Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,throu...Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,through the genomic analysis of Arabidopsis,three Brassica species and 17 other representative species,we found that both cold-related genes(CRGs)and their collinearity were preferentially retained after polyploidization followed by genome instability,while genome-wide gene sets exhibited a variety of other expansion mechanisms.The coldrelated regulatory network was increased in Brassicaceae genomes,which were recursively affected by polyploidization.By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling,we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution.This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence,which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.展开更多
Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the...Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.展开更多
Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh consumption.Here we evaluate patterns of diversity across 33 phenotypes collected ...Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh consumption.Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks,the grape germplasm collection of the United States Department of Agriculture.We find that phenological events throughout the growing season are correlated,and quantify the marked difference in size between table and wine grapes.By pairing publicly available historical phenotype data with genome-wide polymorphism data,we identify large effect loci controlling traits that have been targeted during domestication and breeding,including hermaphroditism,lighter skin pigmentation and muscat aroma.Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited,whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions.We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries.Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.展开更多
Crops face increased risk from heat stress due to climate change.Potato(Solanum tuberosum L.)tubers grown in hot summers often have defects including pre-harvest sprouting(“heat sprouts”).We have used 18 potato cult...Crops face increased risk from heat stress due to climate change.Potato(Solanum tuberosum L.)tubers grown in hot summers often have defects including pre-harvest sprouting(“heat sprouts”).We have used 18 potato cultivars to investigate whether heat stress(HS)conditions alone could cause heat sprouting and dormancy changes in tubers.We also examined transcriptomic responses of potato to HS and whether these responses are like those induced by postharvest sprouting.We demonstrated that HS alone caused heat sprouts and shortened postharvest dormancy period,heat-sprouted tubers became dormant after harvest,and cultivars varied substantially for producing heat spouts but there was no clear association with cultivar maturity earliness.Cultivar Innovator did not show any heat sprouts and still had long dormancy.Dormancy-associated genes(DOG1 and SLP)were downregulated in HS tubers like in postharvest sprouting tubers.We have identified 1201 differentially expressed genes,14 enriched GO terms and 12 enriched KEGG pathways in response to HS in growing tubers of‘Russet Burbank’.Transcriptomic response of‘Russet Burbank’to HS showed significant similarities to that of postharvest non-HS sprouted tubers.Gibberellin biosynthesis pathway was enriched in heat-stressed tubers and was likely involved in heat sprouting and dormancy release.Heat sprouting and postharvest sprouting shared common candidate genes and had significant similarity in gene expression.Our study has significance for selecting potato cultivars for farming,planning storage and utilization of heat-stressed tubers,identifying sprouting-related genes,understanding heat-stress biology,and breeding heat-tolerant potato cultivars,especially for sustainable potato production under climate change.展开更多
Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry...Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.展开更多
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
The apple(Malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit crops.With demand for apples year round,storability has emerged as an important consideration for apple breeding progra...The apple(Malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit crops.With demand for apples year round,storability has emerged as an important consideration for apple breeding programs.Soft scald is a cold storage-related disorder that results in sunken,darkened tissue on the fruit surface.Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round.Traditional breeding approaches are protracted and labor intensive,and therefore marker-assisted selection(MAS)is a valuable tool for breeders.To advance MAS for storage disorders in apple,we used genotyping-by-sequencing(GBS)to generate high-density genetic maps in two F1 apple populations,which were then used for quantitative trait locus(QTL)mapping of soft scald.In total,900 million DNA sequence reads were generated,but after several data filtering steps,only 2%of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms.Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11,an advanced breeding line.This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations,and provides a basis for the advancement of MAS to improve storability of apples.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
Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,ge...Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.展开更多
基金supported by the National Natural Science Foundation of China(31801856 to X.S.,2016YFD0101001 to X.W.)the Hebei Province Higher Education Youth Talents Program(BJ2018016 to X.S.)the Natural Science Foundation of Hebei(C2017209103 to X.S.).
文摘Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,through the genomic analysis of Arabidopsis,three Brassica species and 17 other representative species,we found that both cold-related genes(CRGs)and their collinearity were preferentially retained after polyploidization followed by genome instability,while genome-wide gene sets exhibited a variety of other expansion mechanisms.The coldrelated regulatory network was increased in Brassicaceae genomes,which were recursively affected by polyploidization.By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling,we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution.This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence,which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.
基金supported by the National Natural Science Foundation of China(31801856 to X.S.)the Hebei Province Higher Education Youth Talents Program(BJ2018016 to X.S.)+1 种基金China-Hebei 100 Scholars Supporting Project(E2013100003 to X.W.)the Natural Science Foundation of Hebei(C2017209103 to X.S.).
文摘Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.
基金We acknowledge the funding from the Canada Research Chairs program,the National Sciences and Engineering Research Council of Canada and Genome CanadaZM was supported in part by a Killam Predoctoral Scholarship from Dalhousie University.
文摘Grapes are one of the most economically and culturally important crops worldwide,and they have been bred for both winemaking and fresh consumption.Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks,the grape germplasm collection of the United States Department of Agriculture.We find that phenological events throughout the growing season are correlated,and quantify the marked difference in size between table and wine grapes.By pairing publicly available historical phenotype data with genome-wide polymorphism data,we identify large effect loci controlling traits that have been targeted during domestication and breeding,including hermaphroditism,lighter skin pigmentation and muscat aroma.Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited,whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions.We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries.Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.
基金This research was mainly supported by the National Natural Science Foundation of China(Nos.31860399,31560413 to Huaijun Si)A-base funding of Agriculture and Agri-Food Canada(AAFC),Government of Canada(to Xiu-Qing Li)+3 种基金We thank the China Scholarship Council for its support to Guodong Zhang and Ruimin Tang to work in AAFC under Xiu-Qing Li’s supervisionWe also thank the funding supports from the Natural Science Foundation of Jiangsu Province(No.BK20180519 to Qing Yang)the Key Research Projects Program of Higher Education Institutes in Henan Provinces(21A210029 to Suyan Niu)the funding from the Natural Sciences and Engineering Research Council of Canada Discovery Grant(RGPIN 2017-04589 to Om P.Rajora)。
文摘Crops face increased risk from heat stress due to climate change.Potato(Solanum tuberosum L.)tubers grown in hot summers often have defects including pre-harvest sprouting(“heat sprouts”).We have used 18 potato cultivars to investigate whether heat stress(HS)conditions alone could cause heat sprouting and dormancy changes in tubers.We also examined transcriptomic responses of potato to HS and whether these responses are like those induced by postharvest sprouting.We demonstrated that HS alone caused heat sprouts and shortened postharvest dormancy period,heat-sprouted tubers became dormant after harvest,and cultivars varied substantially for producing heat spouts but there was no clear association with cultivar maturity earliness.Cultivar Innovator did not show any heat sprouts and still had long dormancy.Dormancy-associated genes(DOG1 and SLP)were downregulated in HS tubers like in postharvest sprouting tubers.We have identified 1201 differentially expressed genes,14 enriched GO terms and 12 enriched KEGG pathways in response to HS in growing tubers of‘Russet Burbank’.Transcriptomic response of‘Russet Burbank’to HS showed significant similarities to that of postharvest non-HS sprouted tubers.Gibberellin biosynthesis pathway was enriched in heat-stressed tubers and was likely involved in heat sprouting and dormancy release.Heat sprouting and postharvest sprouting shared common candidate genes and had significant similarity in gene expression.Our study has significance for selecting potato cultivars for farming,planning storage and utilization of heat-stressed tubers,identifying sprouting-related genes,understanding heat-stress biology,and breeding heat-tolerant potato cultivars,especially for sustainable potato production under climate change.
基金supported by the National Natural Science Foundation of China(Grant Nos.32170236,31501333,and 32000405)Natural Science Foundation of Hebei Province(Grant No.C2020209064)the Innovation and Entrepreneurship Training Program for College Students of North China University of Science and Technology(Grant No.X2019252)。
文摘Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.
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This project was funded by the A-Base research(NOI-1238)of Agriculture and Agri-Food CanadaThis research was also supported in part by funding from the Canada Research Chairs program(SM)and the National Sciences and Engineering Research Council of Canada(SM,KM).
文摘The apple(Malus×domestica Borkh.)is one of the world’s most widely grown and valuable fruit crops.With demand for apples year round,storability has emerged as an important consideration for apple breeding programs.Soft scald is a cold storage-related disorder that results in sunken,darkened tissue on the fruit surface.Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round.Traditional breeding approaches are protracted and labor intensive,and therefore marker-assisted selection(MAS)is a valuable tool for breeders.To advance MAS for storage disorders in apple,we used genotyping-by-sequencing(GBS)to generate high-density genetic maps in two F1 apple populations,which were then used for quantitative trait locus(QTL)mapping of soft scald.In total,900 million DNA sequence reads were generated,but after several data filtering steps,only 2%of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms.Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11,an advanced breeding line.This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations,and provides a basis for the advancement of MAS to improve storability of apples.
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.
基金funded in part by Agriculture and Agri-Food Canada(AAFC)project J-001781 awarded to A.M.-G.and by the Enabling Agricultural Research Innovation(EARI)project C1920-0046 awarded to C.W.
基金the Ministry of Science and Technology of the People’s Republic of China(Grant No.2016YFD0101001)the China National Science Foundation(Grant Nos.31371282 to XW,31510333 to JW,and 31661143009 to XW)+1 种基金the Natural Science Foundation of Hebei Province(Grant No.C2015209069 to JW)Tangshan Key Laboratory Project to XW。
文摘Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.
