Aims Within-species genetic and phenotypic variation have well-known effects on evolutionary processes,but less is known about how within-species variation may influence community-level processes.Ecologically meaningf...Aims Within-species genetic and phenotypic variation have well-known effects on evolutionary processes,but less is known about how within-species variation may influence community-level processes.Ecologically meaningful intraspecific variation might be particularly important in the context of anthropogenic impacts on natural systems,such as agriculture and species invasion,because human actions can cause strong selection pressures.Methods In a greenhouse study,we explored intraspecific(30 accessions)and ecotypic variation(representing agricultural and nonagricultural habitats)in biomass and rhizome production in response to inter-and intraspecific competition and soil fertility of Johnsongrass(Sorghum halepense),a widespread invasive species and agricultural weed.Important Findings Contrary to our expectations and previous results,we did not find variation in biomass production among Johnsongrass ecotypes at this early life stage.However,we did find that Johnsongrass biomass varied substantially depending on competitor identity,soil fertility treatments and among accessions.Rhizomes were 11%larger in the agricultural ecotype and up to 3-fold larger in fertilized treatment;while rhizome biomass increased by~50%when fertilized,but did not differ among ecotypes.Interestingly,in competition,Johnsongrass produced 32%less biomass and 20%less rhizome mass with a conspecific than when competing interspecifically with corn.Our results indicate species-specific competitive responses and changes in rhizome allocation in response to neighbor identity;suggesting the possibility of adaptation by Johnsongrass to shift allocation under competition.展开更多
Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their complexity.We have developed a TE genot...Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their complexity.We have developed a TE genotyping pipeline(TEmarker)and applied it to whole-genome genome-wide association study(GWAS)data from 176 Oryza sativa subsp.japonica accessions to identify genetic elements associated with specific agronomic traits.TE markers recovered a large proportion(69%)of single-nucleotide polymorphism(SNP)-based GWAS peaks,and these TE peaks retained ca.25%of the SNPs.The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium(LD)among SNP markers.A genome scan revealed positive selection on TEs associated with agronomic traits.We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs,including an allele of LOC_Os11g08410 associated with plant height and panicle length traits.Together,these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.展开更多
基金We are grateful for the Weed Science Society of America for funding to W.K.,and Virginia Tech College of Agriculture and Life Sciences and grants from the National Institute of Food and Agriculture grants nos.2015-68004-23492 and 2013-67013-21306 to J.N.B.
文摘Aims Within-species genetic and phenotypic variation have well-known effects on evolutionary processes,but less is known about how within-species variation may influence community-level processes.Ecologically meaningful intraspecific variation might be particularly important in the context of anthropogenic impacts on natural systems,such as agriculture and species invasion,because human actions can cause strong selection pressures.Methods In a greenhouse study,we explored intraspecific(30 accessions)and ecotypic variation(representing agricultural and nonagricultural habitats)in biomass and rhizome production in response to inter-and intraspecific competition and soil fertility of Johnsongrass(Sorghum halepense),a widespread invasive species and agricultural weed.Important Findings Contrary to our expectations and previous results,we did not find variation in biomass production among Johnsongrass ecotypes at this early life stage.However,we did find that Johnsongrass biomass varied substantially depending on competitor identity,soil fertility treatments and among accessions.Rhizomes were 11%larger in the agricultural ecotype and up to 3-fold larger in fertilized treatment;while rhizome biomass increased by~50%when fertilized,but did not differ among ecotypes.Interestingly,in competition,Johnsongrass produced 32%less biomass and 20%less rhizome mass with a conspecific than when competing interspecifically with corn.Our results indicate species-specific competitive responses and changes in rhizome allocation in response to neighbor identity;suggesting the possibility of adaptation by Johnsongrass to shift allocation under competition.
文摘Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their complexity.We have developed a TE genotyping pipeline(TEmarker)and applied it to whole-genome genome-wide association study(GWAS)data from 176 Oryza sativa subsp.japonica accessions to identify genetic elements associated with specific agronomic traits.TE markers recovered a large proportion(69%)of single-nucleotide polymorphism(SNP)-based GWAS peaks,and these TE peaks retained ca.25%of the SNPs.The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium(LD)among SNP markers.A genome scan revealed positive selection on TEs associated with agronomic traits.We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs,including an allele of LOC_Os11g08410 associated with plant height and panicle length traits.Together,these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.
