Populations are continually adapting to their environment.Knowledge of which populations and individuals harbor unique and agriculturally useful variations has the potential to accelerate crop adaptation to the increa...Populations are continually adapting to their environment.Knowledge of which populations and individuals harbor unique and agriculturally useful variations has the potential to accelerate crop adaptation to the increasingly challenging environments predicted for the coming century.Landscape genomics,which identifies associations between environmental and genomic variation,provides a means for obtaining this knowledge.However,despite extensive efforts to assemble and characterize ex situ collections of crops and their wild relatives,gaps remain in the genomic and environmental datasets needed to robustly implement this approach.This article outlines the history of landscape genomics,which,to date,has mainly been used in conservation and evolutionary studies,provides an overview of crops and wild relative collections that have the necessary data for implementation and identifies areas where new data genera-tion is needed.We find that 60%of the crops covered by the International Treaty on Plant Genetic Re-sources for Food and Agriculture lack the data necessary to conduct this kind of analysis,necessitating identification of crops in need of more collections,sequencing,or phenotyping.By highlighting these as-pects,we aim to help develop agricultural landscape genomics as a sub-discipline that brings together evolutionary genetics,landscape ecology,and plant breeding,ultimately enhancing the development of resilient and adaptable crops for future environmental challenges.展开更多
Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly importa...Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique flavor of common buckwheat,and provide new resources for future genomics-assisted breeding of this economically important crop.展开更多
Feralization is an important evolutionary process,but the mechanisms behind it remain poorly understood.Here,we use the ancient fiber crop ramie(Boehmeria nivea(L.)Gaudich.)as a model to investigate genomic changes as...Feralization is an important evolutionary process,but the mechanisms behind it remain poorly understood.Here,we use the ancient fiber crop ramie(Boehmeria nivea(L.)Gaudich.)as a model to investigate genomic changes associated with both domestication and feralization.We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes.Next,we gathered 915 accessions from 23 countries,comprising cultivars,major landraces,feral populations,and the wild progenitor.Based on whole-genome resequencing of these accessions,we constructed the most comprehensive ramie genomic variation map to date.Phylogenetic,demographic,and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin,i.e.,descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces.Feral ramie has higher genetic diversity than wild or domesticated ramie,and genomic regions affected by natural selection during feralization differ from those under selection during domestication.Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor,and three environmental variables are associated with habitat-specific adaptation in feral ramie.These findings advance our understanding of feralization,providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.展开更多
文摘Populations are continually adapting to their environment.Knowledge of which populations and individuals harbor unique and agriculturally useful variations has the potential to accelerate crop adaptation to the increasingly challenging environments predicted for the coming century.Landscape genomics,which identifies associations between environmental and genomic variation,provides a means for obtaining this knowledge.However,despite extensive efforts to assemble and characterize ex situ collections of crops and their wild relatives,gaps remain in the genomic and environmental datasets needed to robustly implement this approach.This article outlines the history of landscape genomics,which,to date,has mainly been used in conservation and evolutionary studies,provides an overview of crops and wild relative collections that have the necessary data for implementation and identifies areas where new data genera-tion is needed.We find that 60%of the crops covered by the International Treaty on Plant Genetic Re-sources for Food and Agriculture lack the data necessary to conduct this kind of analysis,necessitating identification of crops in need of more collections,sequencing,or phenotyping.By highlighting these as-pects,we aim to help develop agricultural landscape genomics as a sub-discipline that brings together evolutionary genetics,landscape ecology,and plant breeding,ultimately enhancing the development of resilient and adaptable crops for future environmental challenges.
基金the National Key R&D Program of China(2022YFE0140800)the European Union Horizon 2020 project ECOBREED(771367)+4 种基金the Youth Innovation Program of Chinese Academy of Agricultural Sciences(No.Y2022QC02)Project of Sanya Yazhou Bay Science and Technology City(SCKJ-JYRC-2022-22)National Natural Science Foundation of China(32161143005,31911530772,32111540258)PlantaSYST(SGA No 739582 under FPA No.664620)the BG05M2OP001-1.003-001-C01 project,financed by the European Regional Development Fund through the“Science and Education for Smart Growth”Operational Programme and Slovenian Research Agency,program P4-0077“Genetics and Modern Technologies of Crops”.
文摘Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique flavor of common buckwheat,and provide new resources for future genomics-assisted breeding of this economically important crop.
基金supported by the CAS Strategic Priority Research Program(XDB31000000)the National Natural Science Foundation of China(31970356,42171071,32170398)+5 种基金the Yunnan Young&Elite Talents Projects(YNWR-QNBJ-2020-293,YNWR-QNBJ-2018-146)the Key Research Program of Frontier Sciences,the CAS(ZDBS-LY-7001)the CAS“Light of West China”Program(to Z.-Y.W.and J.L.),the Applied and Fundamental Research Foundation of Yunnan Province(202401AT070190)the CAS Youth Innovation Promotion Association(2019385)the Central Public-interest Scientific Institution Basal Research Fund(Y2023PT11)R.M.and M.C.also thank the CAS President’s International Fellowship Initiative for financial support(2022VBA0004 and 2020VBB0016,respectively).
文摘Feralization is an important evolutionary process,but the mechanisms behind it remain poorly understood.Here,we use the ancient fiber crop ramie(Boehmeria nivea(L.)Gaudich.)as a model to investigate genomic changes associated with both domestication and feralization.We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes.Next,we gathered 915 accessions from 23 countries,comprising cultivars,major landraces,feral populations,and the wild progenitor.Based on whole-genome resequencing of these accessions,we constructed the most comprehensive ramie genomic variation map to date.Phylogenetic,demographic,and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin,i.e.,descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces.Feral ramie has higher genetic diversity than wild or domesticated ramie,and genomic regions affected by natural selection during feralization differ from those under selection during domestication.Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor,and three environmental variables are associated with habitat-specific adaptation in feral ramie.These findings advance our understanding of feralization,providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.
