RT Journal Article
SR Electronic
T1 Impact of SNP calling quality on the detection of transmission ratio distortion in goats
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.06.09.447792
DO 10.1101/2021.06.09.447792
A1 María Gracia Luigi-Sierra
A1 Joaquim Casellas
A1 Amparo Martínez
A1 Juan Vicente Delgado
A1 Javier Fernández Álvarez
A1 Francesc Xavier Such
A1 Jordi Jordana
A1 Marcel Amills
YR 2021
UL http://biorxiv.org/content/early/2021/06/10/2021.06.09.447792.abstract
AB Transmission ratio distortion (TRD) is the preferential transmission of one specific allele to offspring at the expense of the other one. 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 to uncover 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, while 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 one 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, thus evidencing 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 due to technical problems.Competing Interest StatementThe authors have declared no competing interest.