Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economic...Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.展开更多
为缓解河北武安市水资源供需不平衡的突出矛盾,立足水资源精细化管理的需求,构建了武安市GWAS(general water allocation and simulation)模型,并开展规划年(2025年与2030年)不同情景下武安市各乡镇水资源优化配置研究。结果表明:2025年...为缓解河北武安市水资源供需不平衡的突出矛盾,立足水资源精细化管理的需求,构建了武安市GWAS(general water allocation and simulation)模型,并开展规划年(2025年与2030年)不同情景下武安市各乡镇水资源优化配置研究。结果表明:2025年和2030年,平水情景(P=50%)下模型优化配置水量基本可以满足各乡镇水量需求,枯水情景(P=75%)下各乡镇存在不同程度的缺水情况;全市普遍农业缺水,2025年平枯情景农业缺水率分别为6.45%和44.11%,2030年平枯情景农业缺水率分别为5.05%和42.47%;优化后的供水结构改善效果显著,地下水供水量占比在各规划年平枯情景下均有所下降。展开更多
为推进全基因组关联分析(GWAS,genome-wide association study)在葫芦科瓜类作物重要农艺性状关键遗传变异位点精准挖掘中的应用,文章介绍了GWAS的原理和统计模型,归纳了GWAS在鉴定群体中的遗传变异位点、解析植物代谢机制,并对其在实...为推进全基因组关联分析(GWAS,genome-wide association study)在葫芦科瓜类作物重要农艺性状关键遗传变异位点精准挖掘中的应用,文章介绍了GWAS的原理和统计模型,归纳了GWAS在鉴定群体中的遗传变异位点、解析植物代谢机制,并对其在实施精准遗传改良策略中体现出的优势进行了概述,系统梳理了GWAS在西瓜、甜瓜、黄瓜、南瓜等主要葫芦科瓜类作物遗传改良研究中的最新进展,同时对葫芦科作物育种研究中的多组学联合分析和数据库构建进行了展望,以期为葫芦科作物的遗传改良过程中提供更多的依据和参考。展开更多
Malic acid(MA)is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways.It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to unders...Malic acid(MA)is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways.It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes.However,themetabolic accumulation of MA is controlled by complex heredity and environmental factors,making it difficult to predict and regulate the metabolism of MA.In this study,we carried out a genome-wide association study(GWAS)on MA using eight milestone models with two-environment repeats.A series of associated SNP variations were identified from the GWAS,and 15 high-confidence annotated geneswere further predicted based on linkage disequilibrium and lead SNPs.The transcriptome data of candidate geneswere explored within different tomato organs as well as various fruit tissues,and suggested specific expression patterns in fruit pericarp.Based on the genetic parameters of population differentiation and SNP distribution,tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding.In addition,genotype×environment interaction might contribute to the difference in domestication phenotypic data under different environments.This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.展开更多
A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,th...A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge.In this study,we first report a general genetic map which was constructed from 44 published linkage maps.It permits the estimation of genetic distances between any two genetic loci with physical map positions,thereby unifying the linkage relationships between QTL,genes,and genomic markers from multiple genetic populations.Second,we describe QTL mapping in a wheat GWAS panel of 688 accessions,identifying 77 QTL associated with 12 yield and grain-quality traits.Because these QTL have known physical map positions,they could be mapped onto the general map.Finally,we present a design approach to wheat breeding by using known QTL information and computer simulation.Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype,trait correlations in simulated progeny populations,and genetic gain of selected progenies.It is possible to simultaneously improve yield and grain quality by suitable parental selection,progeny population size,and progeny selection scheme.Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment,increasing predictability and efficiency in wheat breeding.展开更多
Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so...Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.展开更多
Adventitious rooting(AR)is critical to the propagation,breeding,and genetic engineering of trees.The capacity for plants to undergo this process is highly heritable and of a polygenic nature;however,the basis of its g...Adventitious rooting(AR)is critical to the propagation,breeding,and genetic engineering of trees.The capacity for plants to undergo this process is highly heritable and of a polygenic nature;however,the basis of its genetic variation is largely uncharacterized.To identify genetic regulators of AR,we performed a genome-wide association study(GWAS)using 1148 genotypes of Populus trichocarpa.GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale;to help overcome this limitation,we developed a computer vision system to measure an array of traits related to adventitious root development in poplar,including temporal measures of lateral and basal root length and area.GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power.These analyses yielded a total of 277 unique associations,suggesting that genes that control rooting include regulators of hormone signaling,cell division and structure,reactive oxygen species signaling,and other processes with known roles in root development.Numerous genes with uncharacterized functions and/or cryptic roles were also identified.These candidates provide targets for functional analysis,including physiological and epistatic analyses,to better characterize the complex polygenic regulation of AR.展开更多
Most variants associated with complex traits and diseases identified by genome-wide association studies(GWAS)map to noncoding regions of the genome with unknown effects.Using ancestrally diverse,biobank-scale GWAS dat...Most variants associated with complex traits and diseases identified by genome-wide association studies(GWAS)map to noncoding regions of the genome with unknown effects.Using ancestrally diverse,biobank-scale GWAS data,massively parallel CRISPR screens,and single-cell transcriptomic and proteomic sequencing,we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci.Using precise variant insertion through base editing,we connected specific variants with gene expression changes.We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs.Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits.This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.展开更多
自提出全基因组关联研究(genome-wide association study,GWAS)设想以来,在人类复杂疾病和水稻农艺性状关联研究方面,GWAS已得到广泛运用。但作为一种典型的单标记研究方法,GWAS不能检测小效应的遗传变异,而稀有变异间的联合效应往往与...自提出全基因组关联研究(genome-wide association study,GWAS)设想以来,在人类复杂疾病和水稻农艺性状关联研究方面,GWAS已得到广泛运用。但作为一种典型的单标记研究方法,GWAS不能检测小效应的遗传变异,而稀有变异间的联合效应往往与表型密切相关,因此,需对GWAS结果进行深入的数据挖掘。基于通路的分析方法(pathway-based analysis,PBA)就是利用基因功能、生物代谢通路等相关信息建立的对GWAS结果进行二次挖掘的方法。该方法能从GWAS结果挖掘出与性状、疾病相关联的通路及具有相同功能的基因集等数据,从而获得更多的遗传信息。现对PBA的出现、计算方法和相关软件进行简要综述,以期为人们进行通路分析提供参考。展开更多
基金supported by the National Key R&D Program of China(2022YFD2400105,2018YFD0900104)Central Publicinterest Scientific Institution Basal Research Fund,CAFS(2021XT0102,2023TD30)+2 种基金Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(2021QNLM050103)Key Research and Development Project of Shandong Province(2021LZGC028)National Marine Genetic Resource Center。
文摘Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.
文摘为缓解河北武安市水资源供需不平衡的突出矛盾,立足水资源精细化管理的需求,构建了武安市GWAS(general water allocation and simulation)模型,并开展规划年(2025年与2030年)不同情景下武安市各乡镇水资源优化配置研究。结果表明:2025年和2030年,平水情景(P=50%)下模型优化配置水量基本可以满足各乡镇水量需求,枯水情景(P=75%)下各乡镇存在不同程度的缺水情况;全市普遍农业缺水,2025年平枯情景农业缺水率分别为6.45%和44.11%,2030年平枯情景农业缺水率分别为5.05%和42.47%;优化后的供水结构改善效果显著,地下水供水量占比在各规划年平枯情景下均有所下降。
文摘为推进全基因组关联分析(GWAS,genome-wide association study)在葫芦科瓜类作物重要农艺性状关键遗传变异位点精准挖掘中的应用,文章介绍了GWAS的原理和统计模型,归纳了GWAS在鉴定群体中的遗传变异位点、解析植物代谢机制,并对其在实施精准遗传改良策略中体现出的优势进行了概述,系统梳理了GWAS在西瓜、甜瓜、黄瓜、南瓜等主要葫芦科瓜类作物遗传改良研究中的最新进展,同时对葫芦科作物育种研究中的多组学联合分析和数据库构建进行了展望,以期为葫芦科作物的遗传改良过程中提供更多的依据和参考。
基金supported by grants from the National Key Research&Development Plan(2022YFD12005022021YFD1200201)+6 种基金the National Natural Science Foundation of China(3197242631991182)the Wuhan Biological Breeding Major Project(2022021302024852)the Key Project of Hubei Hongshan Laboratory(2021hszd007)the Hubei Key Research&Development Plan(2022BBA00622022BBA0066)the Fundamental Research Funds for the Central Universities(2662022YLPY001)and the International Cooperation Promotion Plan of Shihezi University(GJHZ202104)..
文摘Malic acid(MA)is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways.It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes.However,themetabolic accumulation of MA is controlled by complex heredity and environmental factors,making it difficult to predict and regulate the metabolism of MA.In this study,we carried out a genome-wide association study(GWAS)on MA using eight milestone models with two-environment repeats.A series of associated SNP variations were identified from the GWAS,and 15 high-confidence annotated geneswere further predicted based on linkage disequilibrium and lead SNPs.The transcriptome data of candidate geneswere explored within different tomato organs as well as various fruit tissues,and suggested specific expression patterns in fruit pericarp.Based on the genetic parameters of population differentiation and SNP distribution,tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding.In addition,genotype×environment interaction might contribute to the difference in domestication phenotypic data under different environments.This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.
基金the Hainan Yazhou Bay Seed Laboratory(B21Y10209 and B22C10212)China Postdoctoral Science Foundation(2022M713433)+1 种基金National Natural Science Foundation of China(31861143003)Innovation Program of Chinese Academy of Agricultural Sciences.
文摘A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge.In this study,we first report a general genetic map which was constructed from 44 published linkage maps.It permits the estimation of genetic distances between any two genetic loci with physical map positions,thereby unifying the linkage relationships between QTL,genes,and genomic markers from multiple genetic populations.Second,we describe QTL mapping in a wheat GWAS panel of 688 accessions,identifying 77 QTL associated with 12 yield and grain-quality traits.Because these QTL have known physical map positions,they could be mapped onto the general map.Finally,we present a design approach to wheat breeding by using known QTL information and computer simulation.Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype,trait correlations in simulated progeny populations,and genetic gain of selected progenies.It is possible to simultaneously improve yield and grain quality by suitable parental selection,progeny population size,and progeny selection scheme.Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment,increasing predictability and efficiency in wheat breeding.
文摘Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.
文摘Adventitious rooting(AR)is critical to the propagation,breeding,and genetic engineering of trees.The capacity for plants to undergo this process is highly heritable and of a polygenic nature;however,the basis of its genetic variation is largely uncharacterized.To identify genetic regulators of AR,we performed a genome-wide association study(GWAS)using 1148 genotypes of Populus trichocarpa.GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale;to help overcome this limitation,we developed a computer vision system to measure an array of traits related to adventitious root development in poplar,including temporal measures of lateral and basal root length and area.GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power.These analyses yielded a total of 277 unique associations,suggesting that genes that control rooting include regulators of hormone signaling,cell division and structure,reactive oxygen species signaling,and other processes with known roles in root development.Numerous genes with uncharacterized functions and/or cryptic roles were also identified.These candidates provide targets for functional analysis,including physiological and epistatic analyses,to better characterize the complex polygenic regulation of AR.
文摘Most variants associated with complex traits and diseases identified by genome-wide association studies(GWAS)map to noncoding regions of the genome with unknown effects.Using ancestrally diverse,biobank-scale GWAS data,massively parallel CRISPR screens,and single-cell transcriptomic and proteomic sequencing,we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci.Using precise variant insertion through base editing,we connected specific variants with gene expression changes.We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs.Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits.This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.
文摘自提出全基因组关联研究(genome-wide association study,GWAS)设想以来,在人类复杂疾病和水稻农艺性状关联研究方面,GWAS已得到广泛运用。但作为一种典型的单标记研究方法,GWAS不能检测小效应的遗传变异,而稀有变异间的联合效应往往与表型密切相关,因此,需对GWAS结果进行深入的数据挖掘。基于通路的分析方法(pathway-based analysis,PBA)就是利用基因功能、生物代谢通路等相关信息建立的对GWAS结果进行二次挖掘的方法。该方法能从GWAS结果挖掘出与性状、疾病相关联的通路及具有相同功能的基因集等数据,从而获得更多的遗传信息。现对PBA的出现、计算方法和相关软件进行简要综述,以期为人们进行通路分析提供参考。
