The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide populat...The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land.These conditions require increased efficiency in pepper breeding to deal with these imminent challenges.Through resequencing of inbred lines we have completed a valuable haplotype map(HapMap)for the pepper genome based on single-nucleotide polymorphisms(SNP).The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines.A selection of one marker per gene model was utilized to create the PepperSNP16K array,which simultaneously genotyped 16405 SNPs,of which 90.7%were found to be informative.A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array.Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups.The interspecific population created between Tabasco(C.frutescens chile type)and P4(C.annuum blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM.This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper.As a standardized tool for genetic analyses,the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers.Data and information on the array are available through the Solanaceae Genomics Network.展开更多
Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins （NGEMPs）. The expression of these genes is regulated by tissue-specific, developmenta...Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins （NGEMPs）. The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regu- late these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde （nuclear to mitochondrial） and retrograde （mitochondrial to nuclear） signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.展开更多
Background:Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children.The goal of this study is to describe differences in ...Background:Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children.The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access.Methods:Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media,of whom 11 carry the A2ML1 duplication variant.Ear swabs were submitted for 16S rRNA gene sequencing.Results:Genotype-based differences in microbial richness,structure,and composition were identified,but were not statistically significant.Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes,and genus Fusobacterium were nominally increased in carriers compared to non-carriers,but were non-significant after correction for multiple testing.We also detected rare bacteria including Oligella that was reported only once in the middle ear.Conclusions:These findings suggest that A2ML1-related otitis media susceptibility may be mediated by changes in the middle ear microbiome.Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community.展开更多
文摘The Capsicum genus(Pepper)is a part of the Solanacae family.It has been important in many cultures worldwide for its key nutritional components and uses as spices,medicines,ornamentals and vegetables.Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land.These conditions require increased efficiency in pepper breeding to deal with these imminent challenges.Through resequencing of inbred lines we have completed a valuable haplotype map(HapMap)for the pepper genome based on single-nucleotide polymorphisms(SNP).The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines.A selection of one marker per gene model was utilized to create the PepperSNP16K array,which simultaneously genotyped 16405 SNPs,of which 90.7%were found to be informative.A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array.Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups.The interspecific population created between Tabasco(C.frutescens chile type)and P4(C.annuum blocky type)produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM.This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper.As a standardized tool for genetic analyses,the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers.Data and information on the array are available through the Solanaceae Genomics Network.
文摘Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins （NGEMPs）. The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regu- late these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde （nuclear to mitochondrial） and retrograde （mitochondrial to nuclear） signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.
基金supported by:the National Organization for Hearing Research Foundation,the Hearing Health Foundation,and Action On Hearing Loss(to R.L.P.S.C.)the University of the Philippines Manila–National Institutes of Health(to G.T.A.)+1 种基金the Albert and Margaret Alkek Foundation(to J.F.P.)the United States National Institutes of Health-National Institute on Deafness and Other Communication Disorders grants K18 DC013564(to T.C.),R01 DC011651 and R01 DC003594(to S.M.L.)and R01 DC015004(to R.L.P.S.C.).
文摘Background:Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children.The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access.Methods:Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media,of whom 11 carry the A2ML1 duplication variant.Ear swabs were submitted for 16S rRNA gene sequencing.Results:Genotype-based differences in microbial richness,structure,and composition were identified,but were not statistically significant.Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes,and genus Fusobacterium were nominally increased in carriers compared to non-carriers,but were non-significant after correction for multiple testing.We also detected rare bacteria including Oligella that was reported only once in the middle ear.Conclusions:These findings suggest that A2ML1-related otitis media susceptibility may be mediated by changes in the middle ear microbiome.Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community.
