Whole genome sequencing identifies allelic ratio distortion in sperm involving genes related to spermatogenesis in a swine model
Gòdia, Marta (Centre de Recerca en Agrigenòmica)
Casellas Vidal, Joaquim (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Rodríguez Gil, Joan Enric (Universitat Autònoma de Barcelona. Departament de Medicina i Cirurgia Animals)
Castelló Farré, Anna (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Sánchez Bonastre, Armando (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Clop, Alex (Centre de Recerca en Agrigenòmica)
Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia

Date:	2020
Abstract:	Transmission Ratio Distortion (TRD), the uneven transmission of an allele from a parent to its offspring, can be caused by allelic differences affecting gametogenesis, fertilization or embryogenesis. However, TRD remains vaguely studied at a genomic scale. We sequenced the diploid and haploid genomes of three boars from leukocytes and spermatozoa at 50x to shed light into the genetic basis of spermatogenesis-caused Allelic Ratio Distortion (ARD). We first developed a Binomial model to identify ARD by simultaneously analysing all three males. This led to the identification of 55 ARD SNPs, most of which were animal-specific. We then evaluated ARD individually within each pig by a Fisher's exact test and identified two shared genes (TOP3A and UNC5B) and four shared genomic regions harbouring distinct ARD SNPs in the three boars. The shared genomic regions contained candidate genes with functions related to spermatogenesis including AK7, ARID4B, BDKRB2, GSK3B, NID1, NSMCE1, PALB2, VRK1 and ZC3H13. Using the Fisher's test, we also identified 378 genes containing variants with protein damaging potential in at least one boar, a high proportion of which, including FAM120B, TDRD15, JAM2 or AOX4 among others, are associated to spermatogenesis. Overall, our results show that sperm is subjected to ARD with variants associated to a wide variety of genes involved in different stages of spermatogenesis.
Grants:	Ministerio de Economía y Competitividad AGL2013-44978-R Ministerio de Economía y Competitividad AGL2017-86946-R Agència de Gestió d'Ajuts Universitaris i de Recerca 2014/SGR-1528 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017/SGR-01060 Ministerio de Economía y Competitividad SEV-2015-0533 Ministerio de Economía y Competitividad BES-2014-070560
Note:	Altres ajuts: CERCA Programme/Generalitat de Catalunya
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Transmission ratio distortion ; Allelic ratio distortion ; Sperm ; Whole genome sequencing ; Swine
Published in:	DNA research, Vol. 27, Issue 5 (October 2020) , art. dsaa019, ISSN 1756-1663

DOI: 10.1093/dnares/dsaa019
PMID: 32931559

9 p, 319.1 KB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
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Articles > Published articles