Parent–progeny sequencing indicates higher mutation rates in heterozygotes

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Abstract

Mutation rates vary within genomes, but the causes of this remain unclear1. As many prior inferences rely on methods that assume an absence of selection, potentially leading to artefactual results2, we call mutation events directly using a parent–offspring sequencing strategy focusing on Arabidopsis and using rice and honey bee for replication. Here we show that mutation rates are higher in heterozygotes and in proximity to crossover events. A correlation between recombination rate and intraspecific diversity is in part owing to a higher mutation rate in domains of high recombination/diversity. Implicating diversity per se as a cause, we find an 3.5-fold higher mutation rate in heterozygotes than in homozygotes, with mutations occurring in closer proximity to heterozygous sites than expected by chance. In a genome that is a patchwork of heterozygous and homozygous domains, mutations occur disproportionately more often in the heterozygous domains. If segregating mutations predispose to a higher local mutation rate, clusters of genes dominantly under purifying selection (more commonly homozygous) and under balancing selection (more commonly heterozygous), might have low and high mutation rates, respectively. Our results are consistent with this, there being a ten times higher mutation rate in pathogen resistance genes, expected to be under positive or balancing selection. Consequently, we do not necessarily need to evoke extremely weak1,2 selection on the mutation rate to explain why mutational hot and cold spots might correspond to regions under positive/balancing and purifying selection, respectively3,4.

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Figure 1: Pedigree relationship of the sequenced Arabidopsis samples.
Figure 2: Patterns of diversity, recombination and de novo mutation.

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Primary accessions

BioProject

Data deposits

All Illumina reads have been deposited in the BioProject database under accession numbers PRJNA243018, PRJNA252997, PRJNA178613 and PRJNA232554.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (91331205, 91231102 and 31170210), Program for Changjiang Scholars and Innovative Research Team (IRT_14R27) and Jiangsu Collaborative Innovation Center for Modern Crop Production to D.T., S.H. and J.-Q.C., respectively.

Author information

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Authors

Contributions

D.T., L.D.H., S.Y. and J.-Q.C. designed the experiments. S.Y., L.W., J.H., X.Z., L.D.H. and Y.Y. performed the experiments and analysed the data. L.D.H. and D.T. wrote the paper.

Corresponding authors

Correspondence to Laurence D. Hurst or Dacheng Tian.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Details of materials and methods.

a, Schematic diagram of the detection of de novo mutations. b, The calculation of the expected mutations in the meiosis of F2→F3 (EM3) and F3→F4 (EM4). For further explanation see Methods.

Extended Data Figure 2 Mutational properties.

a, Spectra of nucleotide substitutions in Arabidopsis and rice. b, Co-occurrence of mutations and crossover break points in bees. By using the sequence data of 43 honey bee drones and their 3 corresponding queens17, a total of 27 base and 8 indel mutations were detected. Of note, 2 of 35 mutations are found in close proximity with crossover break points in the same sample (distance < 2 kb; P = 0.0012 with 10,000 randomizations), these being illustrated here. The crossover event is between the red and blue line with marker positions annotated. The positions of the mutations are annotated with arrows. c, A schematic diagram of the genomic structures and the possible pairings of two homologous chromosomes during the meiosis at two mutated LRR-TM genes (top) and one mutated NBS-LRR gene (bottom). The top panel shows the genomic structures between Col and Ler at the loci of AT3G23110, the receptor-like protein 37 with a non-synonymous mutation (Chr3:8224726, T→C) at sample of c74, and AT3G23120, the receptor-like protein 38 with a deletion mutation (Chr3:8228194, Del:C, frameshift) at sample of c70. The bottom panel illustrates the genomic structures between two Col chromosomes at AT1G59780 and the mutations detected in a homozygous plant of Col8. Red arrows represent the position of mutation; the hatched areas indicate the highly similar sequences, the other regions being highly diversified; the dotted lines indicate the paired length of the homologues at the highly identical regions. During meiosis, possible pairings between parental chromosomes are illustrated, where the loops indicate the unpaired regions.

Extended Data Figure 3 Correlation between mutations, recombination events, diversity and divergence.

a, The relationship between nucleotide diversity (Col versus Ler) and recombination rate. When the chromosomes were dissected into 100 kb non-overlapping windows, the diversity (polymorphism density) between Col and Ler and the recombination rates in 67 F2 and 32 F4 plants were calculated for each window. When sorting the windows by the diversity and dividing them into 8 equal intervals (for example, from 0 to 0.001, 0.001 to 0.002, 0.002 to 0.003, and so on), the relationships between the average diversity and recombination rate is displayed. Error bars indicate standard error of the mean. b, The relationship between diversity and divergence. The red line represents standard linear regression and is for illustrative purposes only. The statistic is the result of Spearman’s rank correlation. c, Relationship between mutation and distance to polymorphic sites. The mutation data were collected from our 67 F2 samples. Window 0 in the x-axis is the 2 × 100 bp sequence surrounding the position of any given de novo mutation and 1–9 is 100–900 bp away from the mutation on both sides. For each window of 2 × 100 bp sequence, the average diversity is calculated. The black squares denote the average pairwise diversity among the published 80 Arabidopsis ecotypes; the red circles denote the average diversity between Col and the 80 ecotypes; the blue triangles denote the average diversity between Ler and the 80 ecotypes. Error bars indicate standard error of the mean. d, Distribution of the mutations on the chromosomes. The grey vertical bars in the chromosomes denote the position of all collected mutations. When the chromosomes were dissected into 1 Mb non-overlapping windows, the mutation numbers (blue shadow in the figure) were counted in each window. The red lines denote the average pairwise diversity among the published 80 Arabidopsis ecotypes.

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Yang, S., Wang, L., Huang, J. et al. Parent–progeny sequencing indicates higher mutation rates in heterozygotes. Nature 523, 463–467 (2015). https://doi.org/10.1038/nature14649

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