Genome-wide association for testis weight in the diversity outbred mouse population

Abstract

Testis weight is a genetically mediated trait associated with reproductive efficiency across numerous species. We sought to evaluate the genetically diverse, highly recombinant Diversity Outbred (DO) mouse population as a tool to identify and map quantitative trait loci (QTLs) associated with testis weight. Testis weights were recorded for 502 male DO mice and the mice were genotyped on the GIGAMuga array at ~ 143,000 SNPs. We performed a genome-wide association analysis and identified one significant and two suggestive QTLs associated with testis weight. Using bioinformatic approaches, we developed a list of candidate genes and identified those with known roles in testicular size and development. Candidates of particular interest include the RNA demethylase gene Alkbh5, the cyclin-dependent kinase inhibitor gene Cdkn2c, the dynein axonemal heavy chain gene Dnah11, the phospholipase D gene Pld6, the trans-acting transcription factor gene Sp4, and the spermatogenesis-associated gene Spata6, each of which has a human ortholog. Our results demonstrate the utility of DO mice in high-resolution genetic mapping of complex traits, enabling us to identify developmentally important genes in adult mice. Understanding how genetic variation in these genes influence testis weight could aid in the understanding of mechanisms of mammalian reproductive function.

Fig. 1

Testis weight distribution in DO mice (n = 502) Graphics program: SPSS was used to create figure 1

Fig. 2. Genome-wide association mapping of testis weight.

Each point plots the –log₁₀(p- value) for the association between one SNP and testis weight. Values were plotted against their respective positions on the chromosomes. The dashed red and blue lines represent the genome-wide significant (p < 0.05) and genome-wide suggestive (p < 0.1) thresholds, respectively Graphics programs: R and Microsoft PowerPoint were used to create figure 2

Fig. 3

Association mapping of TestWt4 QTL. High resolution view of QTL support interval. Top panel shows SNP marker associations of the eight DO founders. The x-axis displays the distribution along the chromosome in physical distance. The y-axis displays the –log10(p-value) for the SNP mapping. Each data point shows the –log10(p-value) at one SNP; red data points indicate scores above the p < 0.1 threshold. Below each plot is an expanded view showing known genes within the QTL support interval. Gene data retrieved from the UCSC Genome Browser (https://genome.ucsc.edu) Graphics programs: R and Microsoft PowerPoint were used to create figure 3

Fig. 4

Association mapping of TestWt11 QTL. High resolution view of QTL support interval. Top panel shows SNP marker associations of the eight DO founders. The x-axis displays the distribution along the chromosome in physical distance. The y-axis displays the –log10(p-value) for the SNP mapping. Each data point shows the –log10(p-value) at one SNP; red data points indicate scores above the p < 0.1 threshold. Below each plot is an expanded view showing known genes within the QTL support interval. Gene data retrieved from the UCSC Genome Browser (https://genome.ucsc.edu) Graphics programs: R and Microsoft PowerPoint were used to create figure 4

Fig. 5

Association mapping of TestWt12 QTL. High resolution view of QTL support interval. Top panel shows SNP marker associations of the eight DO founders. The x-axis displays the distribution along the chromosome in physical distance. The y-axis displays the –log10(p-value) for the SNP mapping. Each data point shows the –log10(p-value) at one SNP; red data points indicate scores above the p < 0.1 threshold. Below each plot is an expanded view showing known genes within the QTL support interval. Gene data retrieved from the UCSC Genome Browser (https://genome.ucsc.edu) Graphics programs: R and Microsoft PowerPoint were used to create figure 5

Fig. 6

Haplotype effects on chromosome 4 QTL for testis weight. The top panel shows the eight DO founder allele effects (model coefficients) determined by linkage mapping. The x-axis is physical distance in Mb along the chromosome. The y-axis for the top panel is the effect coefficient, and the bottom panel is the LOD score. At ~110 Mb, the NZO/HILtJ alleles (light blue) are associated with larger testis weights. Shading in the bottom panel identifies the 95% credible interval. Graphics programs: R and Microsoft PowerPoint were used to create figure 6

Fig. 7

Haplotype effects on chromosome 11 QTL for testis weight. The top panel shows the eight DO founder allele effects (model coefficients) determined by linkage mapping. The x-axis is physical distance in Mb along the chromosome. The y-axis for the top panel is the effect coefficient, and the bottom panel is the LOD score. At ~61 Mb, PWK/PhJ (red), A/J (yellow), and C57BL/6J (grey) alleles contributed to increased testis weight, while CAST/EiJ (green) and 129S1/SvlmJ (pink) alleles contributed to decreased testis weight. Shading in the bottom panel identifies the 95% credible interval. Graphics programs: R and Microsoft PowerPoint were used to create figure 7

Fig. 8

Haplotype effects on chromosome 12 QTL for testis weight. The top panel shows the eight DO founder allele effects (model coefficients) determined by linkage mapping. The x-axis is physical distance in Mb along the chromosome. The y-axis for the top panel is the effect coefficient, and the bottom panel is the LOD score. At ~117 Mb, the CAST/EiJ (green) and NZO/HILtJ alleles (light blue) are associated with larger testis weights. Shading in the bottom panel identifies the 95% credible interval. Graphics programs: R and Microsoft PowerPoint were used to create figure 8