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The genetic basis of inbreeding depression in potato

Nature Genetics volume 51, pages 374–378 (2019)Cite this article

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Abstract

Inbreeding depression confers reduced fitness among the offspring of genetic relatives. As a clonally propagated crop, potato (Solanum tuberosum L.) suffers from severe inbreeding depression; however, the genetic basis of inbreeding depression in potato is largely unknown. To gain insight into inbreeding depression in potato, we evaluated the mutation burden in 151 diploid potatoes and obtained 344,831 predicted deleterious substitutions. The deleterious mutations in potato are enriched in the pericentromeric regions and are line specific. Using three F2 populations, we identified 15 genomic regions with severe segregation distortions due to selection at the gametic and zygotic stages. Most of the deleterious recessive alleles affecting survival and growth vigor were located in regions with high recombination rates. One of these deleterious alleles is derived from a rare mutation that disrupts a gene required for embryo development. This study provides the basis for genome design of potato inbred lines.

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Fig. 1: Identification of genome-wide deleterious mutations in potato.
Fig. 2: Genome-wide segregation distortions.
Fig. 3: Identification of large-effect deleterious alleles.

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Code availability

The pipeline of parent-independent genotyping in potato was written using custom Python scripts. All codes are available from the corresponding author upon request.

Data availability

The sequencing data that support the findings of this study have been deposited in the Sequence Read Archive (SRA) under accession PRJNA471783. The deleterious mutations datasets are available from the following ftp link: ftp://ftp.agis.org.cn/~zhangchunzhi/.

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Acknowledgements

We thank J. Yan and F. Tian for critical reading of the manuscript; G. Zhu for discussions and project coordination; Z. Peng, X. Xu, and S. Feng for phenotyping and genetic transformation; and Z. Wang, W. Xiao, and D. Zhang from Yinmore Group for greenhouse assistance. This work was supported by the Agricultural Science and Technology Innovation Program (ASTIP-CAAS to S.H.), the Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (CAAS-XTCX2016 to S.H.), Advanced Technology Talents in Yunnan Province (2013HA025 to S.H.), and National Natural Science Foundation of China (31601360 to C.Z.). This work was also supported by the Ministry of Agriculture and Rural Affairs of PRC and the Shenzhen municipal (The Peacock Plan KQTD2016113010482651 to S.H.) and Dapeng district governments.

Author information

Author notes

  1. These authors contributed equally: Chunzhi Zhang, Pei Wang, Die Tang.

Authors and Affiliations

  1. The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China

    Chunzhi Zhang, Pei Wang, Yi Shang & Canhui Li

  2. Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Chunzhi Zhang, Die Tang & Sanwen Huang

  3. Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China

    Chunzhi Zhang & Sanwen Huang

  4. College of Horticulture, Northwest Agriculture and Forest University, Yangling, China

    Zhongmin Yang

  5. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Fei Lu

  6. Inner Mongolia Potato Engineering and Technology Research Centre, Inner Mongolia University, Hohhot, China

    Jianjian Qi

  7. Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore

    Nilesh R. Tawari

Authors
  1. Chunzhi Zhang
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Contributions

S.H. and C.Z. designed the experiments and wrote the manuscript. C.Z., D.T., and F.L. performed the bioinformatics analyses. P.W. carried out the phenotyping assay. Z.Y. performed the cloning and functional analysis of ar1. J.Q. provided the genomic data for wild species S. candolleanum. N.R.T. predicted the deleterious mutations. Y.S. and C.L. coordinated the project.

Corresponding author

Correspondence to Sanwen Huang.

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The authors declare no competing interests.

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Integrated supplementary information

Supplementary Figure 1 S-RNase expression in flowers at the bud stage.

a, The five stages of flower development in PG6226. The numbers indicate the days from flowering. Scale bar, 0.5 cm. b, Relative expression of S-RNase in the mixed carpels of flowers at five developmental stages. The blue dots represent the expression levels of three technical replicates, and the error bars represent the standard errors of three technical replicates. Differential expression was analyzed by t test

Supplementary Figure 2 Deleterious substitutions are enriched in low-recombination regions.

a–c, The distribution of deleterious substitutions in three parental clones, PG6226 (a), PG6235 (b), and PG6359 (c). The x axis indicates the physical position. Red lines indicate the ratio between deleterious substitutions and synonymous mutations in each sliding window (window size, 5 Mb; step, 1 Mb), and black lines indicate the number of recombination events per 5 Mb. Gray-shaded boxes indicate the positions of pericentromeric regions

Supplementary Figure 3 Pipeline for parent-independent genotyping-by-sequencing in potato.

a, High-quality heterozygous SNPs in the F1 clone were extracted. b, The genotype of these SNPs in each F2 individual was identified from low-coverage sequencing data. The breakpoints between homozygous and heterozygous regions were deduced on the basis of the ratio of heterozygous SNPs to all SNPs in each window (window size, 1 Mb; step, 100 kb), and all SNPs in homozygous regions were extracted. c, The longest homozygous region or two overlapping homozygous regions that covered the whole chromosome were chosen as the reference fragments. All homozygous fragments were compared with the reference fragments and divided into two groups based on similarity to the reference fragment. d, Within each group, all SNPs with consensus at each locus were combined to construct the haplotype. e, The weighted value of genotype ‘b’ in each window was used to estimate the breakpoints of recombination. f, The genotype of a bin was defined on the basis of the weighted value of genotype ‘b’ in each bin. Blue, yellow, and gray indicate genotype ‘a’, ‘b’, and ‘h’, respectively. The same procedure was carried out for all 12 chromosomes

Supplementary Figure 4 Bin maps of three selfing populations.

a–c, Bin maps of three selfing populations derived from PG6226 (a), PG6235 (b), and PG6359 (c). Yellow, blue, and gray bars indicate genotype b, a, and h, respectively. Red dashed lines represent the regions with a missing genotype in selfed progeny

Supplementary Figure 5 Distribution of the heterozygous SNPs in parental clones.

a–c, The distribution of heterozygous SNPs in three F1 clones, PG6226 (a), PG6235 (b), and PG6359 (c). The x axis indicates physical position. The upper half of the y axis indicates the number of heterozygous SNPs in each sliding window (window size, 1 Mb; step, 100 kb), and the lower half indicates the average depth of the SNPs (window size, 1 Mb; step, 100 kb)

Supplementary Figure 6 Genetic mapping of the large-effect deleterious alleles affecting survival and growth vigor.

The delta SNP indexes between bulks with normal rooting versus abnormal rooting in the progeny of PG6226 (a), green seedlings and white seedlings in the progeny of PG6235 (b), normal leaves versus yellow-margined leaves in the progeny of PG6226 (c), normal leaves versus yellow leaves in the progeny of PG6359 (d), normal branching versus increased branching in the progeny of PG6235 (e), and normal branching versus strong vegetative growth in the progeny of PG6235 (f). The sliding window size is 1 Mb, and the step is 100 kb. The arrows indicate the positions of the target genes

Supplementary Figure 7 Nucleotide identity between PG6226 and PG6235 at the ar1 locus.

Identify was calculated on the basis of the ratio of the same SNPs and total overlapping SNPs in the haplotype containing the ar1 allele between PG6226 and PG6235 (sliding window size, 5 Mb; step, 500 kb)

Supplementary Figure 8 Genetic mapping of pollen viability and yield.

a–c, Frequency distributions of pollen viability in the selfing populations of PG6226 (a), PG6235 (b), and PG6359 (c). d, The segregation of tuber weight per plant in the selfing population of PG6226. The x axis represents the square root of tuber weight per plant. The arrows in a–d indicate the phenotype of the parental clones. Most progeny showed lower pollen viability and tuber yield than the parental clones. e–g, The delta indexes between bulks with high versus low pollen viability in the selfing populations of PG6226 (e), PG6235 (f), and PG6359 (g). h, The delta index between bulks with high and low tuber weight per plant. The sliding window size in e–h is 1 Mb, and the step size is 100 kb

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Zhang, C., Wang, P., Tang, D. et al. The genetic basis of inbreeding depression in potato. Nat Genet 51, 374–378 (2019). https://doi.org/10.1038/s41588-018-0319-1

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