GBRS

GBRS reconstructs individual diploid genomes and quantifies total and allele-specific gene expression from RNA-Seq data in multiparent populations (MPPs).

Key Features:

• Genotype-Free Genome Reconstruction: Reconstructs diploid genomes without requiring high-density genotyping arrays by leveraging RNA-Seq data from MPPs.
• Alignment to Founder Transcriptomes: Simultaneously aligns RNA-Seq reads to the transcriptomes of inbred founder strains to resolve genetic origin of reads.
• Quantification of Total and Allele-Specific Expression: Produces estimates of both total gene expression and allele-specific expression using RNA-Seq alignments.
• Incorporation of Polymorphic Loci: Incorporates known polymorphic loci into individualized transcriptomes to improve expression quantification and genotype inference.
• Quality Control for Sample Integrity: Detects sample mix-ups or contamination by comparing reconstructed genomes or expression patterns to expected founder contributions.
• Computational Efficiency: Implements a streamlined approach to reduce computational demands associated with constructing and analyzing individualized genomes in diverse populations.

Scientific Applications:

• Analysis of Multiparent Populations (MPPs): Enables genome reconstruction and expression analysis in MPPs derived from multiple inbred founder strains.
• Gene Expression Regulation Studies: Facilitates investigation of regulatory mechanisms by quantifying allele-specific and total expression across individuals.
• Candidate Gene Identification for Complex Traits: Supports identification of candidate genes by linking reconstructed genotypes and expression variation in genetically diverse cohorts.
• Quality Control in Genomic Experiments: Provides a genomic integrity check to identify sample swaps or contamination in RNA-Seq datasets.

Methodology:

GBRS aligns RNA-Seq reads to founder strain transcriptomes and leverages known polymorphic loci incorporated into individualized transcriptomes to reconstruct individual diploid genomes and quantify total and allele-specific gene expression.