Journal of Animal Breeding and Genetics最新文献

{"title":"Modelling the lactation curve in Alpine × Beetal crossbred dairy goats using random regression models fitted with Legendre polynomial and B-spline functions","authors":"Amritanshu Upadhyay,&nbsp;Rani Alex,&nbsp;Mahesh Shivanand Dige,&nbsp;Shweta Sahoo,&nbsp;Kashif Dawood Khan,&nbsp;Pradyut Das,&nbsp;Vikas Vohra,&nbsp;Gopal Ramdasji Gowane","doi":"10.1111/jbg.12849","DOIUrl":"10.1111/jbg.12849","url":null,"abstract":"<p>The current study sought to genetically assess the lactation curve of Alpine × Beetal crossbred goats through the application of random regression models (RRM). The objective was to estimate genetic parameters of the first lactation test-day milk yield (TDMY) for devising a practical breeding strategy within the nucleus breeding programme. In order to model variations in lactation curves, 25,998 TDMY records were used in this study. For the purpose of estimating genetic parameters, orthogonal Legendre polynomials (LEG) and B-splines (BS) were examined in order to generate suitable and parsimonious models. A single-trait RRM technique was used for the analysis. The average first lactation TDMY was 1.22 ± 0.03 kg and peak yield (1.35 ± 0.02 kg) was achieved around the 7th test day (TD). The present investigation has demonstrated the superiority of the B-spline model for the genetic evaluation of Alpine × Beetal dairy goats. The optimal random regression model was identified as a quadratic B-spline function, characterized by six knots to represent the central trend. This model effectively captured the patterns of additive genetic influences, animal-specific permanent environmental effects (c²) and 22 distinct classes of (heterogeneous) residual variance. Additive variances and heritability (h²) estimates were lower in the early lactation, however, moderate across most parts of the lactation studied, ranging from 0.09 ± 0.04 to 0.33 ± 0.06. The moderate heritability estimates indicate the potential for selection using favourable combinations of test days throughout the lactation period. It was also observed that a high proportion of total variance was attributed to the animal's permanent environment. Positive genetic correlations were observed for adjacent TDMY values, while the correlations became less pronounced for more distant TDMY values. Considering better fitting of the lactation curve, the use of B-spline functions for genetic evaluation of Alpine × Beetal goats using RRM is recommended.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 4","pages":"365-378"},"PeriodicalIF":2.6,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139467343","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":"Characteristics of restricted selection indices and geometrical interpretation of restricted breeding values","authors":"Masahiro Satoh","doi":"10.1111/jbg.12845","DOIUrl":"10.1111/jbg.12845","url":null,"abstract":"<p>Restricted selection is used to control genetic changes in one or more characters. Three main selection indices are adopted for this purpose. First, Kempthorne's index is used to maximize aggregate breeding value (BV) with changes in some traits restricted to zero; second, Harville's index is used to maximize aggregate BV with proportional changes for some traits; and third, Yamada's index is mathematically used to achieve the relative desired changes for all traits. Kempthorne's index is equivalent to Harville's index. However, the relationship between Kempthorne's and Yamada's indices has not been clarified. In addition, the characteristics of restricted selection indices and the relationship between BV and restricted BV (RBV) are also unknown. The aim of this study was to clarify the characteristics of restricted selection indices and describe the relationship between BV and RBV by using linear algebra and geometric techniques, respectively. First, I proved that Yamada's index is part of Kempthorne's index. Second, I investigated the relationship between BVs that were estimated using an ordinary selection index (EBVs) and RBVs estimated using a restricted selection index (ERBVs) and proved that the ERBVs of the restricted traits are proportional to the relative desired changes. Third, I proved that RBV is represented by a linear function of BV and geometrically represented the relationship between BV and RBV. In this study, new findings on restricted selection indices and RBV were obtained. This useful clarification of the relationship between BV and RBV will make it possible to evaluate the response to selection using not only a restricted selection index, but also a restricted BLUP in computer simulation studies.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"353-363"},"PeriodicalIF":2.6,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12845","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139418649","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":"Longevity in South African Afrikaner cows as assessed through survival analysis","authors":"Allison M. Bot Steffl,&nbsp;Michael D. MacNeil,&nbsp;Michiel M. Scholtz,&nbsp;Leticia P. Sanglard,&nbsp;Tiago Passafaro,&nbsp;Michael G. Gonda","doi":"10.1111/jbg.12847","DOIUrl":"10.1111/jbg.12847","url":null,"abstract":"<p>The Afrikaner breed of cattle is indigenous to South Africa and, due to their hardiness, was once the most popular breed amongst South African farmers, although in recent years their numbers have decreased. The goal of this study was to assess factors affecting length of productive life, defined as the interval between production of the first and last calf, in Afrikaner cattle using survival analysis. The data spanned 40 years with an observed measure of length of life for 29,379 cows from 374 herds. Relative to similar analyses, few (<i>n</i> = 2964; 8.4%) cows had records that were right censored. The median length of productive life of an Afrikaner cow was just less than 6 years. Cows that were younger at their first parturition had longer productive lives than those that were older at their first calving. Cows that were born in the period from December to February had shorter productive lives than those born between March and November. The estimated animal genetic variance of 0.266 resulted in a heritability estimate for length of productive life in Afrikaner cattle of 0.225. Thus, there appeared to be sufficient additive genetic variance in Afrikaner cattle to enable genetic improvement in their length of productive life.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"343-352"},"PeriodicalIF":2.6,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12847","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139405312","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":"Genome-wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits","authors":"Samuele Bovo,&nbsp;Anisa Ribani,&nbsp;Giuseppina Schiavo,&nbsp;Valeria Taurisano,&nbsp;Francesca Bertolini,&nbsp;Daniela Fornasini,&nbsp;Andrea Frabetti,&nbsp;Luca Fontanesi","doi":"10.1111/jbg.12844","DOIUrl":"10.1111/jbg.12844","url":null,"abstract":"<p>Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from the suckling period, with large negative economic impacts. In this study, from a commercial population of suckling rabbits (derived from 133 litters) that experienced an outbreak of enteropathy, we first selected a few animals that died with severe symptoms of diarrhoea and characterized their microbiota, using 16S rRNA gene sequencing data. <i>Clostridium</i> genus was consistently present in all affected specimens. In addition, with the aim to identify genetic markers in the rabbit genome that could be used as selection tools, we performed genome-wide association studies for symptoms of diarrhoea in the same commercial rabbit population. These studies were also complemented with <i>F</i>_ST analyses between the same groups of rabbits. A total of 332 suckling rabbits (151 with severe symptoms of diarrhoea, 42 with mild symptoms and 129 without any symptoms till the weaning period), derived from 45 different litters (a subset of the 133 litters) were genotyped with the Affymetrix Axiom OrcunSNP Array. In both genomic approaches, rabbits within litters were paired to constitute two groups (susceptible and resistant, including the mildly affected in one or the other group) and run case and control genome-wide association analyses. Genomic heritability estimated in the designed experimental structure integrated in a commercial breeding scheme was 0.19–0.21 (s.e. 0.09–0.10). A total of eight genomic regions on rabbit chromosome 2 (OCU2), OCU3, OCU7, OCU12, OCU13, OCU16 and in an unassembled scaffold had significant single nucleotide polymorphisms (SNPs) and/or markers that trespassed the F_ST percentile distribution. Among these regions, three main peaks of SNPs were identified on OCU12, OCU13 and OCU16. The QTL region on OCU13 encompasses several genes that encode members of a family of immunoglobulin Fc receptors (<i>FCER1G</i>, <i>FCRLA</i>, <i>FCRLB</i> and <i>FCGR2A</i>) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"328-342"},"PeriodicalIF":2.6,"publicationDate":"2023-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12844","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139049807","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":"Investigation of phenotypic, genetic and genomic background of Milk spectra in Sarda dairy sheep","authors":"Michele Congiu,&nbsp;Laura Falchi,&nbsp;Silvia Carta,&nbsp;Alberto Cesarani,&nbsp;Corrado Dimauro,&nbsp;Fabio Correddu,&nbsp;Nicolò Pietro Paolo Macciotta","doi":"10.1111/jbg.12843","DOIUrl":"10.1111/jbg.12843","url":null,"abstract":"<p>Aim of this study was to analyse the genetic background of milk Fourier transform infrared (FTIR) spectra in dairy sheep. Individual milk FTIR spectra, with 1060 wavenumbers each, were available for 793 adult Sarda breed ewes genotyped at 45,813 SNP. The absorbance values of each wavenumber was analysed using a linear mixed model that included dim class, parity and lambing month as fixed effects and flock-test date and animal as random effects. The model was applied to estimate variance components and heritability and to perform a genome-wide association study for each wavenumber. Average h² of wavenumbers absorbance was 0.13 ± 0.08, with the largest values observed in the regions associated with the characteristic bonds of carbonylic and methylenic groups of milk fat (h² = 0.57 at 1724–1728 cm⁻¹; and h² = 0.34 at 2811–2834 cm⁻¹, respectively). The absorbance values of wavenumbers were moderately correlated with the estimated heritabilities. After the Bonferroni correction, a total of nine markers were found to be significantly associated with 32 different wavenumbers. Of particular interest was the SNP s63269.1, mapped on chromosome 2, that was found to be associated with 27 wavenumbers. Genes previously found to be related to traits of interest (e.g. disease resistance, milk yield and quality, cheese firmness) are located close to the significant SNP. As expected, the heritability estimated for the absorbance of each wavenumbers seems to be associated with the related milk components.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"317-327"},"PeriodicalIF":2.6,"publicationDate":"2023-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12843","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139040951","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":"A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle","authors":"Belete Kuraz Abebe,&nbsp;Hongbao Wang,&nbsp;Anning Li,&nbsp;Linsen Zan","doi":"10.1111/jbg.12841","DOIUrl":"10.1111/jbg.12841","url":null,"abstract":"<p>In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"235-256"},"PeriodicalIF":2.6,"publicationDate":"2023-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139038221","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":"Pedigree diversity and implications for genetic selection of Katahdin sheep","authors":"Sara M. Nilson,&nbsp;Joan M. Burke,&nbsp;Brenda M. Murdoch,&nbsp;James L. M. Morgan,&nbsp;Ronald M. Lewis","doi":"10.1111/jbg.12842","DOIUrl":"10.1111/jbg.12842","url":null,"abstract":"<p>The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (<i>n</i> = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (<i>n</i> = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (<i>n</i> = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (<i>N</i>_e) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the <i>N</i>_e is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current <i>N</i>_e suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"304-316"},"PeriodicalIF":2.6,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12842","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138813247","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":"Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds","authors":"Michela Ablondi,&nbsp;Giorgia Stocco,&nbsp;Matteo Cortellari,&nbsp;Antonello Carta,&nbsp;Andrea Summer,&nbsp;Alessio Negro,&nbsp;Silverio Grande,&nbsp;Paola Crepaldi,&nbsp;Claudio Cipolat-Gotet,&nbsp;Stefano Biffani","doi":"10.1111/jbg.12839","DOIUrl":"10.1111/jbg.12839","url":null,"abstract":"<p>Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single-nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels in terms of cost, accuracy, and automation, the transition from MS to SNP markers for parentage verification is still very slow and, so far, only routinely applied in cattle. A major difficulty during this transition period is the need of SNP data for parents and offspring, which in most cases is not yet feasible due to the genotyping cost. To overcome the unavailability of same genotyping platform during the transition period, in this study we aimed to assess the feasibility of a MS imputation pipeline from SNPs in four native sheep dairy breeds: Comisana (<i>N</i> = 331), Massese (<i>N</i> = 210), Delle Langhe (<i>N</i> = 59) and Sarda (<i>N</i> = 1003). Those sheep were genotyped for 11 MS and with the Ovine SNP50 Bead Chip. Prior to imputation, a quality control (QC) was performed, and SNPs located within a window of 2 Mb from each MS were selected. The core of the developed pipeline was made up of three steps: (a) storing of both MS and SNP data in a Variant Call Format file, (b) masking MS information in a random sample of individuals (10%), (c) imputing masked MS based on non-missing individuals (90%) using an imputation program. The feasability of the proposed methodology was assessed also among different training − testing split ratio, population size, number of flanking SNPs as well as within and among breeds. The accuracy of the MS imputation was assessed based on the genotype concordance as well as at parentage verification level in a subset of animals in which assigned parents' MS were available. A total of 8 MS passed the QC, and 505 SNPs were located within the ±2 Mb window from each MS, with an average of 63 SNPs per MS. The results were encouraging since when excluding the worst imputed MS (<i>OARAE129</i>), and regardless on the analyses performed (within and across breeds) for all breeds, we achieved an overall concordance rate over 94%. In addition, on average, the imputed offspring MS resulted in equivalent parentage outcome in 94% of the cases when compared to verification using original MS, highlighting both the feasibility and the eventual practical advantage of using this imputation pipeline.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 3","pages":"278-290"},"PeriodicalIF":2.6,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12839","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138500245","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":"Should performance at different race lengths be treated as genetically distinct traits in Coldblooded trotters?","authors":"Paulina Berglund,&nbsp;Sreten Andonov,&nbsp;Erling Strandberg,&nbsp;Susanne Eriksson","doi":"10.1111/jbg.12837","DOIUrl":"10.1111/jbg.12837","url":null,"abstract":"<p>Speed, in the form of racing time per kilometre (km), is a performance trait of the Swedish–Norwegian Coldblooded trotter included in the joint Swedish–Norwegian genetic evaluation. A few popular stallions have dominated Coldblooded trotter breeding, which has led to an increasing average relationship between individuals in the population. This study investigated the scope for broadening the breeding goal by selecting for racing time per km over different race lengths (short: 1640 m, medium: 2140 m and long: 2640 m), as this could encourage the use of breeding sires that are less related to the population. Performance data on three- to 12-year-old Coldblooded trotters in all Swedish races run 1995–2021 were obtained from the Swedish Trotting Association. These data consisted of 46,356 observations for 8375 horses in short-distance races, 430,512 observations for 11,193 horses in medium-distance races and 11,006 observations for 3341 horses in long-distance races. Variance components and genetic correlations were calculated using a trivariate animal model with Gibbs sampling from the BLUPF90 suite of programs. Breeding values for the three traits were then estimated using univariate animal models with the same fixed and random effects as in the trivariate model. Heritability estimates of 0.27–0.28 and genetic correlations between racing time per km at the different distances of 0.97–0.99 were obtained. Despite the strong genetic correlation between the traits, there was some re-ranking among the top 10 and top 30 stallions based on distance-specific breeding values. Estimated rank correlation between breeding values for racing time per km in short- and medium-distance races was 0.86, while between short- and long-distance races and between medium- and long-distance races it was 0.61. Mean relationship within the top 10 and top 30 stallions based on breeding values for racing time per km at each distance was 0.31–0.33 and 0.23–0.24 while mean relationship to the rest of the population ranged from 0.17 to 0.18 for all groups, although the 10 and 30 top-ranking stallions differed somewhat in the traits. Estimated average increase in inbreeding was 0.1% per year of birth and 1.2% per generation. The strong genetic correlation between racing time per km at different distances did not support their use as genetically distinct traits. Re-ranking of stallions for racing time per km at different race lengths could favour the use of a larger number of stallions in breeding, but according to our results it would not promote the use of stallions that are less related to the total population. Other traits like longevity or health traits, for example, career length and orthopaedic status, may be more relevant in broadening the breeding goal and preventing a few sires dominating future breeding, and this would be interesting to study further.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"220-234"},"PeriodicalIF":2.6,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12837","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441691","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":"Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle","authors":"E. R. Carrara,&nbsp;P. S. Lopes,&nbsp;R. Veroneze,&nbsp;R. J. Pereira,&nbsp;L. E. F. Zadra,&nbsp;M. G. C. D. Peixoto","doi":"10.1111/jbg.12836","DOIUrl":"10.1111/jbg.12836","url":null,"abstract":"<p>For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (<i>F</i>_ROH), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (<i>F</i>_GRM), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (<i>F</i>_{GRM_0.5}), and by the proportion of homozygous loci (<i>F</i>_HOM) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. <i>F</i>_ROH was equal to 0.095 ± 0.084, and its Spearman correlation with <i>F</i>_GRM was low (0.44) and moderate-high with <i>F</i>_HOM (0.79) and with <i>F</i>_{GRM_0.5} (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"207-219"},"PeriodicalIF":2.6,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138447138","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}