Markers with low GenTrain scores can generate spurious signals in genome‐wide scans for transmission ratio distortion

2021 ◽  
Author(s):  
María Gracia Luigi‐Sierra ◽  
Joaquim Casellas ◽  
Amparo Martínez ◽  
Juan Vicente Delgado ◽  
Javier Fernández Álvarez ◽  
...  
Keyword(s):  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Genome Wide ◽  
Ratio Distortion ◽  
Spurious Signals

scholarly journals Impact of SNP calling quality on the detection of transmission ratio distortion in goats

2021 ◽  
Author(s):  
Maria Luigi-Sierra ◽  
Joaquim Casellas ◽  
Amparo Martinez ◽  
Juan Vicente Delgado ◽  
Javier Fernandez Alvarez ◽  
...  
Keyword(s):  
Allele Frequencies ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Technical Problems ◽  
Domestic Species ◽  
Snp Calling ◽  
Genome Wide ◽  
A Genome ◽  
Ratio Distortion ◽  
The Impact

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.

scholarly journals Transmission ratio distortion in the myotonic dystrophy locus in human preimplantation embryos

2006 ◽  
Vol 14 (3) ◽  
pp. 299-306 ◽  
Author(s):  
Nicola L Dean ◽  
J Concepción Loredo-Osti ◽  
T Mary Fujiwara ◽  
Kenneth Morgan ◽  
Seang Lin Tan ◽  
...  
Keyword(s):  
Myotonic Dystrophy ◽  
Transmission Ratio Distortion ◽  
Preimplantation Embryos ◽  
Transmission Ratio ◽  
Ratio Distortion ◽  
Human Preimplantation Embryos

scholarly journals Transmission-Ratio Distortion Through F1 Females at Chromosome 11 Loci Linked to Om in the Mouse DDK Syndrome

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1299-1304
Author(s):  
F Pardo-Manuel de Villena ◽  
C Slamka ◽  
M Fonseca ◽  
A K Naumova ◽  
J Paquette ◽  
...  
Keyword(s):  
Genetic Model ◽  
Inbred Mouse ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
F1 Hybrids ◽  
Mouse Strains ◽  
Inbred Mouse Strains ◽  
Chromosome 11 ◽  
Ratio Distortion

Abstract We determined the genotypes of >200 offspring that are survivors of matings between female reciprocal F1 hybrids (between the DDK and C57BL/6J inbred mouse strains) and C57BL/6J males at markers linked to the Ovum mutant (Om) locus on chromosome 11. In contrast to the expectations of our previous genetic model to explain the “DDK syndrome,” the genotypes of these offspring do not reflect preferential survival of individuals that receive C57BL/6J alleles from the F1 females in the region of chromosome 11 to which the Om locus has been mapped. In fact, we observe significant transmission-ratio distortion in favor of DDK alleles in this region. These results are also in contrast to the expectations of Wakasugi's genetic model for the inheritance of Om, in which he proposed equal transmission of DDK and non-DDK alleles from F1 females. We propose that the results of these experiments may be explained by reduced expression of the maternal DDK Om allele or expression of the maternal DDK Om allele in only a portion of the ova of F1 females

scholarly journals Nondisjunction and transmission ratio distortion ofChromosome 2 in a (2.8) Robertsonian translocation mouse strain

2006 ◽  
Vol 17 (3) ◽  
pp. 239-247 ◽  
Author(s):  
Reiner Schulz ◽  
Lara A. Underkoffler ◽  
Joelle N. Collins ◽  
Rebecca J. Oakey
Keyword(s):  
Mouse Strain ◽  
Robertsonian Translocation ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Ratio Distortion

Concerted evolution of the mouse Tcp-10 gene family: Implications for the functional basis of t haplotype transmission ratio distortion

Genomics ◽  
1992 ◽  
Vol 12 (1) ◽  
pp. 35-41 ◽  
Author(s):  
Stephen H. Pilder ◽  
Cindy L. Decker ◽  
Salim Islam ◽  
Christine Buck ◽  
Judith A. Cebra-Thomas ◽  
...  
Keyword(s):  
Gene Family ◽  
Concerted Evolution ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Functional Basis ◽  
Ratio Distortion ◽  
T Haplotype

scholarly journals The in vivo and in vitro transmission ratio distortion of one complete and two partial t haplotypes in mice

1991 ◽  
Vol 57 (2) ◽  
pp. 153-157 ◽  
Author(s):  
William Garside ◽  
Christine Ruangvoravat ◽  
Patricia Dolan ◽  
Nina Hillman
Keyword(s):  
Genetic Model ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Different Types ◽  
Ratio Distortion

SummaryThe effects of different types of insemination (normal and delayed matings and in vitro fertilization) on the transmission ratio distortion (TRD) of three t haplotypes were determined. The tw73 haplotype which contains all of the loci known to affect TRD is transmitted at equivalent frequencies in normal matings and in in vitro fertilizations (0·84 and 0·85, respectively) but at a significantly lower frequency (0·62) in delayed matings. The distal partial th18 haplotype is transmitted at equivalent frequencies in all types of insemination (0·66 to 0·70) while the proximal partial tw18 haplotype is transmitted in Mendelian frequencies in normal matings and in in vitro inseminations but at a significantly lower frequency in delayed matings. The results are discussed with reference to the current genetic model for transmission ratio distortion.

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