Mapping Data

Experiment

• Experiment
  TEXT-QTL
• Chromosome
  4
• Reference
  J:242563 Shorter JR, et al., Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross. Genetics. 2017 Jun;206(2):557-572
• ID
  MGI:6209503

Genes

Gene	Assay Type
Epid1	visible phenotype
Svwq1	visible phenotype

Notes

• Reference
  The Collaborative Cross (CC) is a large (~1,000 line) panel of recombinant inbred (RI) mouse strains being developed through a community effort (Churchill et al. 2004). The CC combines the genomes of eight genetically diverse founder strains - A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ - to capture nearly 90% of the known variation present in laboratory mice. CC strains are derived using a unique funnel breeding scheme. Once inbred, the RI CC lines can be used to generate thousands of potential 'outbred' but completely reproducible genomes through the generation of recombinant inbred crosses (RIX). The designation 'PreCC' is used to describe a mapping population of CC mice that is still at incipient stages of inbreeding.
  
  CTC (2004), Churchill, G. A., et al.. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet. 36, 1133-7.
  
  
  
• Experiment
  The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population.
  
  Since the start of the CC project in 2004 at ORNL, 707 out of 738 funnels (95%) have been declared extinct. Extinction follows a bimodal distribution and ranges from G1 to G2:F17 (Figure 1A). Males from 347 funnels that became extinct from 2008 to 2011 were included in this study (PreCC#). These males range from generations G2:F2 to G2:F17, with the bulk of the extinction (86%) taking place between G2:F4 and G2:F9 (Figure 1A).
  
  Genotyping for 347 samples was performed with the Mouse Diversity Array (MDA) (Yang et al. 2009). Mice were selected so that only extinct funnel males with reproductive phenotypes were genotyped for analysis. The MDA contains 623,124 SNP probe sets with an average spacing of 4.3 kb.
  
  The marker set was then refined through a set of filters. Informative markers were first selected among the CC founder strains. This informative set was further filtered to select markers that yielded consistent genotypes among the majority of multiple technical and biological replicates from each founder strain available from The Jackson Laboratorys MDA genotype repository of inbred mouse strains (ftp://ftp.jax.org/petrs/MDA/). A final filter removed any genotypes that are inconsistent between predicted and observed genotypes in F1 hybrids derived from crosses of founder inbred strains. A resulting set of 381,351 MDA genotyping markers survived these filtering steps, and only this subset was used in subsequent analyses of the 347 CC lines that were analyzed.
  
  A hidden Markov model (HMM) was used to infer the founder haplotype mosaics from the filtered MDA genotypes. A modified eight-state genotype HMM was used to infer the founder likelihoods at each marker of chromosome X to accommodate hemizygous males. A 500-kb region on the end of chromosome X containing the pseudoautosomal region (PAR) was excluded from the HMM. A significant penalty against the fourth, seventh, and eighth positions of each lines funnel code was also incorporated into the HMMs transition probabilities. This accounts for a constraint imposed by the funnel breeding structure used to develop the CC.
  
  QTL mapping was performed with the R package DOQTL, v1.6.0 (Gatti et al. 2014). Average testes size, body weight, and age were conditionally included as covariates for the reproductive traits. Table S3 contains QTL mapping phenotypes for the 347 mice that were phenotyped and genotyped. Table S4 contains all raw phenotype data for these mice.
  
  A large number of male reproductive traits were assessed in the CC extinct lines, including reproductive organ weights, sperm counts, sperm quality characteristics, and testis histology. Table S4 lists the traits measured in representative males from 347 genotyped lines.
  
  CC extinct lines show large variation in reproductive organ weights and have low sperm motility. Many CC extinct lines have low sperm counts. Sperm morphology varies widely among CC extinct lines, and vacuolization of seminiferous tubules is prevalent in infertile males.
  
  QTL mapping identified nine genomic regions associated with male fertility and reproductive phenotypes:
  
  Ferq1 (genetic fertility QTL 1) maps to ChrX:55-150 Mbp with a peak LOD score of 6.191 at 101 Mbp. PWK/PhJ alleles are associated with lower fertility at Ferq1.
  
  Epid1 (epididymis and vas deferens weight 1) maps to Chr4:90-100 Mbp with a peak LOD score of 10.06 at 95 Mbp. NZO/HlLtJ alleles are associated with an increase in organ weights while PWK/PhJ alleles associated with lower organ weights at Epid1.
  
  Svwq1 (seminal vesicle weight QTL 1) maps to Chr4:90-119 Mbp with a peak LOD score of 8.486 at 117 Mbp. NZO/HlLtJ alleles are associated with an increase in organ weights while PWK/PhJ alleles are associated with lower organ weights at Svwq1.
  
  Svwq2 (seminal vesicle weight QTL 2) maps to ChrX:130-155 Mbp with a peak LOD score of 6.68 at 134 Mbp. A/J alleles are associated with an increase in seminal vesicle weight at Svwq2.
  
  Twq5 (testis weight QTL 5) maps to Chr1:3-185 Mbp with a peak LOD score of 6.728 at 170 Mbp. C57BL/6J alleles are associated with an increase in testis weight at Twq5.
  
  Vclq1 (curvilinear velocity QTL 1) maps to Chr2:62-137 Mbp with a peak LOD score of 7.779 at 72 Mbp. PWK/PhJ and A/J alleles are associated with an increase and decrease in curvilinear velocity at Vclq1, respectively. Vclq1 was confirmed by the authors using a separate CC population.
  
  Alh1 (amplitude of lateral head displacement 1) maps to Chr6:78-97 Mbp with a peak LOD score of 7.93 at 91 Mbp. A/J, NZO/HlLtJ, and WSB/EiJ alleles are associated with an increase in ALH, while C57BL/6J alleles are assocated with decreased ALH at Alh1.
  
  Phsq1 (percent hyperactivated sperm QTL 1) maps to Chr14:3-21 Mbp with a peak LOD score of 7.652 at 19 Mbp. PWK/PhJ alleles are associated with increased percentages of hyperactivated sperm at Phs1.
  
  Pbsq1 (percent broken sperm QTL 1) maps to Chr13:102-112 Mbp with a peak LOD score of 8.299 at 109 Mbp. CAST/EiJ alleles are associated with increased percentages of broken sperm at Pbs1.
  
  In verifying the effect of Vclq1 from the PWK/PhJ haplotype on chromosome 2, the authors performed the first example of cross validation using complementary CC resources in an independent population across multiple generations.