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