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

Autor: Hoopes G; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA., Meng X; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA., Hamilton JP; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA., Achakkagari SR; Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada., de Alves Freitas Guesdes F; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Bolger ME; IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany., Coombs JJ; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA., Esselink D; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Kaiser NR; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Bayer Crop Science, Woodland, CA 95695, USA., Kodde L; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Kyriakidou M; Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada., Lavrijssen B; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., van Lieshout N; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Shereda R; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA., Tuttle HK; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA., Vaillancourt B; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA., Wood JC; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA., de Boer JM; Averis Seeds B.V., 9640 AA Veendam, the Netherlands., Bornowski N; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA., Bourke P; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Douches D; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA., van Eck HJ; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Ellis D; International Potato Center, 1895 Avenida La Molina, Lima, Peru., Feldman MJ; USDA-ARS, Prosser, WA 99350, USA., Gardner KM; Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada., Hopman JCP; Averis Seeds B.V., 9640 AA Veendam, the Netherlands., Jiang J; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA., De Jong WS; School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-1901, USA., Kuhl JC; Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA., Novy RG; USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA., Oome S; HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands., Sathuvalli V; Department of Crop and Soil Science, Oregon State University, Hermiston, OR 97838, USA., Tan EH; School of Biology and Ecology, University of Maine, 5735 Hitchner Hall Orono, ME 04469, USA., Ursum RA; HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands., Vales MI; Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA., Vining K; Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA., Visser RGF; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Vossen J; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Yencho GC; Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA., Anglin NL; International Potato Center, 1895 Avenida La Molina, Lima, Peru; USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA., Bachem CWB; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands., Endelman JB; Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA., Shannon LM; Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA., Strömvik MV; Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada., Tai HH; Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada., Usadel B; IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany; Institute for Biological Data Science, Heinrich Heine University, Düsseldorf, 40225 Düsseldorf, Germany., Buell CR; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA. Electronic address: robin.buell@uga.edu., Finkers R; Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands. Electronic address: richard.finkers@wur.nl.
Jazyk: angličtina
Zdroj: Molecular plant [Mol Plant] 2022 Mar 07; Vol. 15 (3), pp. 520-536. Date of Electronic Publication: 2022 Jan 10.
DOI: 10.1016/j.molp.2022.01.003
Abstrakt: 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.
(Copyright © 2022 The Author. Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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