Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Genevieve Hoopes, Xiaoxi Meng, John P. Hamilton, Sai Reddy Achakkagari, Fernanda de Alves Freitas Guesdes, Marie E. Bolger, Joseph J. Coombs, Danny Esselink, Natalie R. Kaiser, Linda Kodde, Maria Kyriakidou, Brian Lavrijssen, Natascha van Lieshout, Rachel Shereda, Heather K. Tuttle, Brieanne Vaillancourt, Joshua C. Wood, Jan M. de Boer, Nolan Bornowski, Peter BourkeDavid Douches, Herman J. van Eck, Dave Ellis, Max J. Feldman, Kyle M. Gardner, Johannes C.P. Hopman, Jiming Jiang, Walter S. De Jong, Joseph C. Kuhl, Richard G. Novy, Stan Oome, Vidyasagar Sathuvalli, Ek Han Tan, Remco A. Ursum, M.I. Vales, Kelly Vining, Richard G.F. Visser, Jack Vossen, G.C. Yencho, Noelle L. Anglin, Christian W.B. Bachem, Jeffrey B. Endelman, Laura M. Shannon, Martina V. Strömvik, Helen H. Tai, Björn Usadel, Robin Buell*, Richard Finkers*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

82 Citations (Scopus)

Abstract

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Original languageEnglish
Pages (from-to)520-536
Number of pages17
JournalMolecular Plant
Volume15
Issue number3
DOIs
Publication statusPublished - 7 Mar 2022

Keywords

  • allele diversity
  • pan-genome
  • phased assembly
  • polyploid
  • potato
  • wild introgressions

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  • Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

    Hoopes, G. (Creator), Meng, X. (Creator), Hamilton, J. P. (Creator), Achakkagari, S. R. (Creator), de Alves Freitas Guedes, F. (Creator), Bolger, M. E. (Creator), Coombs, J. J. (Creator), Esselink, D. (Creator), Kaiser, N. R. (Creator), Kodde, L. (Creator), Kyriakidou, M. (Creator), Lavrijssen, B. (Creator), van Lieshout, N. (Creator), Shereda, R. (Creator), Tuttle, H. K. (Creator), Vaillancourt, B. (Creator), Wood, J. C. (Creator), de Boer, J. M. (Creator), Bornowski, N. (Creator), Bourke, P. (Creator), Douches, D. (Creator), van Eck, H. (Creator), Ellis, D. (Creator), Feldman, M. J. (Creator), Gardner, K. M. (Creator), Hopman, J. C. P. (Creator), Jiang, J. (Creator), De Jong, W. S. (Creator), Kuhl, J. C. (Creator), Novy, R. G. (Creator), Oome, S. (Creator), Sathuvalli, V. (Creator), Tan, E. H. (Creator), Ursum, R. A. (Creator), Vales, I. (Creator), Vining, K. (Creator), Visser, R. (Creator), Vossen, J. (Creator), Yencho, C. (Creator), Anglin, N. L. (Creator), Bachem, C. (Creator), Endelman, J. B. (Creator), Shannon, L. M. (Creator), Strömvik, M. V. (Creator), Tai, H. H. (Creator), Usadel, B. (Creator), Buell, R. (Creator) & Finkers, R. (Creator), Michigan State University, 27 Jan 2022

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