Markers with low GenTrain scores can generate spurious signals in genome-wide scans for transmission ratio distortion
Luigi Sierra, Maria Gracia (Centre de Recerca en Agrigenòmica)
Casellas Vidal, Joaquim (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Martinez, Amparo (Universidad de Córdoba. Departamento de Genética)
Delgado Bermejo, Juan Vicente (Universidad de Córdoba. Departamento de Genética)
Fernández Álvarez, Javier (Universidad de Córdoba. Departamento de Genética)
Such i Martí, Francesc Xavier (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Jordana i Vidal, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Amills i Eras, Marcel (Centre de Recerca en Agrigenòmica)

Data:	2021
Resum:	Transmission ratio distortion (TRD) is the preferential transmission of one specific allele to offspring at the expense of the other. The existence of TRD is mostly explained by the segregation of genetic variants with deleterious effects on the developmental processes that go from the formation of gametes to fecundation and birth. A few years ago, a statistical methodology was implemented in order to detect TRD signals on a genome-wide scale as a first step toward uncovering the biological basis of TRD and reproductive success in domestic species. In the current work, we have analyzed the impact of SNP calling quality on the detection of TRD signals in a population of Murciano-Granadina goats. Seventeen bucks and their offspring (N = 288) were typed with the Goat SNP50 BeadChip, whereas the genotypes of the dams were lacking. Performance of a genome-wide scan revealed the existence of 36 SNPs showing significant evidence of TRD. When we calculated GenTrain scores for each of the SNPs, we observed that 25 SNPs showed scores below 0. 8. The allele frequencies of these SNPs in the offspring were not correlated with the allele frequencies estimated in the dams with statistical methods, providing evidence that flawed SNP calling quality might lead to the detection of spurious TRD signals. We conclude that, when performing TRD scans, the GenTrain scores of markers should be taken into account to discriminate SNPs that are truly under TRD from those yielding spurious signals owing to technical problems.
Ajuts:	Agencia Estatal de Investigación PID2019-105805RB-I00 Ministerio de Ciencia e Innovación CEX2019-000902-S Ministerio de Economía y Competitividad BES-C-2017-079709
Drets:	Tots els drets reservats.
Llengua:	Anglès
Document:	Article ; recerca ; Versió acceptada per publicar
Publicat a:	Animal Genetics, Vol. 52, Issue 5 (October 2021) , p. 779-781, ISSN 1365-2052

DOI: 10.1111/age.13107
PMID: 34189737

Postprint 14 p, 663.5 KB

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