The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 ...The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.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funding from the National Sciences and Engineering Research Council of Canada and Canada Research Chairs programme(SM).
文摘The apple(Malus domestica)is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years.Here,we genetically characterise over 1000 apple accessions from the United States Department of Agriculture(USDA)germplasm collection using over 30,000 singlenucleotide polymorphisms(SNPs).We con fi rm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversii from Central Asia,and fi nd that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris,than do dessert apples.We determine that most of the USDA collection is a large complex pedigree:over half of the collection is interconnected by a series of fi rst-degree relationships.In addition,15%of the accessions have a fi rst-degree relationship with one of the top 8 cultivars produced in the USA.With the exception of‘Honeycrisp',the top 8 cultivars are interconnected to each other via pedigree relationships.The cultivars‘Golden Delicious'and‘Red Delicious'were found to have over 60 fi rst-degree relatives,consistent with their repeated use by apple breeders.We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased fi rmness.Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will bene fi t from increased exploitation of its tremendous natural genetic diversity.
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.
