Identification of Specific Nuclear Genetic Loci and Genes That Interact With the Mitochondrial Genome and Contribute to Fecundity in Caenorhabditis elegans

Abstract

Previous studies have found that fecundity is a multigenic trait regulated, in part, by mitochondrial-nuclear (mit-n) genetic interactions. However, the identification of specific nuclear genetic loci or genes interacting with the mitochondrial genome and contributing to the quantitative trait fecundity is an unsolved issue. Here, a panel of recombinant inbred advanced intercrossed lines (RIAILs), established from a cross between the N2 and CB4856 strains of C. elegans, were used to characterize the underlying genetic basis of mit-n genetic interactions related to fecundity. Sixty-seven single nucleotide polymorphisms (SNPs) were identified by association mapping to be linked with fecundity among 115 SNPs linked to mitotype. This indicated significant epistatic effects between nuclear and mitochondria genetics on fecundity. In addition, two specific nuclear genetic loci interacting with the mitochondrial genome and contributing to fecundity were identified. A significant reduction in fecundity was observed in the RIAILs that carried CB4856 mitochondria and a N2 genotype at locus 1 or a CB4856 genotype at locus 2 relative to the wild-type strains. Then, a hybrid strain (CNC10) was established, which was bred as homoplasmic for the CB4856 mtDNA genome and N2 genotype at locus 1 in the CB4856 nuclear background. The mean fecundity of CNC10 was half the fecundity of the control strain. Several functional characteristics of the mitochondria in CNC10 were also influenced by mit-n interactions. Overall, experimental evidence was presented that specific nuclear genetic loci or genes have interactions with the mitochondrial genome and are associated with fecundity. In total, 18 genes were identified using integrative approaches to have interactions with the mitochondrial genome and to contribute to fecundity.

Keywords: C. elegans; epistasis; fecundity; genes; genetics; mitochondria; nuclear.

FIGURE 1

Lifetime fecundity of wild type and hybrid C. elegans. The number of offspring of C. elegans was counted for more than 8 days until there were no more eggs laid. Data shown are the median (10–90% percentile). ^∗P < 0.05, ^∗∗P < 0.01, ^∗∗∗P < 0.001, Student’s t-test.

FIGURE 2

Fecundity of 83 N2-CB4856 recombinant inbred advanced intercross lines (RIAILs). The brood sizes for each of the 83 RIAILs (x-axis) provided by Dr. Kruglyak.

FIGURE 3

The effect of N2 and CB4856 alleles of the npr-1 gene and mitochondrial type on fecundity. Box plots show a summary of phenotype data of nematode RIAILs that carried different mitochondria or genotypes of npr-1 (Bristol in black (N2) and Hawaii in red (CB4856)). The effect of N2 and CB4856 alleles of the npr-1 gene and mitochondrial type on fecundity in the 83 RIAILs (A) and the 192 RIAILs published by Andersen et al. (B). The interaction effect between the npr-1 gene and mitochondrial type on fecundity in the 83 RIAILs (C) and the 192 RIAILs published by Andersen et al. (D). Data shown are the median (10% - 90% percentile). ^∗P < 0.05, ^∗∗∗P < 0.001, Student’s t-test.

FIGURE 4

Fecundity of RIAILs C. elegans. Box plots show summary phenotype data of the RIAILs that carried different mitochondria or genotypes at one of two loci on the chromosomes [Bristol in black (N2) and Hawaii in red (CB4856)]. Lifespan brood sizes were counted by standard laboratory agar plate assays (A–C). Normalized brood sizes of the RIAILs C. elegans were counted by high-throughput assays of nematodes grown in 96-well microtiter plates (D–F) and from data downloaded from previously published dataset (Andersen et al., 2015). Data shown are the median (10–90% percentile). ^∗P < 0.05, ^∗∗∗P < 0.001, Student’s t-test.

FIGURE 5

Wild-type and hybrid strain variations in fecundity, hatching rate and functional characteristics of mitochondria. The CNC10 hybrid strain was bred as homoplasmic for the CB4856 mtDNA genome and for N2 genotype at locus 1 in the CB4856 nuclear background. The CCC10 strain was bred as homoplasmic for the CB4856 mtDNA genome and for CB4856 genotype at locus 1 in the CB4856 nuclear background. (A) Variation in fecundity. (B) Variation in hatching rate. (C) The variation in relative level of mtDNA. (D) The variation in relative ATP levels. (E) The variation in relative ROS levels. Data shown are the median (10–90% percentile) in (A) and means ± SEM in (C–E). ^∗P < 0.05, ^∗∗∗P < 0.001, Student’s t-test.