期刊
MOLECULAR PLANT
卷 15, 期 3, 页码 520-536出版社
CELL PRESS
DOI: 10.1016/j.molp.2022.01.003
关键词
potato; allele diversity; phased assembly; polyploid; pan-genome; wild introgressions
资金
- AAFC-Genome Quebec [GQAAC-2019-2]
- Agriculture and Agri-Food Canada Genomics Research and Development Initiative [J-002367]
- Compute Canada, Research Portals and Platforms (RPP) award
- Compute Canada, Resources for Research Groups (RRG) award
- DFG Germany's Excellence Strategy [EXC2048/1, 390686111]
- Dutch TKI top-sector project Novel genetic and genomic tools for polyploid crops [BO26.03-009-004, BO-50-002-022]
- European Union [862858]
- Germany Ministry of Education and Research BMBF [FKZ031A536C]
- GIZ on behalf of the of the Federal Ministry for Economic Cooperation and Development, Germany
- National Science Foundation [IOS 2140176]
- National Science Foundation NRT-IMPACTS fellowship [1828149]
- NC Agricultural Research Service
- NC State University
- NSF [IOS-1929982]
- NWO-domein Toegepaste en Technische Wetenschappen MAMY project [16889]
- Potato Variety Management Institute
- State of Minnesota, Minnesota Department of Agriculture
- United States-Israel Binational Agricultural Research and Development Funds [IS-5038-17C, IS-5317-20C]
- Texas A M University
- Clen P. and Emma L. Atchley Potato Research Faculty Excellence Endowment
- University of Maine
- USDA AFRI NIFA Pre-doctoral Fellowship project [2019-07160]
- USDA Multistate Research Funds [1004958]
- USDA Hatch Act [2019-03162]
- USDA NIFA [2020-67034-31731]
- USDA-NIFA [2016-34141-25707]
- USDA-NIFA-SCRI [2019-51181-30021]
- Dutch TKI top-sector project Genetics Assisted Assembly of Complex Genomes [BO-68-001033-WPR]
- LWV20.112 Application of sequence-based multi-allelic markers in genetics and breeding of polyploids [BO-68001-042-WPR]
- Wageningen UR Plant Breeding
- Washington State Potato Commission
- Division Of Graduate Education
- Direct For Education and Human Resources [1828149] Funding Source: National Science Foundation
- NIFA [2016-34141-25707, 914133] Funding Source: Federal RePORTER
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars revealed extensive allelic diversity and structural variation, resulting in a complex transcriptome and predicted proteome. Wild species contribute to the allelic diversity in tetraploid cultivars. Understanding the complexity of the potato genome is key for precision breeding and hybridization.
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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