Genetics Selection Evolution最新文献

{"title":"Correction: Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis","authors":"Jesús Valdés-Hernández, Josep M. Folch, Daniel Crespo-Piazuelo, Magí Passols, Cristina Sebastià, Lourdes Criado-Mesas, Anna Castelló, Armand Sánchez, Yuliaxis Ramayo-Caldas","doi":"10.1186/s12711-024-00885-8","DOIUrl":"https://doi.org/10.1186/s12711-024-00885-8","url":null,"abstract":"<p><b>Correction: Genetics Selection Evolution (2024) 56:12</b><b>https://doi.org/10.1186/s12711-024-00882-x</b></p><p>After publication of original article [1], we noticed that two errors were introduced during production:</p><ol>\u0000<li>\u0000<span>(1)</span>\u0000<p>In the <b>Bioinformatic and statistical analyses</b> section, the corresponding information on the <b>X</b> and <b>Y</b> matrices has been removed in three places:</p>\u0000<p>The part “A regularized canonical correlation analysis (rCCA) was performed using the expression dataset of the 12,381 genes (matrix) and the 15 FA traits (matrix) measured on the 129 individuals. The rCCA multivariate approach is implemented in the mixOmics v6.14.1 package [12], which allows subsets of canonical variables that maximize the correlation between two datasets (“and”, respectively of sizes n × p and n × q) to be identified [22].”</p>\u0000<p>Should be “A regularized canonical correlation analysis (rCCA) was performed using the expression dataset of the 12,381 genes (matrix <b>Y</b>) and the 15 FA traits (matrix <b>X</b>) measured on the 129 individuals. The rCCA multivariate approach is implemented in the mixOmics v6.14.1 package [10], which allows to identify the subsets of canonical variables that maximize the correlation between two datasets (“<b>X</b> and <b>Y</b>”, respectively of sizes n × p and n × q) [22].”</p>\u0000</li>\u0000<li>\u0000<span>(2)</span>\u0000<p>In the Funding section, the following term “https://doi.org/” has been automatically added to the funding source in three places. In fact, the correct funding source should be “MCIN/AEI/10.13039/501100011033” and not “MCIN/AEI/https://doi.org/10.13039/501100011033”.</p>\u0000</li>\u0000</ol><ol data-track-component=\"outbound reference\"><li data-counter=\"1.\"><p>Valdés-Hernández J, Folch JM, Crespo-Piazuelo D, Passols M, Sebastià C, Criado-Mesas L, Castelló A, Sánchez A, Ramayo-Caldas Y. Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis. Genet Sel Evol. 2024;56:12. https://doi.org/10.1186/s12711-024-00882-x.</p><p>Article CAS PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><h3>Authors and Affiliations</h3><ol><li><p>Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain</p><p>Jesús Valdés-Hernández, Josep M. Folch, Magí Passols, Cristina Sebastià, Lourdes Criado-Mesas, Anna Castelló & Armand Sánchez</p></li><li><p>Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain</p><p>Jesús Valdés-Hernández, Josep M. Folch, Cristina Sebastià, Anna Castelló & Armand Sánchez</p></li><li><p>Departament de Genètica i Millora Animal, Institut de Recerca y Tecnologia Agraroalimentàri","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"138 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139967315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)","authors":"Katy Paul, Gwendal Restoux, Florence Phocas","doi":"10.1186/s12711-024-00884-9","DOIUrl":"https://doi.org/10.1186/s12711-024-00884-9","url":null,"abstract":"Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"11 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139925532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis","authors":"Jesús Valdés-Hernández, Josep M. Folch, Daniel Crespo-Piazuelo, Magí Passols, Cristina Sebastià, Lourdes Criado-Mesas, Anna Castelló, Armand Sánchez, Yuliaxis Ramayo-Caldas","doi":"10.1186/s12711-024-00882-x","DOIUrl":"https://doi.org/10.1186/s12711-024-00882-x","url":null,"abstract":"Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and putative regulators involved in FA composition, we performed a multivariate integrative analysis between intramuscular FA and transcriptome profiles of porcine longissimus dorsi (LD) muscle. We also carried out a combination of network, regulatory impact factor (RIF), in silico prediction of putative target genes, and functional analyses to better support the biological relevance of our findings. For this purpose, we used LD RNA-Seq and intramuscular FA composition profiles of 129 Iberian × Duroc backcrossed pigs. We identified 378 correlated variables (13 FA and 365 genes), including six FA (C20:4n-6, C18:2n-6, C20:3n-6, C18:1n-9, C18:0, and C16:1n-7) that were among the most interconnected variables in the predicted network. The detected FA-correlated genes include genes involved in lipid and/or carbohydrate metabolism or in regulation of IMF deposition (e.g., ADIPOQ, CHUK, CYCS, CYP4B1, DLD, ELOVL6, FBP1, G0S2, GCLC, HMGCR, IDH3A, LEP, LGALS12, LPIN1, PLIN1, PNPLA8, PPP1R1B, SDR16C5, SFRP5, SOD3, SNW1, and TFRC), meat quality (GALNT15, GOT1, MDH1, NEU3, PDHA1, SDHD, and UNC93A), and transport (e.g., EXOC7 and SLC44A2). Functional analysis highlighted 54 over-represented gene ontology terms, including well-known biological processes and pathways that regulate lipid and carbohydrate metabolism. RIF analysis suggested a pivotal role for six transcription factors (CARHSP1, LBX1, MAFA, PAX7, SIX5, and TADA2A) as putative regulators of gene expression and intramuscular FA composition. Based on in silico prediction, we identified putative target genes for these six regulators. Among these, TADA2A and CARHSP1 had extreme RIF scores and present novel regulators in pigs. In addition, the expression of TADA2A correlated (either positively or negatively) with C20:4n-6, C18:2n-6, C20:3n-6, C18:1n-9, and that of CARHSP1 correlated (positively) with the C16:1n-7 lipokine. We also found that these two transcription factors share target genes that are involved in lipid metabolism (e.g., GOT1, PLIN1, and TFRC). This integrative analysis of muscle transcriptome and intramuscular FA profile revealed valuable information about key candidate genes and potential regulators for FA and lipid metabolism in pigs, among which some transcription factors are proposed to control gene expression and modulate FA composition differences.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"237 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139720404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test","authors":"Jigme Dorji, Antonio Reverter, Pamela A. Alexandre, Amanda J. Chamberlain, Christy J. Vander-Jagt, James Kijas, Laercio R. Porto-Neto","doi":"10.1186/s12711-024-00879-6","DOIUrl":"https://doi.org/10.1186/s12711-024-00879-6","url":null,"abstract":"The study of ancestral alleles provides insights into the evolutionary history, selection, and genetic structures of a population. In cattle, ancestral alleles are widely used in genetic analyses, including the detection of signatures of selection, determination of breed ancestry, and identification of admixture. Having a comprehensive list of ancestral alleles is expected to improve the accuracy of these genetic analyses. However, the list of ancestral alleles in cattle, especially at the whole genome sequence level, is far from complete. In fact, the current largest list of ancestral alleles (~ 42 million) represents less than 28% of the total number of detected variants in cattle. To address this issue and develop a genomic resource for evolutionary studies, we determined ancestral alleles in cattle by comparing prior derived whole-genome sequence variants to an out-species group using a population-based likelihood ratio test. Our study determined and makes available the largest list of ancestral alleles in cattle to date (70.1 million) and includes 2.3 million on the X chromosome. There was high concordance (97.6%) of the determined ancestral alleles with those from previous studies when only high-probability ancestral alleles were considered (29.8 million positions) and another 23.5 million high-confidence ancestral alleles were novel, expanding the available reference list to improve the accuracies of genetic analyses involving ancestral alleles. The high concordance of the results with previous studies implies that our approach using genomic sequence variants and a likelihood ratio test to determine ancestral alleles is appropriate. Considering the high concordance of ancestral alleles across studies, the ancestral alleles determined in this study including those not previously listed, particularly those with high-probability estimates, may be used for further genetic analyses with reasonable accuracy. Our approach that used predetermined variants in species and the likelihood ratio test to determine ancestral alleles is applicable to other species for which sequence level genotypes are available.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"11 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139695588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle.","authors":"Maulana Mughitz Naji, José Luis Gualdrón Duarte, Natalia Soledad Forneris, Tom Druet","doi":"10.1186/s12711-024-00878-7","DOIUrl":"10.1186/s12711-024-00878-7","url":null,"abstract":"<p><strong>Background: </strong>Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding.</p><p><strong>Methods: </strong>We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (F_PED), on the correlation between uniting gametes (F_UNI), on the genomic relationship matrix (F_GRM), on excess homozygosity (F_HET), or on homozygous-by-descent (HBD) segments (F_HBD).</p><p><strong>Results: </strong>F_UNI and F_GRM were sensitive to used allele frequencies, whereas F_HET and F_HBD were more robust. We detected significant ID for four traits related to height and length; F_HBD and F_UNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments.</p><p><strong>Conclusions: </strong>Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"56 1","pages":"10"},"PeriodicalIF":4.1,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10832232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139652237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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":"Correction: Validation of reaction norm breeding values for robustness in Australian sheep","authors":"Dominic L. Waters, Sam A. Clark, Daniel J. Brown, Samuel F. Walkom, Julius H. J. van der Werf","doi":"10.1186/s12711-024-00877-8","DOIUrl":"https://doi.org/10.1186/s12711-024-00877-8","url":null,"abstract":"&lt;p&gt;\u0000&lt;b&gt;Correction: Genetics Selection Evolution (2024) 56:4 &lt;/b&gt;&lt;b&gt;https://doi.org/10.1186/s12711-023-00872-5&lt;/b&gt;&lt;/p&gt;&lt;p&gt;After publication of this original article [1], we noticed that an error was introduced in Eq. (2) page 3 which should be:&lt;/p&gt;&lt;span&gt;$$mathbf{y}=mathbf{X}mathbf{b}+{mathbf{Z}}_{1}{mathbf{a}}_{mathbf{0}}+{mathbf{Z}}_{mathbf{2}}{mathbf{a}}_{mathbf{1}}+{mathbf{Z}}_{mathbf{3}}mathbf{c}+mathbf{Q}mathbf{g}+{mathbf{e}},$$&lt;/span&gt;(2)&lt;p&gt;instead of :&lt;/p&gt;&lt;span&gt;$$mathbf{y}=mathbf{X}mathbf{b}+{Pmathbf{Z}}_{mathbf{1}}{mathbf{a}}_{mathbf{0}}+{mathbf{Z}}_{mathbf{2}}{mathbf{a}}_{mathbf{1}}+{mathbf{Z}}_{mathbf{3}}mathbf{c}+mathbf{Q}mathbf{g}+{mathbf{e}}.$$&lt;/span&gt;&lt;ol data-track-component=\"outbound reference\"&gt;&lt;li data-counter=\"1.\"&gt;&lt;p&gt;Waters DL, Clark SA, Brown DJ, Walkom SF, van der Werf HJ. Validation of reaction norm breeding values for robustness in Australian sheep. Genet Sel Evol. 2024;56:4. https://doi.org/10.1186/s12711-023-00872-5.&lt;/p&gt;&lt;p&gt;Article PubMed PubMed Central Google Scholar &lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;p&gt;Download references&lt;svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"&gt;&lt;use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"&gt;&lt;/use&gt;&lt;/svg&gt;&lt;/p&gt;&lt;h3&gt;Authors and Affiliations&lt;/h3&gt;&lt;ol&gt;&lt;li&gt;&lt;p&gt;School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia&lt;/p&gt;&lt;p&gt;Dominic L. Waters, Sam A. Clark &amp; Julius H. J. van der Werf&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;p&gt;Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, 2351, Australia&lt;/p&gt;&lt;p&gt;Dominic L. Waters, Daniel J. Brown &amp; Samuel F. Walkom&lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;span&gt;Authors&lt;/span&gt;&lt;ol&gt;&lt;li&gt;&lt;span&gt;Dominic L. Waters&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Sam A. Clark&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Daniel J. Brown&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Samuel F. Walkom&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;li&gt;&lt;span&gt;Julius H. J. van der Werf&lt;/span&gt;View author publications&lt;p&gt;You can also search for this author in &lt;span&gt;PubMed&lt;span&gt; &lt;/span&gt;Google Scholar&lt;/span&gt;&lt;/p&gt;&lt;/li&gt;&lt;/ol&gt;&lt;h3&gt;Corresponding author&lt;/h3&gt;&lt;p&gt;Correspondence to Dominic L. Waters.&lt;/p&gt;&lt;h3&gt;Publisher’s Note&lt;/h3&gt;&lt;p&gt;Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.&lt;/p&gt;&lt;p&gt;The online version of the original article can be found at https://doi.org/10.1186/s12711-023-00872-5.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Open Access&lt;/b&gt; This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate cred","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"5 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139551074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The potential of microbiota information to better predict efficiency traits in growing pigs fed a conventional and a high-fiber diet","authors":"Vanille Déru, Francesco Tiezzi, Céline Carillier-Jacquin, Benoit Blanchet, Laurent Cauquil, Olivier Zemb, Alban Bouquet, Christian Maltecca, Hélène Gilbert","doi":"10.1186/s12711-023-00865-4","DOIUrl":"https://doi.org/10.1186/s12711-023-00865-4","url":null,"abstract":"Improving pigs’ ability to digest diets with an increased dietary fiber content is a lever to improve feed efficiency and limit feed costs in pig production. The aim of this study was to determine whether information on the gut microbiota and host genetics can contribute to predict digestive efficiency (DE, i.e. digestibility coefficients of energy, organic matter, and nitrogen), feed efficiency (FE, i.e. feed conversion ratio and residual feed intake), average daily gain, and daily feed intake phenotypes. Data were available for 1082 pigs fed a conventional or high-fiber diet. Fecal samples were collected at 16 weeks, and DE was estimated using near‑infrared spectrometry. A cross-validation approach was used to predict traits within the same diet, for the opposite diet, and for a combination of both diets, by implementing three models, i.e. with only genomic (Gen), only microbiota (Micro), and both genomic and microbiota information (Micro+Gen). The predictive ability with and without sharing common sires and breeding environment was also evaluated. Prediction accuracy of the phenotypes was calculated as the correlation between model prediction and phenotype adjusted for fixed effects. Prediction accuracies of the three models were low to moderate (< 0.47) for growth and FE traits and not significantly different between models. In contrast, for DE traits, prediction accuracies of model Gen were low (< 0.30) and those of models Micro and Micro+Gen were moderate to high (> 0.52). Prediction accuracies were not affected by the stratification of diets in the reference and validation sets and were in the same order of magnitude within the same diet, for the opposite diet, and for the combination of both diets. Prediction accuracies of the three models were significantly higher when pigs in the reference and validation populations shared common sires and breeding environment than when they did not (P < 0.001). The microbiota is a relevant source of information to predict DE regardless of the diet, but not to predict growth and FE traits for which prediction accuracies were similar to those obtained with genomic information only. Further analyses on larger datasets and more diverse diets should be carried out to complement and consolidate these results.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"32 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139494692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation of dual-purpose chicken breeding programs implementing gene editing.","authors":"Edward Y S Chuang, Robin Wellmann, Franck L B Meijboom, Jens Tetens, Jörn Bennewitz","doi":"10.1186/s12711-023-00874-3","DOIUrl":"10.1186/s12711-023-00874-3","url":null,"abstract":"<p><strong>Background: </strong>In spite of being controversial and raising ethical concerns, the application of gene editing is more likely to be accepted when it contributes to improving animal welfare. One of the animal welfare and ethical issues in chicken breeding is chick culling, the killing of the male layer chicks after hatching due to the poor fattening performance. Although establishing dual-purpose chicken lines could solve this problem, unfavorable genetic correlations between egg and meat production traits hindered their competitiveness. Although it is also controversial in ethical terms, gene editing may accelerate genetic progress in dual-purpose chicken and alleviate the ethical concerns from chick culling.</p><p><strong>Results: </strong>The simulation compared the utility improvement in dual-purpose use under two breeding schemes: one consisting in the improvement of the laying hens, and the second in the improvement of a synthetic line obtained from a layer broiler cross. In each breeding scheme, the breeding programs were simulated with and without gene editing. Polygenic breeding values and 500 simulated quantitative trait loci (QTL) with different levels of pleiotropy caused negative correlations between egg production, meat production, and overall health. The results of the simulation demonstrated that genetic gain could be accelerated by at most 81% for several generations if gene editing was used. The actual increase in genetic gain depended on the number of single nucleotide polymorphisms (SNPs) being edited per animal. The rate of genetic improvement became equal in scenarios with and without gene editing after 20 generations. This is because the remaining segregating QTL had small effects and their edition would have negative overall health effects from potential off-target edits. Although gene editing can improve genetic gain in quantitative traits, it can only be recommended as long as QTL with reasonable effect sizes are segregating and detectable.</p><p><strong>Conclusions: </strong>This simulation demonstrates the potential of gene editing to accelerate the simultaneous improvement of negatively correlated traits. When the risk of negative consequences from gene editing persists, the number of SNPs to be edited should be chosen carefully to obtain the optimal genetic gain.</p>","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"56 1","pages":"7"},"PeriodicalIF":4.1,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10795215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139486818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy","authors":"David Wragg, Wengang Zhang, Sarah Peterson, Murthy Yerramilli, Richard Mellanby, Jeffrey J. Schoenebeck, Dylan N. Clements","doi":"10.1186/s12711-024-00875-w","DOIUrl":"https://doi.org/10.1186/s12711-024-00875-w","url":null,"abstract":"Low-pass whole-genome sequencing and imputation offer significant cost savings, enabling substantial increases in sample size and statistical power. This approach is particularly promising in livestock breeding, providing an affordable means of screening individuals for deleterious alleles or calculating genomic breeding values. Consequently, it may also be of value in companion animal genomics to support pedigree breeding. We sought to evaluate in dogs the impact of low coverage sequencing and reference-guided imputation on genotype concordance and association analyses. DNA isolated from saliva of 30 Labrador retrievers was sequenced at low (0.9X and 3.8X) and high (43.5X) coverage, and down-sampled from 43.5X to 9.6X and 17.4X. Genotype imputation was performed using a diverse reference panel (1021 dogs), and two subsets of the former panel (256 dogs each) where one had an excess of Labrador retrievers relative to other breeds. We observed little difference in imputed genotype concordance between reference panels. Association analyses for a locus acting as a disease proxy were performed using single-marker (GEMMA) and haplotype-based (XP-EHH) tests. GEMMA results were highly correlated (r ≥ 0.97) between 43.5X and ≥ 3.8X depths of coverage, while for 0.9X the correlation was lower (r ≤ 0.8). XP-EHH results were less well correlated, with r ranging from 0.58 (0.9X) to 0.88 (17.4X). Across a random sample of 10,000 genomic regions averaging 17 kb in size, we observed a median of three haplotypes per dog across the sequencing depths, with 5% of the regions returning more than eight haplotypes. Inspection of one such region revealed genotype and phasing inconsistencies across sequencing depths. We demonstrate that saliva-derived canine DNA is suitable for whole-genome sequencing, highlighting the feasibility of client-based sampling. Low-pass sequencing and imputation require caution as incorrect allele assignments result when the subject possesses alleles that are absent in the reference panel. Larger panels have the capacity for greater allelic diversity, which should reduce the potential for imputation error. Although low-pass sequencing can accurately impute allele dosage, we highlight issues with phasing accuracy that impact haplotype-based analyses. Consequently, if accurately phased genotypes are required for analyses, we advocate sequencing at high depth (> 20X).","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"94 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in understanding the genetic architecture of antibody response to paratuberculosis in sheep by heritability estimate and LDLA mapping analyses and investigation of candidate regions using sequence-based data","authors":"Mario Graziano Usai, Sara Casu, Tiziana Sechi, Sotero L. Salaris, Sabrina Miari, Giuliana Mulas, Maria Giovanna Cancedda, Ciriaco Ligios, Antonello Carta","doi":"10.1186/s12711-023-00873-4","DOIUrl":"https://doi.org/10.1186/s12711-023-00873-4","url":null,"abstract":"Paratuberculosis is a contagious and incurable disease that is caused by Mycobacterium avium subsp. paratuberculosis (MAP) with significant negative effects on animal welfare and farm profitability. Based on a large naturally infected flock over 12 years, we analyzed repeated enzyme-linked immunosorbent assay tests (ELISA), OvineSNP50 BeadChip genotypes and whole-genome sequences imputed from 56 influential animals. The main goals were to estimate the genetic parameters of proxy traits for resistance to MAP, identify genomic regions associated with the host’s immune response against MAP and search for candidate genes and causative mutations through association and functional annotation analyses of polymorphisms identified by sequencing. Two variables were derived from ELISA tests. The first, a binary variable, assessed the infection status of each animal over the entire productive life, while the second considered the level of antibody recorded over time. Very similar results were obtained for both variables. Heritability estimates of about 0.20 were found and a significant region capturing 18% and 13% of the genetic variance was detected on ovine chromosome 20 by linkage disequilibrium and linkage analysis on OvineSNP50 positions. Functional annotation and association analyses on the imputed sequence polymorphisms that were identified in this region were carried out. No significant variants showed a functional effect on the genes that mapped to this region, most of which belong to the major histocompatibility complex class II (MHC II). However, the conditional analysis led to the identification of two significant polymorphisms that can explain the genetic variance associated with the investigated genomic region. Our results confirm the involvement of the host’s genetics in susceptibility to MAP in sheep and suggest that selective breeding may be an option to limit the infection. The estimated heritability is moderate with a relevant portion being due to a highly significant region on ovine chromosome 20. The results of the combined use of sequence-based data and functional analyses suggest several genes belonging to the MHC II as the most likely candidates, although no mutations in their coding regions showed a significant association. Nevertheless, information from genotypes of two highly significant polymorphisms in the region can enhance the efficiency of selective breeding programs.","PeriodicalId":55120,"journal":{"name":"Genetics Selection Evolution","volume":"68 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139407893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}