Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population

Abstract

Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts toward inbreeding undertaken by the UNC Systems Genetics Core. The timing reflects our competing mandates to release to the public as many CC strains as possible while achieving an acceptable level of inbreeding. The new six strains have a higher than average founder contribution from non- domesticus strains than the previously released CC strains. Five of the six strains also have high residual heterozygosity (>14%), which may be related to non- domesticus founder contributions. Finally, we report on updated estimates on residual heterozygosity across the entire CC population using a novel, simple and cost effective genotyping platform on three mice from each strain. We observe a reduction in residual heterozygosity across all previously released CC strains. We discuss the optimal use of different genetic resources available for the CC population.

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

“…The founder haplotype contributions for each CC strain was previously reconstructed by the UNC Systems Genetics Core (http://csbio.unc.edu/CCstatus/index.py?run=FounderProbs) with a Hidden Markov Model [58] on genotype calls [MegaMUGA array [59]] from multiple animals per strain, representing ancestors to the analyzed mice. Notably, QTL mapping power is reduced at loci with segregating variants in these ancestors, and where these specific animals likely differ [60]. To reduce the number of statistical tests, adjacent genomic regions were merged through averaging if the founder mosaics for all mice were similar, defined as L2 distance � 10% of the maximum L2 distance ( ffi ffi ffi 2 p for a probability vector).…”

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

“…Genes with 502 TMM-normalized TPM values ≤ 1 and chromatin windows with normalized counts ≤ 5 503 for ≥ 50% of samples were excluded (as in [22]) in order to avoid the detection of QTL 504 that result from highly influential non-zero observations when most of the sample have 505 low to no expression. For each gene and chromatin window, we applied K-means 506 clustering with K = 2 to identify outcomes containing outlier observations that could where these specific animals likely differ [33]. To reduce the number of statistical tests, 517 adjacent genomic regions were merged through averaging if the founder mosaics for all 518 mice were similar, defined as L2 distance ≤ 10% of the maximum L2 distance ( √ 2 for a 519 probability vector).…”

The Collaborative Cross Graphical Genome

“…The CC are popular genetic reference populations due to a huge expansion of phenotypic variation observed for most traits measured using them (Aylor et al 2011;Philip et al 2011;Bottomly et al 2012;Kelada et al 2012;Leist et al 2016;Manet et al 2019). This has motivated the creation of new CC-related genomic resources (Srivastava et al 2017;Shorter et al 2019) and analysis tools (Holt et al 2013;Huang et al 2014) to aid in sorting out the underlying phenotypic correlates to the genetic sources of variation. In the summer of 2017 the sequence data from 69 CC mouse strains were published, from a single male from each available line with 20×-30× genome coverage (Srivastava et al 2017).…”

“…In the summer of 2017 the sequence data from 69 CC mouse strains were published, from a single male from each available line with 20×-30× genome coverage (Srivastava et al 2017). In early 2019, sequence data from six additional CC strains were published (Shorter et al 2019). Meanwhile in the fall of 2018, classical "linear" genome assemblies were released for sixteen common laboratory mouse strains, which included seven of the eight CC founders (Lilue et al 2018).…”

“…Here, we present a first draft of the CCGG pangenome resource. This version was constructed by merging the standard mouse reference with de novo assemblies of the 7 founder genomes (Lilue et al 2018) guided by the short-read sequence data from CC-line samples (Srivastava et al 2017;Shorter et al 2019 founder assemblies. Anchor nodes provide a coordinate framework that allows annotations to be placed in a common genomic context that is easier to maintain as the assemblies are improved.…”