- -

A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: Sosa-Madrid;Santa ...
Tamaño: 295.5Kb
Formato: PDF
Descripción: Versión del Autor.
Abrir
[Cerrado]
Nombre: jbg.12451.pdf
Tamaño: 1.791Mb
Formato: PDF
Descripción: Versión editorial
Solicitar una copia al autor
dc.contributor.author Sosa-Madrid, Bolivar Samuel es_ES
dc.contributor.author Santacreu Jerez, María Antonia es_ES
dc.contributor.author Blasco Mateu, Agustín es_ES
dc.contributor.author Fontanesi, Luca es_ES
dc.contributor.author Pena, R. es_ES
dc.contributor.author Ibáñez-Escriche, Noelia es_ES
dc.date.accessioned 2020-10-07T03:35:12Z
dc.date.available 2020-10-07T03:35:12Z
dc.date.issued 2020-03 es_ES
dc.identifier.issn 0931-2668 es_ES
dc.identifier.uri http://hdl.handle.net/10251/151311
dc.description.abstract [EN] Uterine capacity (UC), defined as the total number of kits from unilaterally ovariectomized does at birth, has a high genetic correlation with litter size. The aim of our research was to identify genomic regions associated with litter size traits through a genome-wide association study using rabbits from a divergent selection experiment for UC. A high-density SNP array (200K) was used to genotype 181 does from a control population, high and low UC lines. Traits included total number born (TNB), number born alive (NBA), number born dead, ovulation rate (OR), implanted embryos (IE), and embryo, foetal and prenatal survivals at second parity. We implemented the Bayes B method and the associations were tested by Bayes factors and the percentage of genomic variance (GV) explained by windows. Different genomic regions associated with TNB, NBA, IE, and OR were found. These regions explained 7.36%, 1.27%, 15.87%, and 3.95% of GV, respectively. Two consecutive windows on chromosome 17 were associated with TNB, NBA, and IE. This genomic region accounted for 6.32% of GV of TNB. In this region, we found the BMP4, PTDGR, PTGER2, STYX and CDKN3 candidate genes which presented functional annotations linked to some reproductive processes. Our findings suggest that a genomic region on chromosome 17 has an important effect on litter size traits. However, further analyses are needed to validate this region in other maternal rabbit lines. es_ES
dc.description.sponsorship The work was funded by project AGL2014-55921-C2-1-P from the National Programme for Fostering Excellence in Scientific and Technical Research Project I+D. B. Samuel Sosa-Madrid was supported by a grant from the National Secretariat of Science, Technology, and Innovation of Panama (SENACYT) for a master's degree (the first stage of this study): BECA-2199-40-2012. Also, he was supported by an FPI grant from the Ministry of Economy and Competitiveness of Spain (the second stage of this study): BES-2015-074194. es_ES
dc.language Inglés es_ES
dc.publisher Blackwell Publishing es_ES
dc.relation.ispartof Journal of Animal Breeding and Genetics es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject Divergent selection es_ES
dc.subject Genome-wide association studies es_ES
dc.subject Litter size es_ES
dc.subject Quantitative trait loci es_ES
dc.subject Rabbits es_ES
dc.subject Uterine capacity es_ES
dc.subject.classification PRODUCCION ANIMAL es_ES
dc.title A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1111/jbg.12451 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//AGL2014-55921-C2-1-P/ES/ESTUDIO GENOMICO Y METABOLOMICO DE VARIAS LINEAS DE SELECCION DIVERGENTE EN CONEJO: EL CONEJO COMO MODELO EXPERIMENTAL/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BES-2015-074194/ES/BES-2015-074194/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/SENACYT//BECA-2199-40-2012/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ciencia Animal - Departament de Ciència Animal es_ES
dc.description.bibliographicCitation Sosa-Madrid, BS.; Santacreu Jerez, MA.; Blasco Mateu, A.; Fontanesi, L.; Pena, R.; Ibáñez-Escriche, N. (2020). A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits. Journal of Animal Breeding and Genetics. 137(2):123-138. https://doi.org/10.1111/jbg.12451 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1111/jbg.12451 es_ES
dc.description.upvformatpinicio 123 es_ES
dc.description.upvformatpfin 138 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 137 es_ES
dc.description.issue 2 es_ES
dc.identifier.pmid 31657065 es_ES
dc.relation.pasarela S\395254 es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder Secretaría Nacional de Ciencia, Tecnología e Innovación, Panamá es_ES
dc.description.references Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., … Searle, S. M. J. (2016). The Ensembl gene annotation system. Database, 2016, baw093. doi:10.1093/database/baw093 es_ES
dc.description.references Al-Samerria, S., Al-Ali, I., McFarlane, J. R., & Almahbobi, G. (2015). The impact of passive immunisation against BMPRIB and BMP4 on follicle development and ovulation in mice. REPRODUCTION, 149(5), 403-411. doi:10.1530/rep-14-0451 es_ES
dc.description.references Argente, M. J., Merchán, M., Peiró, R., García, M. L., Santacreu, M. A., Folch, J. M., & Blasco, A. (2010). Candidate gene analysis for reproductive traits in two lines of rabbits divergently selected for uterine capacity1. Journal of Animal Science, 88(3), 828-836. doi:10.2527/jas.2009-2324 es_ES
dc.description.references Argente, M. J., Santacreu, M. A., Climent, A., Bolet, G., & Blasco, A. (1997). Divergent selection for uterine capacity in rabbits. Journal of Animal Science, 75(9), 2350. doi:10.2527/1997.7592350x es_ES
dc.description.references Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25-29. doi:10.1038/75556 es_ES
dc.description.references Ballester, M., Castelló, A., Peiró, R., Argente, M. J., Santacreu, M. A., & Folch, J. M. (2012). Identification of differentially expressed genes in the oviduct of two rabbit lines divergently selected for uterine capacity using suppression subtractive hybridization. Animal Genetics, 44(3), 296-304. doi:10.1111/age.12005 es_ES
dc.description.references Bergfelder-Drüing, S., Grosse-Brinkhaus, C., Lind, B., Erbe, M., Schellander, K., Simianer, H., & Tholen, E. (2015). A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive. PLOS ONE, 10(3), e0117468. doi:10.1371/journal.pone.0117468 es_ES
dc.description.references Blasco, A., Argente, M. J., Haley, C. S., & Santacreu, M. A. (1994). Relationships between components of litter size in unilaterally ovariectomized and intact rabbit does. Journal of Animal Science, 72(12), 3066-3072. doi:10.2527/1994.72123066x es_ES
dc.description.references Blasco, A., Ortega, J. A., Climent, A., & Santacreu, M. A. (2005). Divergent selection for uterine capacity in rabbits. I. Genetic parameters and response to selection1. Journal of Animal Science, 83(10), 2297-2302. doi:10.2527/2005.83102297x es_ES
dc.description.references Blasco, A., & Pena, R. N. (2018). Current Status of Genomic Maps: Genomic Selection/GBV in Livestock. Animal Biotechnology 2, 61-80. doi:10.1007/978-3-319-92348-2_4 es_ES
dc.description.references Browning, B. L., & Browning, S. R. (2009). A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals. The American Journal of Human Genetics, 84(2), 210-223. doi:10.1016/j.ajhg.2009.01.005 es_ES
dc.description.references Carneiro, M., Afonso, S., Geraldes, A., Garreau, H., Bolet, G., Boucher, S., … Ferrand, N. (2011). The Genetic Structure of Domestic Rabbits. Molecular Biology and Evolution, 28(6), 1801-1816. doi:10.1093/molbev/msr003 es_ES
dc.description.references Carneiro, M., Rubin, C.-J., Di Palma, F., Albert, F. W., Alfoldi, J., Barrio, A. M., … Andersson, L. (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science, 345(6200), 1074-1079. doi:10.1126/science.1253714 es_ES
dc.description.references Cartuche, L., Pascual, M., Gómez, E. A., & Blasco, A. (2014). Economic weights in rabbit meat production. World Rabbit Science, 22(3), 165. doi:10.4995/wrs.2014.1747 es_ES
dc.description.references Cesar, A. S., Regitano, L. C., Mourão, G. B., Tullio, R. R., Lanna, D. P., Nassu, R. T., … Coutinho, L. L. (2014). Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle. BMC Genetics, 15(1), 39. doi:10.1186/1471-2156-15-39 es_ES
dc.description.references Christenson, R. K., Leymaster, K. A., & Young, L. D. (1987). Justification of Unilateral Hysterectomy-Ovariectomy as a Model to Evaluate Uterine Capacity in Swine. Journal of Animal Science, 65(3), 738-744. doi:10.2527/jas1987.653738x es_ES
dc.description.references Ding, X., Zhang, X., Mu, Y., Li, Y., & Hao, J. (2012). Effects of BMP4/SMAD signaling pathway on mouse primordial follicle growth and survival via up-regulation ofSohlh2andc-kit. Molecular Reproduction and Development, 80(1), 70-78. doi:10.1002/mrd.22138 es_ES
dc.description.references Fan, B., Du, Z.-Q., Gorbach, D. M., & Rothschild, M. F. (2010). Development and Application of High-density SNP Arrays in Genomic Studies of Domestic Animals. Asian-Australasian Journal of Animal Sciences, 23(7), 833-847. doi:10.5713/ajas.2010.r.03 es_ES
dc.description.references Garrick, D. J., & Fernando, R. L. (2013). Implementing a QTL Detection Study (GWAS) Using Genomic Prediction Methodology. Genome-Wide Association Studies and Genomic Prediction, 275-298. doi:10.1007/978-1-62703-447-0_11 es_ES
dc.description.references Goggolidou, P., Soneji, S., Powles-Glover, N., Williams, D., Sethi, S., Baban, D., … Norris, D. P. (2013). A chronological expression profile of gene activity during embryonic mouse brain development. Mammalian Genome, 24(11-12), 459-472. doi:10.1007/s00335-013-9486-7 es_ES
dc.description.references Jiao, X., Sherman, B. T., Huang, D. W., Stephens, R., Baseler, M. W., Lane, H. C., & Lempicki, R. A. (2012). DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics, 28(13), 1805-1806. doi:10.1093/bioinformatics/bts251 es_ES
dc.description.references Kass, R. E., & Raftery, A. E. (1995). Bayes Factors. Journal of the American Statistical Association, 90(430), 773-795. doi:10.1080/01621459.1995.10476572 es_ES
dc.description.references Kessner, D., & Novembre, J. (2015). Power Analysis of Artificial Selection Experiments Using Efficient Whole Genome Simulation of Quantitative Traits. Genetics, 199(4), 991-1005. doi:10.1534/genetics.115.175075 es_ES
dc.description.references Konno, T., Pinho Melo, E., Lopes, C., Mehmeti, I., Lenzen, S., Ron, D., & Avezov, E. (2015). ERO1-independent production of H2O2 within the endoplasmic reticulum fuels Prdx4-mediated oxidative protein folding. Journal of Cell Biology, 211(2), 253-259. doi:10.1083/jcb.201506123 es_ES
dc.description.references Laborda, P., Mocé, M. L., Blasco, A., & Santacreu, M. A. (2012). Selection for ovulation rate in rabbits: Genetic parameters and correlated responses on survival rates1. Journal of Animal Science, 90(2), 439-446. doi:10.2527/jas.2011-4219 es_ES
dc.description.references Laborda, P., Mocé, M. L., Santacreu, M. A., & Blasco, A. (2011). Selection for ovulation rate in rabbits: Genetic parameters, direct response, and correlated response on litter size1. Journal of Animal Science, 89(10), 2981-2987. doi:10.2527/jas.2011-3906 es_ES
dc.description.references Lehermeier, C., Wimmer, V., Albrecht, T., Auinger, H.-J., Gianola, D., Schmid, V. J., & Schön, C.-C. (2013). Sensitivity to prior specification in Bayesian genome-based prediction models. Statistical Applications in Genetics and Molecular Biology, 12(3). doi:10.1515/sagmb-2012-0042 es_ES
dc.description.references Li, Y., & Parast, M. M. (2014). BMP4 regulation of human trophoblast development. The International Journal of Developmental Biology, 58(2-3-4), 239-246. doi:10.1387/ijdb.130341mp es_ES
dc.description.references López de Maturana, E., Ibáñez-Escriche, N., González-Recio, Ó., Marenne, G., Mehrban, H., Chanock, S. J., … Malats, N. (2014). Next generation modeling in GWAS: comparing different genetic architectures. Human Genetics, 133(10), 1235-1253. doi:10.1007/s00439-014-1461-1 es_ES
dc.description.references Marras, G., Rossoni, A., Schwarzenbacher, H., Biffani, S., Biscarini, F., & Nicolazzi, E. L. (2016). zanardi: an open-source pipeline for multiple-species genomic analysis of SNP array data. Animal Genetics, 48(1), 121-121. doi:10.1111/age.12485 es_ES
dc.description.references Matzuk, M. M., & Lamb, D. J. (2002). Genetic dissection of mammalian fertility pathways. Nature Cell Biology, 4, S33-S40. doi:10.1038/ncb-nm-fertilitys41 es_ES
dc.description.references Merchán, M., Peiró, R., Argente, M. J., Santacreu, M. A., García, M. L., Blasco, A., & Folch, J. M. (2009). Analysis of theoviductal glycoprotein 1polymorphisms and their effects on components of litter size in rabbits. Animal Genetics, 40(5), 756-758. doi:10.1111/j.1365-2052.2009.01898.x es_ES
dc.description.references Mocé, M. L., Santacreu, M. A., Climent, A., & Blasco, A. (2004). The effect of divergent selection for uterine capacity on fetal and placental development at term in rabbits: Maternal and embryonic genetic effects1. Journal of Animal Science, 82(4), 1046-1052. doi:10.1093/ansci/82.4.1046 es_ES
dc.description.references Mocé, M. L., Santacreu, M. A., Climent, A., & Blasco, A. (2005). Divergent selection for uterine capacity in rabbits. III. Responses in uterine capacity and its components estimated with a cryopreserved control population1. Journal of Animal Science, 83(10), 2308-2312. doi:10.2527/2005.83102308x es_ES
dc.description.references Onteru, S. K., Fan, B., Du, Z.-Q., Garrick, D. J., Stalder, K. J., & Rothschild, M. F. (2011). A whole-genome association study for pig reproductive traits. Animal Genetics, 43(1), 18-26. doi:10.1111/j.1365-2052.2011.02213.x es_ES
dc.description.references Onteru, S. K., Gorbach, D. M., Young, J. M., Garrick, D. J., Dekkers, J. C. M., & Rothschild, M. F. (2013). Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig. PLoS ONE, 8(6), e61756. doi:10.1371/journal.pone.0061756 es_ES
dc.description.references Peiró, R., Merchán, M., Santacreu, M. A., Argente, M. J., García, M. L., Folch, J. M., & Blasco, A. (2008). Identification of Single-Nucleotide Polymorphism in the Progesterone Receptor Gene and Its Association With Reproductive Traits in Rabbits. Genetics, 180(3), 1699-1705. doi:10.1534/genetics.108.090779 es_ES
dc.description.references Piles, M., García, M. L., Rafel, O., Ramon, J., & Baselga, M. (2006). Genetics of litter size in three maternal lines of rabbits: Repeatability versus multiple-trait models. Journal of Animal Science, 84(9), 2309-2315. doi:10.2527/jas.2005-622 es_ES
dc.description.references Quinton, V. M., Wilton, J. W., Robinson, J. A., & Mathur, P. K. (2006). Economic weights for sow productivity traits in nucleus pig populations. Livestock Science, 99(1), 69-77. doi:10.1016/j.livprodsci.2005.06.002 es_ES
dc.description.references Ragab, M., Sánchez, J. P., Mínguez, C., Vicente, J. S., & Baselga, M. (2014). Litter size components in a full diallel cross of four maternal lines of rabbits1. Journal of Animal Science, 92(8), 3231-3236. doi:10.2527/jas.2013-7286 es_ES
dc.description.references Rosenbloom, K. R., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., … Kent, W. J. (2014). The UCSC Genome Browser database: 2015 update. Nucleic Acids Research, 43(D1), D670-D681. doi:10.1093/nar/gku1177 es_ES
dc.description.references Ros-Freixedes, R., Gol, S., Pena, R. N., Tor, M., Ibáñez-Escriche, N., Dekkers, J. C. M., & Estany, J. (2016). Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs. PLOS ONE, 11(3), e0152496. doi:10.1371/journal.pone.0152496 es_ES
dc.description.references Rossitto, M., Ujjan, S., Poulat, F., & Boizet-Bonhoure, B. (2015). Multiple roles of the prostaglandin D2 signaling pathway in reproduction. REPRODUCTION, 149(1), R49-R58. doi:10.1530/rep-14-0381 es_ES
dc.description.references Santacreu, M. A., Mocé, M. L., Climent, A., & Blasco, A. (2005). Divergent selection for uterine capacity in rabbits. II. Correlated response in litter size and its components estimated with a cryopreserved control population1. Journal of Animal Science, 83(10), 2303-2307. doi:10.2527/2005.83102303x es_ES
dc.description.references Schneider, J. F., Nonneman, D. J., Wiedmann, R. T., Vallet, J. L., & Rohrer, G. A. (2014). Genomewide association and identification of candidate genes for ovulation rate in swine12. Journal of Animal Science, 92(9), 3792-3803. doi:10.2527/jas.2014-7788 es_ES
dc.description.references Schneider, J. F., Rempel, L. A., Snelling, W. M., Wiedmann, R. T., Nonneman, D. J., & Rohrer, G. A. (2012). Genome-wide association study of swine farrowing traits. Part II: Bayesian analysis of marker data1,2. Journal of Animal Science, 90(10), 3360-3367. doi:10.2527/jas.2011-4759 es_ES
dc.description.references Stelzer, G., Rosen, N., Plaschkes, I., Zimmerman, S., Twik, M., Fishilevich, S., … Lancet, D. (2016). The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Current Protocols in Bioinformatics, 54(1). doi:10.1002/cpbi.5 es_ES
dc.description.references Stephens, M., & Balding, D. J. (2009). Bayesian statistical methods for genetic association studies. Nature Reviews Genetics, 10(10), 681-690. doi:10.1038/nrg2615 es_ES
dc.description.references Toosi, A., Fernando, R. L., & Dekkers, J. C. M. (2018). Genome-wide mapping of quantitative trait loci in admixed populations using mixed linear model and Bayesian multiple regression analysis. Genetics Selection Evolution, 50(1). doi:10.1186/s12711-018-0402-1 es_ES
dc.description.references H.M., Y., Kumar, S., Dubey, P. P., Modi, R. P., Chaudhary, R., A., S. K., … B., S. (2017). Profiling of sperm gene transcripts in crossbred ( Bos taurus x Bos indicus ) bulls. Animal Reproduction Science, 177, 25-34. doi:10.1016/j.anireprosci.2016.12.003 es_ES
dc.description.references Zeisel, S. H. (2011). The supply of choline is important for fetal progenitor cells. Seminars in Cell & Developmental Biology, 22(6), 624-628. doi:10.1016/j.semcdb.2011.06.002 es_ES
dc.description.references Ziadi, C., Mocé, M. L., Laborda, P., Blasco, A., & Santacreu, M. A. (2013). Genetic selection for ovulation rate and litter size in rabbits: Estimation of genetic parameters and direct and correlated responses1. Journal of Animal Science, 91(7), 3113-3120. doi:10.2527/jas.2012-6043 es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem