Fig 1.
Diagram of the intercross design using wild-derived strains (a) between subspecies of M. m. musculus and M. m. castaneus, represented by castCAST and muscPWD, and (b) within subspecies of M. m. domesticus, represented by domGI and domWSB. F2s in both crosses are a mix from reciprocal cross directions. The abbreviations for each strain in bold are used throughout.
Fig 2.
Progression of spermatocyte images through image analysis.
On the left, cytological images of a pachytene spermatocyte from a castCAST × muscPWD F2 (top) and a domGI × domWSB F2 (bottom). Chromosome spreads stained for SYCP3 in red, MLH1 in green, and DAPI in blue. Scale bar = 10μm. The respective images after isolating, balancing, and thresholding the red channel (middle); and their single-pixel-wide representation after applying the skeletonize algorithm (right).
Fig 3.
SC lengths from automated versus manual analysis.
Each point represents the SC length from a single spermatocyte image in the test set. SC lengths of spermatocytes from domGI × domWSB F2 individuals are shown in purple (coefficient of determination, R2 = 0.74); those from castCAST × muscPWD F2 individuals are shown in orange (R2 = 0.81).
Fig 4.
Plots show significant QTL for SC length in the (a) castCAST × muscPWD cross on chromosomes 3, 4, and X and in the (b) domGI × domWSB cross on chromosomes 5 and X. Dashed line shows genome-wide significance level, α = 0.05.
Table 1.
QTL for synaptonemal complex length.
Fig 5.
Estimated QTL effects by genotype.
Effects on F2 individuals estimated at the position of peak LOD on chromosomes with significant QTL for mean SC length (top) and MLH1 foci count (bottom). Error bars show ±1 SE.(a) castCAST × muscPWD cross; cC – castCAST, mP−muscPWD SC QTL: (Chr. 3, 38.0 cM); (Chr. 4, 44.0 cM); (Chr. X, 31.9 cM) MLH1 QTL: (Chr. 3, 66.0 cM); (Chr. 4, 25.0 cM); (Chr. X, 31.9 cM) (b) domGI × domWSB cross; dG−domGI, dW−domWSB SC QTL: (Chr. 5, 44.8 cM); (Chr. X, 54.0 cM) MLH1 QTL: (Chr. 5, 36.9 cM).
Table 2.
Overlapping QTL.
Table 3.
Candidate genes and mutations for the evolution of SC length within M. m. domesticus.
Fig 6.
Mean MLH1 foci count and SC length from each cross.
Mean MLH1 count and SC length from the same F2 individuals. Those from the castCAST × muscPWD cross in orange (regression slope (SE): 0.13 (0.01) foci/μm) and from the domGI × domWSB cross in purple (regression slope: 0.01 (0.01) foci/μm).
Fig 7.
A QTL for the SC/CO ratio in the domGI × domWSB cross.
(a) LOD plot for SC/CO ratio shows a significant QTL on chromosome 5. Dashed line shows genome-wide significance level, α = 0.05. (b) Estimated effects of the QTL on chromosome 5 for SC/CO ratio among domGI × domWSB F2s by genotype; dG –domGI, dW−domWSB. Error bars show ±1 SE.
Table 4.
Regression coefficients and mediation at pleiotropic loci.