Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost efficient approach

BioRxiv : the Preprint Server for Biology
Yanjun ZanOrjan Carlborg


Background: Experimental intercrosses between outbred founder populations are powerful resources for mapping loci contributing to complex traits (Quantitative Trait Loci or QTL). Here, we present an approach and accompanying software for high-resolution genotype imputation in such populations using whole-genome high coverage sequence data on founder individuals (~30x) and low coverage sequence data on intercross individuals (~0.4x). The method is illustrated in a large F2 pedigree between lines of chickens that have been divergently selected for 40 generations for the same trait (body weight at 8 weeks of age). Results: Described is how hundreds of individuals were whole-genome sequenced in a cost- and time-efficient manner using a Tn5-based library preparation protocol optimized for this application. In total, 7.6M markers segregated in this pedigree and 10.0 to 13.7% were informative for imputing the founder line genotypes within the F0-F2 families. The genotypes imputed from low coverage sequence data were consistent with the founder line genotypes estimated using SNP and microsatellite markers both at individual imputed sites (92%) and across the genome of individual chickens (93%). The resolution of the recombination break...Continue Reading

Related Concepts

Computer Software
Biological Markers
Short Tandem Repeat
Quantitative Trait Loci
Equine Laminitis
F2 gene
Recombination, Genetic
Weighing Patient
Genetic Pedigree

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