Projects per year
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 language | English |
---|---|
Pages (from-to) | 520-536 |
Number of pages | 17 |
Journal | Molecular Plant |
Volume | 15 |
Issue number | 3 |
DOIs | |
Publication status | Published - 7 Mar 2022 |
Keywords
- allele diversity
- pan-genome
- phased assembly
- polyploid
- potato
- wild introgressions
Fingerprint
Dive into the research topics of 'Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity'. Together they form a unique fingerprint.Datasets
-
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
Dataset
-
LWV20085 Genetics Assisted Assembly of Complex Genomes (BO-68-001-033)
Hooykaas, M. (Project Leader)
1/01/21 → 31/12/24
Project: LVVN project
-
LWV20.112 Application of sequence-based multi-allelic markers in genetics and breeding of polyploids (BO-68-001-042)
Arens, P. (Project Leader)
1/01/21 → 1/03/25
Project: LVVN project
-
ADAPT: Accelerated Development of multiple-stress tolerAnt PoTato
1/07/20 → 31/10/24
Project: EU research project