000048097 001__ 48097
000048097 005__ 20200221144334.0
000048097 0247_ $$2doi$$a10.1186/s12711-016-0189-x
000048097 0248_ $$2sideral$$a93731
000048097 037__ $$aART-2016-93731
000048097 041__ $$aeng
000048097 100__ $$aVerardo, L.L.
000048097 245__ $$aRevealing new candidate genes for reproductive traits in pigs: Combining Bayesian GWAS and functional pathways
000048097 260__ $$c2016
000048097 5060_ $$aAccess copy available to the general public$$fUnrestricted
000048097 5203_ $$aBackground: Reproductive traits such as number of stillborn piglets (SB) and number of teats (NT) have been evaluated in many genome-wide association studies (GWAS). Most of these GWAS were performed under the assumption that these traits were normally distributed. However, both SB and NT are discrete (e.g. count) variables. Therefore, it is necessary to test for better fit of other appropriate statistical models based on discrete distributions. In addition, although many GWAS have been performed, the biological meaning of the identified candidate genes, as well as their functional relationships still need to be better understood. Here, we performed and tested a Bayesian treatment of a GWAS model assuming a Poisson distribution for SB and NT in a commercial pig line. To explore the biological role of the genes that underlie SB and NT and identify the most likely candidate genes, we used the most significant single nucleotide polymorphisms (SNPs), to collect related genes and generated gene-transcription factor (TF) networks. Results: Comparisons of the Poisson and Gaussian distributions showed that the Poisson model was appropriate for SB, while the Gaussian was appropriate for NT. The fitted GWAS models indicated 18 and 65 significant SNPs with one and nine quantitative trait locus (QTL) regions within which 18 and 57 related genes were identified for SB and NT, respectively. Based on the related TF, we selected the most representative TF for each trait and constructed a gene-TF network of gene-gene interactions and identified new candidate genes. Conclusions: Our comparative analyses showed that the Poisson model presented the best fit for SB. Thus, to increase the accuracy of GWAS, counting models should be considered for this kind of trait. We identified multiple candidate genes (e.g. PTP4A2, NPHP1, and CYP24A1 for SB and YLPM1, SYNDIG1L, TGFB3, and VRTN for NT) and TF (e.g. NF-¿B and KLF4 for SB and SOX9 and ELF5 for NT), which were consistent with known newborn survival traits (e.g. congenital heart disease in fetuses and kidney diseases and diabetes in the mother) and mammary gland biology (e.g. mammary gland development and body length).
000048097 540__ $$9info:eu-repo/semantics/openAccess$$aby$$uhttp://creativecommons.org/licenses/by/3.0/es/
000048097 590__ $$a2.964$$b2016
000048097 591__ $$aAGRICULTURE, DAIRY & ANIMAL SCIENCE$$b2 / 57 = 0.035$$c2016$$dQ1$$eT1
000048097 591__ $$aGENETICS & HEREDITY$$b70 / 166 = 0.422$$c2016$$dQ2$$eT2
000048097 592__ $$a1.534$$b2016
000048097 593__ $$aAnimal Science and Zoology$$c2016$$dQ1
000048097 593__ $$aMedicine (miscellaneous)$$c2016$$dQ1
000048097 593__ $$aEcology, Evolution, Behavior and Systematics$$c2016$$dQ1
000048097 593__ $$aGenetics$$c2016$$dQ2
000048097 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000048097 700__ $$aSilva, F.F.
000048097 700__ $$aLopes, M.S.
000048097 700__ $$aMadsen, O.
000048097 700__ $$aBastiaansen, J.W.M.
000048097 700__ $$aKnol, E.F.
000048097 700__ $$aKelly, M.
000048097 700__ $$0(orcid)0000-0001-6256-5478$$aVarona, L.$$uUniversidad de Zaragoza
000048097 700__ $$aLopes, P.S.
000048097 700__ $$aGuimarães, S.E.F.
000048097 7102_ $$11001$$2420$$aUniversidad de Zaragoza$$bDpto. Anatom.,Embri.Genét.Ani.$$cÁrea Genética
000048097 773__ $$g48, 1 (2016), 189 [13 pp]$$pGenet. sel. evol.$$tGENETICS SELECTION EVOLUTION$$x0999-193X
000048097 8564_ $$s2575610$$uhttps://zaguan.unizar.es/record/48097/files/texto_completo.pdf$$yVersión publicada
000048097 8564_ $$s95339$$uhttps://zaguan.unizar.es/record/48097/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000048097 909CO $$ooai:zaguan.unizar.es:48097$$particulos$$pdriver
000048097 951__ $$a2020-02-21-13:46:29
000048097 980__ $$aARTICLE