Figure 1. Representative example of the pattern of oxygen consumption for assessment of mitochondrial function. The dashed line represents values from.

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Figure 1. Representative example of the pattern of oxygen consumption for assessment of mitochondrial function. The dashed line represents values from a cow of the AA genotype, and the blue line the values for a cow of the GG genotype. Excess electron transport system capacity was calculated as the ratio of maximum respiration and routine respiration. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Figure 2. Models of the three-dimensional structure of COQ9 Figure 2. Models of the three-dimensional structure of COQ9. (A) Variant G, corresponding to the major allele; (B) variant A corresponding to the minor allele; (C) superimposed models of both isoforms of the protein. The residue affected by the SNP is shown in red in panel A and in green in panels B and C. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Figure 3. Phylogeny of the mutation in COQ9 Figure 3. Phylogeny of the mutation in COQ9. The reference allele is indicated in red. All species distal to the common ancestor had the same reference allele unless indicated by placement of a distinct letter. For B. taurus, both alleles are presented (major/minor). The allele underlined is the one associated with superior fertility. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Figure 4. Association of COQ9 genotype with body weight changes after calving during the first and second lactation of Holstein cows. Values are least-squares means ± SEM of daily body weights averaged for each week. The number of cows for each genotype was 86 AA, 223 AG, and 106 GG. Body weight was affected by the interaction between genotype and week after calving (P < 0.001) for both lactations. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Figure 5. Expression of COQ9 in the endometrium, oocyte, and preimplantation embryo. All values are least-squares means ± SEM of the fold change of expression relative to the geometric mean of three housekeeping genes. (A) Changes in COQ9 expression in the endometrium during the first 7 days of the estrous cycle. Expression of COQ9 was measured for samples from 3 to 4 cows per day. There was no significant effect of day of the estrous cycle (P = 0.412). (B) COQ9 expression in the matured oocyte and early embryo. A total of four pools of 30 oocytes or embryos per pool were assessed for each stage. COQ9 expression was higher for oocytes and two-cell embryos than for embryos at other stages (P < 0.001). A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Figure 6. Expression of COQ9 in genotype-identified cumulus cells (A) and oocytes (B). Values are least-squares means ± SEM. The number of pools of oocytes or cumulus cells evaluated was 11 for AA, 20 for AG, and 12 for GG. Expression in cumulus cells was not affected by genotype (P = 0.1370), but expression in oocytes was affected by genotype (P < 0.001), with oocytes of the AG genotype having greater expression than either homozygote. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Figure 7. Association of COQ9 genotype with markers of oocyte quality Figure 7. Association of COQ9 genotype with markers of oocyte quality. (A) Expression of BMP15 and GDF9 in oocytes of the three genotypes for COQ9. Values are least-squares means ± SEM. There were 11 pools of oocytes for AA, 20 for AG, and 12 for GG. There was no effect of genotype on expression of BMP15 (P = 0.779) or GDF9 (P = 0.685). (B) Mitochondrial copy number in oocytes of the three genotypes for COQ9. Values are least-squares means ± SEM. There were 11 pools of oocytes for 11 AA, 20 for AG, and 12 for GG. There was an additive effect of genotype on mitochondrial copy number in favor of the A allele (P < 0.0001) and a dominance effect (P < 0.0001). A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows† Biol Reprod. 2017;96(3):652-663. doi:10.1093/biolre/iox004 Biol Reprod | © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com