Haplotype-resolved genome analyses of a heterozygous diploid potato

Qian Zhou, Dié Tang, Wu Huang, Zhongmin Yang, Yu Zhang, John P. Hamilton, Richard G.F. Visser, Christian W.B. Bachem, C. Robin Buell, Zhonghua Zhang, Chunzhi Zhang, Sanwen Huang*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Abstract

Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.

Original languageEnglish
Pages (from-to)1018-1023
Number of pages6
JournalNature Genetics
Volume52
Issue number10
DOIs
Publication statusPublished - 1 Oct 2020

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