Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity
作者机构：Department of Plant BiologyMichigan State UniversityEast LansingMI 48824USA Department of Horticultural ScienceUniversity of MinnesotaSt.PaulMN 55108USA Department of Plant ScienceMcGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant BreedingWageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IBG-4 BioinformaticsForschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of PlantSoiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA Bayer Crop ScienceWoodlandCA 95695USA Averis Seeds B.V.9640 AA Veendamthe Netherlands International Potato Center1895 Avenida La MolinaLimaPeru USDA-ARSProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development CentreFrederictonNB E3B 4Z7Canada School of Integrative Plant ScienceCornell UniversityIthacaNY 14853-1901USA Department of Plant SciencesUniversity of IdahoMoscowID 83844USA USDA-ARSSmall Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research B.V.Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil ScienceOregon State UniversityHermistonOR 97838USA School of Biology and EcologyUniversity of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural SciencesTexas A&M UniversityCollege StationTX 77843-2133USA Department of HorticultureOregon State UniversityCorvallisOR 97331USA Department of Horticultural ScienceNorth Carolina State UniversityRaleighNC 27695-7609USA Department of HorticultureUniversity of Wisconsin-MadisonMadisonWI 53706USA Department of HorticultureMichigan State UniversityEast LansingMI 48824USA Institute for Biological Data ScienceHeinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience InstituteMichigan State UniversityEast LansingMI 48824USA Present address:GenNovation B.V.Wageningenthe Netherlands
出 版 物：《Molecular Plant》 (分子植物（英文版）)
年 卷 期：2022年第15卷第3期
页 面：520-536页
核心收录：
基 金：We acknowledge financial support from AAFC-Genome Quebec GQAAC-2019-2 to M.V.S.,Agriculture and Agri-Food Canada Genomics Research and Development Initiative grant number J-002367 to H.H.T.and K.M.G Compute Canada,Research Portals and Platforms(RPP)award to M.V.S,Compute Canada,Resources for Research Groups(RRG)award to M.V.S.,DFG Germany’s Excellence Strategy(EXC2048/1-Project 390686111)to B.U.,Dutch TKI top-sector project Novel genetic and genomic tools for polyploid crops(project numbers BO26.03-009-004 and BO-50-002-022)to P.M.B.,European Union’s Horizon 2020 research and innovation programme under grant agreement no 862858(ADAPT)to C.W.B.B.,Germany Ministry of Education and Research BMBF FKZ031A536C to B.U.,Germany Ministry of Education and Research BMBF FKZ031A536C to M.E.B.,GIZ on behalf of the of the Federal Ministry for Economic Cooperation and Development,Germany to D.Ellis and N.L.A.,National Science Foundation(IOS 2140176)to C.R.B National Science Foundation NRT-IMPACTS fellowship(1828149)to N.B.,NC Agricultural Research Service to G.C.Y.,NC State University to G.C.Y.,NSF IOS-1929982 to C.R.B NWO-domein Toegepaste en Technische Wetenschappen MAMY project ID 16889 to C.W.B.B.and N.L.,Potato Variety Management Institute to K.V.and V.S.,State of Minnesota,Minnesota Department of Agriculture to L.M.S.,the United States-Israel Binational Agricultural Research and Development Funds IS-5038-17C and IS-5317-20C to J.J Texas A&M University to M.I.V.,The Clen P.and Emma L.Atchley Potato Research Faculty Excellence Endowment to J.C.K.,University of Maine to E.H.T.,USDA AFRI NIFA Pre-doctoral Fellowship project 2019-07160 to N.R.K.,USDA Multistate Research Funds accession 1004958 to W.S.D.J USDA Hatch Act 2019-03162 to C.R.B.,USDA NIFA 2020-67034-31731 to G.H USDA-NIFA 2016-34141-25707 to L.M.S.,USDA-NIFA-SCRI 2019-51181-30021 to L.M.S.,Dutch TKI top-sector project Genetics Assisted Assembly of Complex Genomes(project number BO-68-001-033-WPR) LWV20.112 Application of sequence-based multi-allelic markers in genetics and breeding of polyploids(project number BO-68-001-042-WPR) Wageningen UR Plant Breeding to R.F.,Wageningen UR Plant Breeding to R.G.F.V.,and Washington State Potato Commission to M.J.F.We would like to thank Emily McCoy and Martin Lague for assistance with data analysis
主 题：potato allele diversity phased assembly polyploid pan-genome wild introgressions
摘 要：Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** 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 *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** 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 *** 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 *** 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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