Journal of Animal Breeding and Genetics最新文献

{"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}

{"title":"Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight","authors":"Candela Ojeda-Marín,&nbsp;Juan Pablo Gutiérrez,&nbsp;Nora Formoso-Rafferty,&nbsp;Félix Goyache,&nbsp;Isabel Cervantes","doi":"10.1111/jbg.12835","DOIUrl":"10.1111/jbg.12835","url":null,"abstract":"<p>Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH-based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H-Line), 766 individuals for the low variability line (L-Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (<i>F</i>_PED) information, on ROH identified using the SW method (<i>F</i>_ROHSW) and on ROH identified using the CR method (<i>F</i>_ROHCR). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between <i>F</i>_PED and <i>F</i>_ROH were high, particularly for <i>F</i>_ROHSW. Moreover, correlations between <i>F</i>_ROHSW and <i>F</i>_PED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of <i>F</i>_ROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH-based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with <i>F</i>_PED. Differences in robustness between lines were not attributable to a higher homozygosis in the L-Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"193-206"},"PeriodicalIF":2.6,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12835","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138292448","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":"Candidate genes for longitudinal traits under sequential sampling in beef cattle","authors":"Virgínia Mara Pereira Ribeiro,&nbsp;Gabriela Canabrava Gouveia,&nbsp;Fabio Luiz Buranelo Toral","doi":"10.1111/jbg.12833","DOIUrl":"10.1111/jbg.12833","url":null,"abstract":"<p>Both the measurement age of a longitudinal trait and the common pre-sampling procedures used in beef cattle herds may affect the identification of a functional candidate gene (FCG) that is potentially associated with a trait. To identify the FCG that takes part in the genetic control of body weight at five different ages in a beef cattle population with and without sequential sampling, the animals were weighed at different measurement events, around 330, 385, 440, 495 and 550 days old. Genetic parameters were estimated for body weight at each age using a single trait (STM) and a random regression model (RRM). In addition, two different databases were used to estimate the genetic parameters: the first (DB100) was formed by all animals that were weighed in the five measurement events, and the second (DB70) has records of the same population, considering that 70% of the heaviest animals were selected after each measurement event. For DB100, genome-wide association studies (GWAS) were performed with 21,667 SNP markers to identify genomic windows that explained at least 1% of the genetic variance. Additionally, prioritization analyses were performed and FCGs were selected. We associated seven different FCGs with body weight at different ages. Among them, the gene DUSP10 was suggested as FCG in all five ages evaluated. Genetic parameters estimated for body weight using DB100 were similar when STM and RRM were applied. However, when DB70 was used as phenotypic data, there were differences between the two models. When the STM was applied, there were differences between the genetic parameters estimated for body weight when DB100 or DB70 were used as sources of phenotypes, but not for the estimates obtained with RRM. The importance of each gene for animal growth can change at different ages, and different genes may be more relevant to body weight at each different growth stage for beef cattle. Besides, sequential sampling can affect the GWAS results of a longitudinal trait. The age of the animal when a longitudinal trait is measured and pre-sampling can also contribute to inconsistencies in GWAS results for body weight in beef cattle, depending on the time when that data were collected, and consequently on the identification of FCG between studies, even when models that consider a covariance structure are used.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"179-192"},"PeriodicalIF":2.6,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429306","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 background of biotypes related to growth, carcass and meat quality traits in Duroc pigs based on principal component analysis","authors":"Hannah E. Green,&nbsp;Hinayah Rojas de Oliveira,&nbsp;Amanda Botelho Alvarenga,&nbsp;Stacy Scramlin-Zuelly,&nbsp;Daniela Grossi,&nbsp;Allan P. Schinckel,&nbsp;Luiz F. Brito","doi":"10.1111/jbg.12831","DOIUrl":"10.1111/jbg.12831","url":null,"abstract":"<p>As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes with different sets of phenotypic measurements. Principal component analysis (PCA) and genome-wide association studies (GWAS) can be combined to understand the genetic architecture and biological mechanisms by defining biological types (biotypes) that relate these valuable traits. Therefore, the main objectives of this study were to: (1) estimate genomic-based genetic parameters; (2) define animal biotypes utilizing PCA; and (3) utilize GWAS to link the biotypes to candidate genes and quantitative trait loci (QTL). The phenotypic dataset included 2583 phenotypic records from female Duroc pigs from a terminal sire line. The pedigree file contained 193,764 animals and the genotype file included 21,309 animals with 35,651 single nucleotide polymorphisms (SNPs). Eight principal components (PCs), accounting for a total of 99.7% of the population variation, were defined for three growth, eight conventional carcass, 10 pork quality and 18 novel carcass traits. The eight biotypes defined from the PCs were found to be related to growth rate, maturity, meat quality and body structure, which were then related to candidate genes. Of the 175 candidate genes found, six of them [<i>LDHA</i> (SSC1), <i>PIK3C3</i> (SSC6), <i>PRKAG3</i> (SSC15), <i>VRTN</i> (SSC7), <i>DLST</i> (SSC7) and <i>PAPPA</i> (SSC1)] related to four PCs were found to be associated with previously defined QTL, linking the biotypes with biological processes involved with muscle growth, fat deposition, glycogen levels and skeletal development. Further functional analyses helped to make connections between biotypes, relating them through common KEGG pathways and gene ontology (GO) terms. These findings contribute to a better understanding of the genetic relationships between growth, carcass and meat quality traits in Duroc pigs, enabling breeders to better understand the biological mechanisms underlying the phenotypic expression of these traits.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"163-178"},"PeriodicalIF":2.6,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12831","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415339","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 multivariate gametic model for the analysis of purebred and crossbred data. An example between two populations of Iberian pigs","authors":"Houssemeddine Srihi,&nbsp;David López-Carbonell,&nbsp;Noelia Ibáñez-Escriche,&nbsp;Joaquim Casellas,&nbsp;Pilar Hernández,&nbsp;Sara Negro,&nbsp;Luis Varona","doi":"10.1111/jbg.12832","DOIUrl":"10.1111/jbg.12832","url":null,"abstract":"<p>Crossbreeding plays a pivotal role within pig breeding programmes, aiming to maximize heterosis and improve reproductive traits in crossbred maternal lines. Nevertheless, there is evidence indicating that the performance of reciprocal crosses between two genetic lines might exhibit variability. These variations in performance can be attributed to differences in the correlations between gametic effects, acting as either sire or dam, within purebred and crossbred populations. To address this issue, we propose a multivariate gametic model that incorporates up to four correlated gametic effects for each parental population. The model is employed on a data set comprising litter size data (total number of piglets born—TNB- and number of piglets born alive—NBA-) derived from a reciprocal cross involving two Iberian pig populations: Entrepelado and Retinto. The data set comprises 6933 records from 1564 purebred Entrepelado (EE) sows, 4995 records from 1015 Entrepelado × Retinto (ER) crosses, 2977 records from 756 Retinto × Entrepelado (RE) crosses and 7497 records from 1577 purebred Retinto (RR) sows. The data set is further supplemented by a pedigree encompassing 6007 individual-sire-dam entries. The statistical model also included the order of parity (with six levels), the breed of the service sire (five levels) and the herd-year-season effects (141 levels). Additionally, the model integrates random dominant and permanent environmental sow effects. The analysis employed a Bayesian approach, and the results revealed all the posterior estimates of the gametic correlations to be positive. The range of the posterior mean estimates of the correlations varied across different gametic effects and traits, with a range between 0.04 (gametic correlation between the paternal effects for purebred and the maternal for crossbred in Retinto) and 0.53 (gametic correlation between the paternal effects for purebred and the paternal for crossbred in Entrepelado). Furthermore, the posterior mean variance estimates of the maternal gametic effects were consistently surpassed those for paternal effects within all four populations. The results suggest the possible influence of imprinting effects on the genetic control of litter size, and underscore the importance of incorporating crossbred data into the breeding value predictions for purebred individuals.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"153-162"},"PeriodicalIF":2.6,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12832","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54232360","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":"Early life jumping traits: Are they good proxies for success in show jumping competitions in Belgian warmblood horses?","authors":"Léa Chapard,&nbsp;Roel Meyermans,&nbsp;Wim Gorssen,&nbsp;Katrijn Hooyberghs,&nbsp;Inge Meurrens,&nbsp;Stefaan De Smet,&nbsp;Nadine Buys,&nbsp;Steven Janssens","doi":"10.1111/jbg.12834","DOIUrl":"10.1111/jbg.12834","url":null,"abstract":"<p>The main goal of the Belgian Warmblood horse studbook (BWP) is to breed successful competition horses, with emphasis on show jumping. However, competition results are only available later in life and competition traits are lowly heritable. Hence, the use of phenotypes that record performance-related traits at an early life stage could help increase genetic progress. In this study, we evaluated the potential of eleven linear scored early life jumping traits assessed during jumping in freedom (2–5 years old) or under the saddle (4–6 years old) as proxies for later success in show jumping competitions. To this end, we estimated their heritabilities and genetic correlations with the competition trait, adjusted fence height, by using 2170 free jumping records, 1588 jumping under saddle records, 674,527 show jumping competition records and almost 81,000 informative horses in the pedigree. As participation of young horses in these contests is on a voluntary basis, a pre-selection most probably exists. To verify this hypothesis, we investigated the association between participation to young horse contests and participation to show jumping competitions later on (called here start status phenotype). We also estimated heritabilities for “start status in free jumping contest”, “start status in jumping under saddle contest” and “start status in free jumping or jumping under saddle contest” by fitting threshold models. Furthermore, we calculated genetic correlations between these traits and adjusted fence height and calculated the correlations between EBVs for start status in young horse contests and EBVs for success in competitions. Estimated heritabilities of early life jumping traits ranged between 0.05 and 0.30. Their genetic correlations with adjusted fence height were moderate to high (<i>r</i>_<i>g</i> = 0.37–0.63). Relatively more horses that participated in young horse contests competed later on compared to horses that did not participate in young horse contests (<i>p</i>-value &lt; 0.001). They were also significantly more successful in show jumping competitions. Furthermore, start status in young horse contests was moderately heritable in BWP horses (<i>h</i>² = 0.56–0.65) and moderately to highly correlated with later success in competitions (<i>r</i>_<i>g</i> = 0.30–0.77). Hence, we showed that ELJ traits are good proxies for later success in competitions and that a pre-selection of horses occurs in young horse contests. It is suggested to stimulate participation to young horse contests to achieve a more representative sample of the population. Early life jumping traits can therefore optimize the genetic progress for show jumping performance.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"138-152"},"PeriodicalIF":2.6,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12834","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50163824","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 prediction and genome-wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high-density SNP genotypes in Yunong-black pigs","authors":"Ziyi Wu,&nbsp;Tengfei Dou,&nbsp;Liyao Bai,&nbsp;Jinyi Han,&nbsp;Feng Yang,&nbsp;Kejun Wang,&nbsp;Xuelei Han,&nbsp;Ruimin Qiao,&nbsp;Xiu-Ling Li,&nbsp;Xin-Jian Li","doi":"10.1111/jbg.12830","DOIUrl":"10.1111/jbg.12830","url":null,"abstract":"<p>Body composition traits are complex traits controlled by minor genes and, in hybrid populations, are impacted by additive and nonadditive effects. We aimed to identify candidate genes and increase the accuracy of genomic prediction of body composition traits in crossbred pigs by including dominance genetic effects. Genomic selection (GS) and genome-wide association studies were performed on seven body composition traits in 807 Yunong-black pigs using additive genomic models (AM) and additive-dominance genomic models (ADM) with an imputed high-density single nucleotide polymorphism (SNP) array and the Illumina Porcine SNP50 BeadChip. The results revealed that the additive heritabilities estimated for AM and ADM using the 50 K SNP data ranged from 0.20 to 0.34 and 0.11 to 0.30, respectively. However, the ranges of additive heritability for AM and ADM in the imputed data ranged from 0.20 to 0.36 and 0.12 to 0.30, respectively. The dominance variance accounted for 23% and 27% of the total variance for the 50 K and imputed data, respectively. The accuracy of genomic prediction improved by 5% on average for 50 K and imputed data when dominance effect were considered. Without the dominance effect, the accuracies for 50 K and imputed data were 0.35 and 0.38, respectively, and 0.41 and 0.43, respectively, upon considering it. A total of 12 significant SNP and 16 genomic regions were identified in the AM, and 14 significant SNP and 21 genomic regions were identified in the ADM for both the 50 K and imputed data. There were five overlapping SNP in the 50 K and imputed data. In the AM, a significant SNP (CNC10041568) was found in both body length and backfat thickness traits, which was in the <i>PLAG1</i> gene strongly and significantly associated with body length and backfat thickness in pigs. Moreover, a significant SNP (CNC10031356) with a heterozygous dominant genotype was present in the ADM. Furthermore, several functionally related genes were associated with body composition traits, including <i>MOS</i>, <i>RPS20</i>, <i>LYN</i>, <i>TGS1</i>, <i>TMEM68</i>, <i>XKR4</i>, <i>SEMA4D</i> and <i>ARNT2</i>. These findings provide insights into molecular markers and GS breeding for the Yunong-black pigs.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"124-137"},"PeriodicalIF":2.6,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220471","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 evaluation of gestation length in Italian Holstein breed","authors":"Ferdinando Galluzzo,&nbsp;Giulio Visentin,&nbsp;Johannes B. C. H. M. van Kaam,&nbsp;Raffaella Finocchiaro,&nbsp;Stefano Biffani,&nbsp;Angela Costa,&nbsp;Maurizio Marusi,&nbsp;Martino Cassandro","doi":"10.1111/jbg.12828","DOIUrl":"10.1111/jbg.12828","url":null,"abstract":"<p>Gestation length (GL) can potentially affect health and performance of both the dam and the newborn calf, and it is controlled by two genetic components, direct and maternal. This means that both the calf (direct effect) and the cow (maternal effect) genotypes contribute to determine GL and its variability. The aims of the present study were to estimate direct and maternal variance components of GL, develop a routine genetic evaluation of GL in Italian Holstein and evaluate potential (un)favourable associations with traits for which selection is undertaken in this population. A multiple-trait repeatability linear animal model was employed for the estimation of variance components considering GL in first and later parities as different traits. The posterior mean (PM) of heritability of the direct effect was 0.43 for first parity and 0.35 for later parities. The PM of heritability of the maternal effect was lower, being 0.08 for primiparae and 0.06 for pluriparae. The posterior standard deviation (PSD) of the heritability estimates was small, ranging from 0.001 to 0.005. The relationship of direct and maternal effects with important traits such as milk yield and fertility indicated that selecting for extreme GL, longer or shorter, may have negative consequences on several traits, suggesting that GL has an intermediate optimum in dairy cattle. In conclusion, this study reveals that selecting an intermediate GL in the Italian Holstein population is advisable. Although scarcely variable compared to other conventional traits for which Italian Holstein is selected, GL is heritable and a deeper knowledge can be useful for decision-making at the farm level.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 2","pages":"113-123"},"PeriodicalIF":2.6,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41220420","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":"Ascertaining the genetic background of the Celtic-Iberian pig strain: A signatures of selection approach","authors":"Katherine D. Arias,&nbsp;Hanboreum Lee,&nbsp;Riccardo Bozzi,&nbsp;Isabel Álvarez,&nbsp;Juan Pablo Gutiérrez,&nbsp;Iván Fernandez,&nbsp;Juan Menéndez,&nbsp;Albano Beja-Pereira,&nbsp;Félix Goyache","doi":"10.1111/jbg.12829","DOIUrl":"10.1111/jbg.12829","url":null,"abstract":"<p>Celtic-Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic-Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic-Iberian genetic lineage. A total of 153 DNA samples of Celtic-Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise-comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP-EHH, <i>F</i>_ST and <i>Δ</i>DAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two-by-two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic-Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic-Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (<i>NOL12</i>, <i>LGALS1</i>, <i>PDXP</i>, <i>SH3BP1</i>, <i>GGA1</i>, <i>WIF1</i>, and <i>LYPD6</i>). Other studies reported that the <i>WIF1</i> gene is associated with ear size, one of the characteristic traits of the Celtic-Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non-improved pig strain traditionally exploited under semi-extensive conditions.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":"141 1","pages":"96-112"},"PeriodicalIF":2.6,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jbg.12829","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157396","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}