Stripes

Stripes reconstructs founder mosaic genotypes in intercross offspring from outbred founder populations using low-coverage whole-genome sequencing of intercross individuals and high-coverage founder sequences to enable high-resolution QTL mapping of complex traits.

Key Features:

• Low-coverage sequencing reconstruction: Reconstructs genome-wide genotypes from very low-coverage (< 0.5×) sequencing data of intercross individuals.
• High-resolution genotyping: Identifies founder-line informative markers fixed for alternative alleles in divergent founder lines, enabling precise inference of recombination breakpoints with 50% localized to regions shorter than 10 kb.
• Consistency and accuracy: Genotypes inferred from low-coverage data show over 95% agreement with individual SNP genotyping.
• Optimized imputation algorithm: Incorporates an optimized imputation algorithm tailored for founder-mosaic genotype reconstruction across large pedigrees.
• Tn5-based library preparation: Utilizes a Tn5-based library preparation protocol to enable whole-genome genotyping in hundreds of individuals.

Scientific Applications:

• QTL mapping: Enables high-resolution mapping of quantitative trait loci contributing to complex traits using reconstructed founder mosaics.
• Experimental pedigrees and F2 studies: Supports analyses of large F2 pedigrees derived from divergently selected lines, including intercrosses between chicken populations.

Methodology:

Selects founder-line informative markers within each full-sib family and markers fixed for alternative alleles in divergent founder lines, reconstructs mosaic genotypes and infers recombination breakpoints using high-coverage (~30×) founder whole-genome sequencing and very low-coverage (< 0.5×) intercross sequencing, and applies an optimized imputation algorithm.