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- Crooks, Lucy, et al.
(författare)
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An Improved Method for Estimating Chromosomal Line Origin in QTL Analysis of Crosses Between Outbred Lines
- 2011
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 1, s. 57-64
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Tidskriftsartikel (refereegranskat)abstract
- Estimating the line origin of chromosomal sections from marker genotypes is a vital step in quantitative trait loci analyses of outbred line crosses. The original, and most commonly used, algorithm can only handle moderate numbers of partially informative markers. The advent of high-density genotyping with SNP chips motivates a new method because the generic sets of markers on SNP chips typically result in long stretches of partially informative markers. We validated a new method for inferring line origin, triM (tracing inheritance with Markov models), with simulated data. A realistic pattern of marker information was achieved by replicating the linkage disequilibrium from an existing chicken intercross. There were approximately 1500 SNP markers and 800 F-2 individuals. The performance of triM was compared to GridQTL, which uses a variant of the original algorithm but modified for larger datasets. triM estimated the line origin with an average error of 2%, was 10% more accurate than GridQTL, considerably faster, and better at inferring positions of recombination. GridQTL could not analyze all simulated replicates and did not estimate line origin for around a third of individuals at many positions. The study shows that triM has computational benefits and improved estimation over available algorithms and is valuable for analyzing the large datasets that will be standard in future.
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- Crooks, Lucy, et al.
(författare)
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Comparison of analyses of the QTLMAS XII common dataset. II : genome-wide association and fine mapping.
- 2009
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Ingår i: BMC Proceedings. - 1753-6561. ; 3 Suppl 1
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Tidskriftsartikel (refereegranskat)abstract
- As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We have evaluated the findings from the groups that reported fine mapping and genome-wide association (GWA) efforts to map quantitative trait loci (QTL). Generally the power to detect QTL was high and the Type 1 error was low. Estimates of QTL locations were generally very accurate. Some methods were much better than others at estimating QTL effects, and with some the accuracy depended on simulated effect size or minor allele frequency. There were also indications of bias in the effect estimates. No epistasis was simulated, but the two studies that included searches for epistasis reported several interacting loci, indicating a problem with controlling the Type I error rate in these analyses. Although this study is based on a single dataset, it indicates that there is a need to improve fine mapping and GWA methods with respect to estimation of genetic effects, appropriate choice of significance thresholds and analysis of epistasis.
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- Crooks, Lucy
(författare)
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Consequences of Epistasis on Growth in an Erhualian x White Duroc Pig Cross
- 2017
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Epistasis describes an interaction between the effects of loci. We included epistasis in quantitative trait locus (QTL) mapping of growth at a series of ages in a cross of a Chinese pig breed, Erhualian, with a commercial line, White Duroc. Erhualian pigs have much lower growth rates than White Duroc. We improved a method for genomewide testing of epistasis and present a clear analysis workflow. We also suggest a new approach for interpreting epistasis results where significant additive and dominance effects of a locus in specific backgrounds are determined. In total, seventeen QTL were found and eleven showed epistasis. Loci on chromosomes 2, 3, 4 and 7 were highlighted as affecting growth at more than one age or forming an interaction network. Epistasis resulted in both the QTL on chromosomes 3 and 7 having effects in opposite directions. We believe it is the first time for the chromosome 7 locus that an allele from a Chinese breed has been found to decrease growth. The consequences of epistasis were diverse. Results were impacted by using growth rather than body weight as the phenotype and by correcting for an effect of mother. Epistasis made a considerable contribution to growth in this population and modelling epistasis was important for accurately determining QTL effects.
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- Crooks, Lucy, et al.
(författare)
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Identification of Null Alleles and Deletions from SNP Genotypes for an Intercross Between Domestic and Wild Chickens
- 2013
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 3:8, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed genotypes from similar to 10K single-nucleotide polymorphisms (SNPs) in two families of an F-2 intercross between Red Junglefowl and White Leghorn chickens. Possible null alleles were found by patterns of incompatible and missing genotypes. We estimated that 2.6% of SNPs had null alleles compared with 2.3% with genotyping errors and that 40% of SNPs in which a parent and offspring were genotyped as different homozygotes had null alleles. Putative deletions were identified by null alleles at adjacent markers. We found two candidate deletions that were supported by fluorescence intensity data from a 60K SNP chip. One of the candidate deletions was from the Red Junglefowl, and one was present in both the Red Junglefowl and White Leghorn. Both candidate deletions spanned protein-coding regions and were close to a previously detected quantitative trait locus affecting body weight in this population. This study demonstrates that the similar to 50K SNP genotyping arrays now available for several agricultural species can be used to identify null alleles and deletions in data from large families. We suggest that our approach could be a useful complement to linkage analysis in experimental crosses.
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