Experiment
The current study is a quantitative trait loci (QTL) mapping study designed to identify loci that interact with myostatin to impact growth traits in mice.
An F2 mapping population was derived from reciprocal crosses between two founder strains, myostatin-null C57BL/6 and M16i high body weight mice. Four myostatin null male mice were mated with eight M16i females to produce 35 male and 37 female F1 offspring. In addition, two M16i males and seven myostatin-null females were crossed to generate 31 male and 55 female F1 offspring. Within each of these two crosses, F1 mice were intercrossed to produce the F2 mapping population.
A total of 1000 F2 generation progeny that were either homozygous myostatin wild type or homozygous myostatin-null were collected for genotype and phenotype information. Among these 1000 F2 mice, 552 mice were from the myostatin-null male by M16i female cross, whereas 448 mice were from the reciprocal cross. Each of the F2 individuals had its body weight recorded at 7, 14, 21, 28, 35 and 42 days of age.
On the basis of the measurements of body weights, growth rate was calculated for different growth periods. For the pre-weaning period, average daily gain was calculated for the 2nd week and 3rd week, along with the 1st-3rd week interval. During the post-weaning period, average daily gain was calculated for the 4th week, 5th week, 6th week, and the 4th-6th week interval. Average daily gain for the 1st-6th week interval was calculated and included as a measurement of overall growth rate. Genomic DNA from each of the F0, F1 and F2 generation mice was purified by a phenol chloroform method.
152 SNPs were genotyped that were distributed on 17 autosomes (no informative SNPs were present on chromosome 15 and 16) and the X chromosome. A linkage map was constructed in Kosambi centimorgans with Cri-map. QTL mapping analysis was performed based the linkage map. GridQTL, a web-based QTL analysis program, was used to identify QTL associated with the 14 growth traits by interval mapping. The QTL model included the main effects of myostatin genotype, coat color, sex and reciprocal cross, and the interaction effects of sex x myostatin genotype, sex x reciprocal cross, myostatin genotype x reciprocal cross, sex x coat color and sex myostatin genotype x reciprocal cross along with the additive and dominance effect at the single QTL position.
For each trait, both F-values and logarithm of the odds (LOD) values were provided by GridQTL. Genome-wide significance levels (1 and 5%) were determined by the genome-wide permutation procedure implemented in GridQTL, using 1000 permutations. Additive and dominance effects were estimated for each significant QTL peak. A positive estimate indicates that the effect of the recurrent quantitative trait loci genotype is larger than the effect of the heterozygous genotype - see Estimate Table 2.
Four pre-weaning body weight QTL were identified on Chromosomes 2 and 4; Table 2:
QTL Pwbwq1 (pre-weaning body weight QTL 1) mapped to Chr 2 with an F-value of 14.21, a LOD score of 6.08, peaking at 81 cM between flanking markers rs3144393 and rs13476878.
QTL Pwbwq2 (pre-weaning body weight QTL 2) mapped to Chr 2 with an F-value of 10.27, a LOD score of 4.41, peaking at 101 cM between flanking markers rs13476878 and rs3143843.
QTL Pwbwq3 (pre-weaning body weight QTL 3) mapped to Chr 2 with an F-value of 10.46, a LOD score of 4.47, peaking at 103 cM between flanking markers rs3143843 and rs6335805.
QTL Pwbwq4 ( pre-weaning body weight QTL 4) mapped to Chr 4 with an F-value of 7.95, a LOD score of 3.42, peaking at 64 cM between flanking markers rs6324470 and rs3659226.
Eight pre-weaning growth rate QTL were identified on Chrs 2,4,6,10,12 and 18, Table 2:
QTL Pwgrq1 (pre-weaning growth rate QTL 1) mapped to Chr 2 with an F-value of 26.27, a LOD
score of 11.11, peaking at 71 cM between flanking markers rs3144393 and rs13476878.
QTL Pwgrq2 (pre-weaning growth rate QTL 2) mapped to Chr 2 with an F-value of 15.18, a LOD score of 6.49, peaking at 79 cM between flanking markers rs3144393 and rs13476878.
QTL Pwgrq3 (pre-weaning growth rate QTL 3) mapped to Chr 2 with an F-value of 8.13, a LOD score of 3.5, peaking at 96 cM between flanking markers rs13476878 and rs3143843.
QTL Pwgrq4 (pre-weaning growth rate QTL 4) mapped to Chr 4 with an F-value of 10.15, a LOD score of 4.36, peaking between flanking markers rs6324470 and rs3659226.
QTL Pwgrq5 (pre-weaning growth rate QTL 5) mapped to Chr 6 with an F-value of 8.11, a LOD score of 3.49, peaking at 23 cM between flanking markers rs13478727 and rs13478839.
QTL Pwgrq6 (pre-weaning growth rate QTL 6) mapped to Chr 10 with an F-value of 10.82, a LOD score of 4.64, peaking at 32 cM between flanking markers CEL-10_58149652 and rs13480647.
QTL Pwgrq7 (pre-weaning growth rate QTL 7) mapped to Chr 12 with an F-value of 8.91, a LOD score of 3.8, peaking at 61 cM between flanking markers rs6288403 and rs6390948.
QTL Pwgrq8 ( pre-weaning growth rate QTL 8) mapped to Chr 18 with an F-value of 8.59, a LOD score of 3.69, peaking at 38 cM between flanking markers rs3670254 and rs3718618.
Fourteen post-weaning body weight QTL were identified on Chrs 2,3,4,6,10,11 and 18; Table 2:
QTL Pwbwq5 (post-weaning body weight QTL 5) mapped to Chr 2 with an F-value of 11.88, a LOD score of 5.09, peaking at 79 cM between flanking markers rs3144393 and rs13476878.
QTL Pwbwq6 (post-weaning body weight QTL 6) mapped to Chr 3 with an F-value of 10.78, a LOD score of 4.63, peaking at 61 cM between flanking markers rs3663873 and rs13477430.
QTL Pwbwq7 (post-weaning body weight QTL 7) mapped to Chr 3 with an F-value of 8.95, a LOD score of 3.85, peaking at 64 cM between flanking markers rs3663873 and rs13477430.
QTL Pwbwq8 (post-weaning body weight QTL 8) mapped to Chr 4 with an F-value of 10.64, a LOD score of 4.57, peaking at 64 cM between flanking markers rs6324470 and rs3659226.
QTL Pwbwq9 (post-weaning body weight QTL 9) mapped to Chr 4 with an F-value of 8.08, a LOD score of 3.48, peaking at 67 cM between flanking markers rs6324470 and rs3659226.
QTL Pwbwq10 (post-weaning body weight QTL 10) mapped to Chr 6 with an F-value of 14.07, a LOD score of 6.02, peaking at 27 cM between flanking markers rs13478727 and rs13478839.
QTL Pwbwq11 (post-weaning body weight QTL 11) mapped to Chr 6 with an F-value of 16.54, a LOD score of 7.06, peaking at 27 cM between flanking markers rs13478727 and rs13478839.
QTL Pwbwq12 (post-weaning body weight QTL 12) mapped to Chr 6 with an F-value of 15.88, a LOD score of 6.78, peaking at 28 cM between flanking markers rs13478727 and rs13478839.
QTL Pwbwq13 (post-weaning body weight QTL 13) mapped to Chr 10 with an F-value of 9.08, a LOD score of 3.90, peaking at 37 cM between flanking markers CEL-10_58149655 and rs13480650.
QTL Pwbwq14 (post-weaning body weight QTL 14) mapped to Chr 11 with an F-value of 18.86, a LOD score of 8.03, peaking at 28 cM between flanking markers rs6276300 and rs6199956.
QTL Pwbwq15 (post-weaning body weight QTL 15) mapped to Chr 11 with an F-value of 13.66, a LOD score of 5.85, peaking at 29 cM between flanking markers rs6276300 and rs6199956.
QTL Pwbwq16 (post-weaning body weight QTL 16) mapped to Chr 11 with an F-value of 17.53, a LOD score of 7.48, peaking at 29 cM between flanking markers rs6276300 and rs6199956.
QTL Pwbwq17 (post-weaning body weight QTL 17) mapped to Chr 18 with an F-value of 9.15, a LOD score of 3.93, peaking at 8 cM between flanking markers rs13483233 and rs3723947.
QTL Pwbwq18 (post-weaning body weight QTL 18) mapped to Chr 18 with an F-value of 8.61, a LOD score of 3.70, peaking at 8 cM between flanking markers rs13483233 and rs3723947.
Twelve post-weaning growth rate QTL were identified on Chrs 1,3,5,6,10,11 and 18; Table 2:
QTL Pwgrq9 (post-weaning growth rate QTL 9) mapped to Chr 1 with an F-value of 15.83, a LOD score of 6.76, peaking at 22 cM between flanking markers rs3696088 and rs13472794.
QTL Pwgrq10 (post-weaning growth rate QTL 10) mapped to Chr 1 with an F-value of 25.91, a LOD score of 10.96, peaking at 23 cM between flanking markers rs3696088 and rs13472794.
QTL Pwgrq11 (post-weaning growth rate QTL 11) mapped to Chr 1 with an F-value of 10.63, a LOD score of 4.56, peaking at 24 cM between flanking markers rs3696088 and rs13472794.
QTL Pwgrq12 (post-weaning growth rate QTL 12) mapped to Chr 3 with an F-value of 13.32, a LOD score of 5.70, peaking at 25 cM between flanking markers rs3663409 and rs13477132.
QTL Pwgrq13 (post-weaning growth rate QTL 13) mapped to Chr 3 with an F-value of 10.55, a LOD score of 4.53, peaking at 30 cM between flanking markers rs3663409 and rs13477132.
QTL Pwgrq14 (post-weaning growth rate QTL 14) mapped to Chr 3 with an F-value of 8.85, a LOD score of 3.81, peaking at 120 cM between flanking markers rs3724562 and CEL-3_159340478.
QTL Pwgrq15 (post-weaning growth rate QTL 15) mapped to Chr 5 with an F-value of 8.94, a LOD score of 3.85, peaking at 78 cM between flanking markers rs3720626 and rs3706737.
QTL Pwgrq16 (post-weaning growth rate QTL 16) mapped to Chr 6 with an F-value of 16.65, a LOD score of 7.11, peaking at 30 cM between flanking markers rs13478727 and rs13478839.
QTL Pwgrq17 (post-weaning growth rate QTL 17) mapped to Chr 10 with an F-value of 10.65, a LOD score of 4.57, peaking at 32 cM between flanking markers CEL-10_58149653 and rs13480648.
QTL Pwgrq18 (post-weaning growth rate QTL 18) mapped to Chr 10 with an F-value of 8.77, a LOD score of 3.77, peaking at 36 cM between flanking markers CEL-10_58149654 and rs13480649.
QTL Pwgrq19 (post-weaning growth rate QTL 19) mapped to Chr 10 with an F-value of 8.39, a LOD score of 3.61, peaking at 44 cM between flanking markers rs3717445 and rs13480707.
QTL Pwgrq20 (post-weaning growth rate QTL 20) mapped to Chr 11 with an F-value of 17.78, a LOD score of 7.58, peaking at 26 cM between flanking markers rs6276300 and rs6199956.
Six overall growth rate QTL were identified on Chrs 3,5,6,10,11 and 18; Table 2:
QTL Ogrq1 (overall growth rate QTL 1) mapped to Chr 3 with an F-value of 12.94, a LOD score of 5.54, peaking at 58 cM between flanking markers rs3663873 and rs13477430.
QTL Ogrq2 (overall growth rate QTL 2) mapped to Chr 5 with an F-value of 8.52, a LOD score of 3.66, peaking at 76 cM between flanking markers rs3720626 and rs3706737.
QTL Ogrq3 (overall growth rate QTL 3) mapped to Chr 6 with an F-value of 16.40, a LOD score of 7.0, peaking at 29 cM between flanking markers rs13478727 and rs13478839.
QTL Ogrq4 (overall growth rate QTL 4) mapped to Chr 10 with an F-value of 10.05, a LOD score of 4.32, peaking at 47 cM between flanking markers rs13480707 and rs13480754.
QTL Ogrq5 (overall growth rate QTL 5) mapped to Chr 11 with an F-value of 20.51, a LOD score of 8.72, peaking at 28 cM between flanking markers rs6276300 and rs6199956.
QTL Ogrq6 (overall growth rate QTL 6) mapped to Chr 18 with an F-value of 8.53, a LOD score of 3.67, peaking at 8 cM between flanking markers rs13483233 and rs3723947.
The average phenotypic variation accounted for by each of the 44 QTL was about 2.5%. The contribution from each specific QTL is listed in Table 2.
Twelve QTL that significantly interacted (p<0.01, p<0.05) with the myostatin genotype were also identified, Table 4. Eleven and fourteen QTL were detected with a significant interaction with reciprocal cross and sex, respectively (Supp Tables 2 and 3). In all, 21 of these additive or dominant QTL were also detected when the genome scan was performed on the full dataset. The other 16 did not have a significant QTL effect when the whole F2 population was analyzed. The amount of total phenotypic variation of each trait explained by the interactions ranged from 1.18-6.36%.
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