbsp;Luciano B. Ribeiro","doi":"10.1111/jbg.12870","DOIUrl":"10.1111/jbg.12870","url":null,"abstract":"<p>We estimated heritabilities and genetic and phenotypic correlation estimates for maintenance energy requirements (NEmR), residual feed intake (RFI), growth, carcass and reproductive indicator traits, using data from 41 feed efficiency trials in Brazil, comprising 4381 males and females. Continuous traits were analysed using a linear animal model and threshold traits were analysed using a threshold animal model. The heritability estimates were low for RFI (0.190) and NEmR (0.193); other heritabilities were mainly moderate (growth and carcass traits) or high (sexual precocity traits). The genetic correlation of RFI with NEmR was high (0.701). The genetic correlations of NEmR were low with carcass and reproductive traits, and moderate with growth traits. Thus, selection to improve weaning weight and female sexual precocity indicator traits would not affect maintenance energy requirement. Genetic selection to reduce maintenance energy requirements is feasible and would also reduce DMI and RFI. Selection to improve RFI can be used to identify animals with lower maintenance energy requirements. Long-term selection to reduce RFI and NEmR would have favourable effects on yearling weight, carcass muscle indicator traits and female sexual precocity. Genetic (co)variance component estimates for NEmR, in conjunction with economic values of selection criteria, may be used to develop novel approaches for genetic selection to improve efficiency of beef production.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"643-655"},"PeriodicalIF":1.9,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12870","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140873579","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":"Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile","authors":"João Inácio Gomes Vieira,&nbsp;Larissa Graciano Braga,&nbsp;Tatiane C. S. Chud,&nbsp;Pablo Henrique Ferreira,&nbsp;Simone Eliza Facioni Guimarães,&nbsp;Marta Fonseca Martins,&nbsp;João Cláudio do Carmo Panetto,&nbsp;Marco Antonio Machado,&nbsp;Danielly Beraldo dos Santos Silva,&nbsp;Cristina Moreira Bonafé,&nbsp;Ana Fabrícia Braga Magalhães,&nbsp;Marcos Vinícius G. B. da Silva,&nbsp;Lucas Lima Verardo","doi":"10.1111/jbg.12869","DOIUrl":"10.1111/jbg.12869","url":null,"abstract":"<p>The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5′ UTR and coding region. Through the gene–biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene–TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. <i>LIPE</i>, <i>MFSD2A</i> and <i>SREBF1</i> genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"628-642"},"PeriodicalIF":1.9,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869177","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 parameters for mid-infrared-spectroscopy-predicted mastitis phenotypes and related traits","authors":"Lisa Rienesl,&nbsp;Birgit Fuerst-Waltl,&nbsp;Gábor Mészáros,&nbsp;Astrid Koeck,&nbsp;Christa Egger-Danner,&nbsp;Nicolas Gengler,&nbsp;Clément Grelet,&nbsp;Johann Sölkner","doi":"10.1111/jbg.12868","DOIUrl":"10.1111/jbg.12868","url":null,"abstract":"<p>Genetic improvement of udder health in dairy cows is of high relevance as mastitis is one of the most prevalent diseases. Since it is known that the heritability of mastitis is low and direct data on mastitis cases are often not available in large numbers, auxiliary traits, such as somatic cell count (SCC) are used for the genetic evaluation of udder health. In previous studies, models to predict clinical mastitis based on mid-infrared (MIR) spectral data and a somatic cell count-derived score (SCS) were developed. Those models can provide a probability of mastitis for each cow at every test-day, which is potentially useful as an additional auxiliary trait for the genetic evaluation of udder health. Furthermore, MIR spectral data were used to estimate contents of lactoferrin, a glycoprotein positively associated with immune response. The present study aimed to estimate heritabilities (h²) and genetic correlations (r_a) for clinical mastitis diagnosis (CM), SCS, MIR-predicted mastitis probability (MIRprob), MIR + SCS-predicted mastitis probability (MIRSCSprob) and lactoferrin estimates (LF). Data for this study were collected within the routine milk recording and health monitoring system of Austria from 2014 to 2021 and included records of approximately 54,000 Fleckvieh cows. Analyses were performed in two datasets, including test-day records from 5 to 150 or 5 to 305 days in milk. Prediction models were applied to obtain MIR- and SCS-based phenotypes (MIRprob, MIRSCSprob, LF). To estimate heritabilities and genetic correlations bivariate linear animal models were applied for all traits. A lactation model was used for CM, defined as a binary trait, and a test-day model for all other continuous traits. In addition to the random animal genetic effect, the fixed effects year-season of calving and parity-age at calving and the random permanent environmental effect were considered in all models. For CM the random herd-year effect, for continuous traits the random herd-test day effect and the covariate days in milk (linear and quadratic) were additionally fitted. The obtained genetic parameters were similar in both datasets. The heritability found for CM was expectedly low (h² = 0.02). For SCS and MIRSCSprob, heritability estimates ranged from 0.23 to 0.25, and for MIRprob and LF from 0.15 to 0.17. CM was highly correlated with SCS and MIRSCSprob (r_a = 0.85 to 0.88). Genetic correlations of CM were moderate with MIRprob (r_a = 0.26 and 0.37) during 150 and 305 days in milk, respectively and low with LF (h² = 0.10 and 0.11). However, basic selection index calculations indicate that the added value of the new MIR-predicted phenotypes is limited for genetic evaluation of udder health.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"614-627"},"PeriodicalIF":1.9,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12868","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140855585","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 investigations on backfat thickness and body condition score in German Holstein cattle","authors":"Christin Schmidtmann,&nbsp;Julius Mugambe,&nbsp;Iulia Blaj,&nbsp;Carsten Harms,&nbsp;Georg Thaller","doi":"10.1111/jbg.12867","DOIUrl":"10.1111/jbg.12867","url":null,"abstract":"<p>Up to now, little has been known about backfat thickness (BFT) in dairy cattle. The objective of this study was to investigate the lactation curve and genetic parameters for BFT as well as its relationship with body condition score (BCS) and milk yield (MKG). For this purpose, a dataset was analysed including phenotypic observations of 1929 German Holstein cows for BFT, BCS and MKG recorded on a single research dairy farm between September 2005 and December 2022. Additionally, pedigree and genomic information was available. Lactation curves were predicted and genetic parameters were estimated for all traits in first to third lactation using univariate random regression models. For BCS, lactation curves had nadirs at 94 DIM, 101 DIM and 107 DIM in first, second and third lactation. By contrast, trajectories of BFT showed lowest values later in lactation at 129 DIM, 117 DIM and 120 DIM in lactation numbers 1 to 3, respectively. Although lactation curves of BCS and BFT had similar shapes, the traits showed distinct sequence of curves for lactation number 2 and 3. Cows in third lactation had highest BCS, whereas highest BFT values were found for second parity animals. Average heritabilities were 0.315 ± 0.052, 0.297 ± 0.048 and 0.332 ± 0.061 for BCS in lactation number 1 to 3, respectively. Compared to that, BFT had considerably higher heritability in all lactation numbers with estimates ranging between 0.357 ± 0.028 and 0.424 ± 0.034. Pearson correlation coefficients between estimated breeding values for the 3 traits were negative between MKG with both BCS (<i>r</i> = −0.245 to −0.322) and BFT (<i>r</i> = −0.163 to −0.301). Correlation between traits BCS and BFT was positive and consistently high (<i>r</i> = 0.719 to 0.738). Overall, the results of this study suggest that BFT and BCS show genetic differences in dairy cattle, which might be due to differences in depletion and accumulation of body reserves measured by BFT and BCS. Therefore, routine recording of BFT on practical dairy farms could provide valuable information beyond BCS measurements and might be useful, for example, to better assess the nutritional status of cows.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"602-613"},"PeriodicalIF":1.9,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12867","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140861545","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":"Effects of reference population size and structure on genomic prediction of maternal traits in two pig lines using whole-genome sequence-, high-density- and combined annotation-dependent depletion genotypes","authors":"Maria V. Kjetså,&nbsp;Arne B. Gjuvsland,&nbsp;Eli Grindflek,&nbsp;Theo Meuwissen","doi":"10.1111/jbg.12865","DOIUrl":"10.1111/jbg.12865","url":null,"abstract":"<p>The aim of this study was to investigate the reference population size required to obtain substantial prediction accuracy within- and across-lines and the effect of using a multi-line reference population for genomic predictions of maternal traits in pigs. The data consisted of two nucleus pig populations, one pure-bred Landrace (L) and one Synthetic (S) Yorkshire/Large White line. All animals were genotyped with up to 30 K animals in each line, and all had records on maternal traits. Prediction accuracy was tested with three different marker data sets: High-density SNP (HD), whole genome sequence (WGS), and markers derived from WGS based on pig combined annotation dependent depletion-score (pCADD). Also, two different genomic prediction methods (GBLUP and Bayes GC) were compared for four maternal traits; total number piglets born (TNB), total number of stillborn piglets (STB), Shoulder Lesion Score and Body Condition Score. The main results from this study showed that a reference population of 3 K–6 K animals for within-line prediction generally was sufficient to achieve high prediction accuracy. However, when the number of animals in the reference population was increased to 30 K, the prediction accuracy significantly increased for the traits TNB and STB. For multi-line prediction accuracy, the accuracy was most dependent on the number of within-line animals in the reference data. The S-line provided a generally higher prediction accuracy compared to the L-line. Using pCADD scores to reduce the number of markers from WGS data in combination with the GBLUP method generally reduced prediction accuracies relative to GBLUP using HD genotypes. The BayesGC method benefited from a large reference population and was less dependent on the different genotype marker datasets to achieve a high prediction accuracy.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 6","pages":"587-601"},"PeriodicalIF":1.9,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12865","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337730","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":"Prevalence of sex-chromosome aneuploidy estimated using SNP genotype intensity information in a large population of juvenile dairy and beef cattle","authors":"Cliona A. Ryan,&nbsp;Deirdre C. Purfield,&nbsp;Daragh Matthews,&nbsp;Carla Canedo-Ribeiro,&nbsp;Ainhoa Valldecabres,&nbsp;Donagh P. Berry","doi":"10.1111/jbg.12866","DOIUrl":"10.1111/jbg.12866","url":null,"abstract":"<p>Aneuploidy is a genetic condition characterized by the loss or gain of one or more chromosomes. Aneuploidy affecting the sex chromosomes can lead to infertility in otherwise externally phenotypically normal cattle. Early identification of cattle with sex chromosomal aneuploidy is important to minimize the costs associated with rearing infertile cattle and futile breeding attempts. As most livestock breeding programs routinely genotype their breeding populations using single nucleotide polymorphism (SNP) arrays, this study aimed to assess the feasibility of integrating an aneuploidy screening tool into the existing pipelines that handle dense SNP genotype data. A further objective was to estimate the prevalence of sex chromosome aneuploidy in a population of 146,431 juvenile cattle using available genotype intensity data. Three genotype intensity statistics were used: the LogR Ratio (LRR), <i>R</i>-value (the sum of X and Y SNP probe intensities), and B-allele frequency (BAF) measurements. Within the female-verified population of 124,958 individuals, the estimated prevalence rate was 0.0048% for XO, 0.0350% for XXX, and 0.0004% for XXY. The prevalence of XXY in the male-verified population was 0.0870% (i.e., 18 out of 20,670 males). Cytogenetic testing was used to verify 2 of the XXX females who were still alive. The proposed approach can be readily integrated into existing genomic pipelines, serving as an efficient, large-scale screening tool for aneuploidy. Its implementation could enable the early identification of infertile animals with sex-chromosome aneuploidy.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 5","pages":"571-585"},"PeriodicalIF":1.9,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12866","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319890","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":"Genomic analyses of nitrogen utilization efficiency, its indicator trait blood urea nitrogen and the relationship to classical growth performance and feed efficiency traits in a Landrace × Piétrain crossbred population","authors":"Markus Schmid,&nbsp;Ramona Weishaar,&nbsp;Jana Seifert,&nbsp;Amélia Camarinha-Silva,&nbsp;Markus Rodehutscord,&nbsp;Jörn Bennewitz","doi":"10.1111/jbg.12864","DOIUrl":"10.1111/jbg.12864","url":null,"abstract":"&lt;p&gt;Improving the nutrient efficiency in pork production is required to reduce the resource competition between human food and animal feed regarding diet components edible for humans and to minimize emissions relevant to climate or the environment. Thereby, protein utilization efficiency and its equivalent nitrogen utilization efficiency (NUE) play a major role. Breeding for more nitrogen (N) efficient pigs bears a promising strategy to improve such traits, however, directly phenotyping NUE based on N balance data is neither cost-efficient nor straightforward and not applicable for routine evaluations. Blood urea nitrogen (BUN) levels in the pig are suitable to predict the NUE and, therefore, might be an indicator trait for NUE because BUN is a relatively easy-to-measure trait. This study investigated the suitability of NUE as a selection trait in future breeding programs. The relationships to classical growth performance and feed efficiency traits were analysed as well as the relationship to BUN to infer the role of BUN as an indicator trait to improve NUE via breeding. The analyzes were based on a Landrace F1 cross population consisting of 502 individuals who descended from 20 Piétrain sires. All animals were genotyped for 48,525 SNPs. They were phenotyped in two different fattening phases, i.e., FP1 and FP2, during the experiment. Uni- and bivariate analyses were run to estimate variance components and to determine the genetic correlation between different traits or between the same trait measured at different time points. Moderate heritabilities were estimated for all traits, whereby the heritability for NUE was &lt;i&gt;h&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.293 in FP1 and &lt;i&gt;h&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.163 in FP2 and BUN had the by far highest heritability (&lt;i&gt;h&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.415 in FP1 and &lt;i&gt;h&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.460 in FP2). The significant genetic correlation between NUE and BUN showed the potential of BUN to be considered an indicator trait for NUE. This was particularly pronounced when NUE was measured in FP1 (genetic correlations &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;r&lt;/mi&gt;\u0000 &lt;mi&gt;g&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;mn&gt;0.631&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; and &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;r&lt;/mi&gt;\u0000 &lt;mi&gt;g&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;mn&gt;0.688&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; between NUE and BUN measured in FP1 and FP2, respectively). The genetic correlations of NUE and BUN with important production traits suggest selecting pigs with high growth rates and low BUN levels to breed more efficient","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 5","pages":"559-570"},"PeriodicalIF":1.9,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12864","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208271","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 heritability with genomic information by method R","authors":"Mary Kate Hollifield,&nbsp;Daniela Lourenco,&nbsp;Ignacy Misztal","doi":"10.1111/jbg.12863","DOIUrl":"10.1111/jbg.12863","url":null,"abstract":"<p>Estimating heritabilities with large genomic models by established methods such as restricted maximum likelihood (REML) or Bayesian via Gibbs sampling is computationally expensive. Alternatively, heritability can be estimated indirectly by method R and by maximum predictivity, referred to as MaxPred here, at a much lower computing cost. By method R, the heritability used for predictions with whole and partial data is considered the best estimate when the predictions based on partial data are unbiased relative to those with the complete data. By MaxPred, the heritability estimate is the one that maximizes predictivity. This study compared heritability estimation with genomic information using average information REML (AI–REML), method R and MaxPred. A simulated population was generated with ten generations of 5000 animals each and an effective population size of 80. Each animal had one record for a trait with a heritability of 0.3, a phenotypic variance of 10.0 and was genotyped at 50 k SNP. In method R, the heritability estimate is found when the expectation of a regression coefficient is equal to one. The regression is the EBV of selection candidates calculated with the whole dataset regressed on the EBV of candidates calculated from a partial dataset. In this study, we used the GBLUP framework and therefore, GEBV was calculated. The partial dataset was created by removing the last generation of phenotypes. Predictivity was defined as the correlation between the adjusted phenotypes of the selection candidates and their GEBV calculated from the partial data. We estimated the heritability for populations that included between three and 10 generations. In every scenario, predictivity increased as more data was used and was the highest at the simulated heritability. However, the predictivity for all data subsets and all heritabilities compared did not differ more than 0.01, suggesting MaxPred is not the best indication for heritability estimation. For the whole dataset, the heritability was estimated as 0.30 ± 0.01, 0.26 ± 0.01 and 0.30 ± 0.04 for AI–REML without genomics, AI–REML with genomics and method R with genomics, respectively. Heritability estimation with genomics by method R reduced timing by 83%, implying a reduction in computing time from 9.5 to 1.6 h, on average, compared to AI–REML with genomics. Method R has the potential to estimate heritabilities with large genomic information at a low cost when many generations of animals are present; however, the standard error can be high when only a few iterations are used.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 5","pages":"550-558"},"PeriodicalIF":1.9,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12863","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208201","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}