Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the fa...Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the family of nucleotide-binding,leucine-rich-repeat(NLR)genes.To identify effective disease resistance genes in established varieties,we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d.The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score.Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator,SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1,Rpi-R2-like,Rpi-R3a,and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations.All benchmark genes were identified with an F1 score of 1,which indicates absolute linkage in the panel.This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode(PCN)species Globodera pallida(pathotypes Pa2/3).Assuming that NLRs are involved in controlling many types of resistances,SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.展开更多
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 alleli...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.展开更多
基金supported by the Rural&Environment Science&Analytical Services(RESAS)Division of the Scottish Government through project JHI-B1-1,the Biotechnology and Biological Sciences Research Council(BBSRC)through award BB/S015663/1 and the Royal Society through award NAF\R1\201061YW was supported through the CSC scholarship program,China.LB was supported through the East of Scotland Bioscience Doctoral Training Partnership(EASTBIO DTP)funded by the BBSRC award BB/T00875X/1.AK was supported through a Research Leaders 2025 fellowship funded by European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement no.754380.
文摘Potato is the thirdmost important food crop in theworld.Diverse pathogens threaten sustainable crop production but can be controlled,in many cases,through the deployment of disease resistance genes belonging to the family of nucleotide-binding,leucine-rich-repeat(NLR)genes.To identify effective disease resistance genes in established varieties,we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d.The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score.Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator,SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1,Rpi-R2-like,Rpi-R3a,and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations.All benchmark genes were identified with an F1 score of 1,which indicates absolute linkage in the panel.This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode(PCN)species Globodera pallida(pathotypes Pa2/3).Assuming that NLRs are involved in controlling many types of resistances,SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
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.+6 种基金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.
文摘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.
