Journal Article

FZJ-2022-01120

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

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

2022
Oxford Univ. Press Oxford

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Please use a persistent id in citations: http://hdl.handle.net/2128/30935  doi:10.1016/j.molp.2022.01.003

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.

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Contributing Institute(s):

1. Bioinformatik (IBG-4)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)

Appears in the scientific report 2022

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Database coverage:
; ; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 20 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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