Common wheat(Triticum aestivum L.)is a leading cereal crop,but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and mai...Common wheat(Triticum aestivum L.)is a leading cereal crop,but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize.The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets.Meanwhile,the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals.One such productive avenue is combining metabolomics approaches with genetic designs.However,this trial is not as widespread as that for sequencing technologies,especially when the acquisition,understanding,and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized.In this review,we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes.Considerable progress has been made in delivering improved varieties,suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and,as such,this procedure could serve as an-omics-informed roadmap for executing similar improvement strategies in wheat and other species.展开更多
Global crop productivity faces a significant threat from climate change-induced drought stress(DS),which is vital for sustainable agriculture and global food security.Uncovering DS adaptation and tolerance mechanisms ...Global crop productivity faces a significant threat from climate change-induced drought stress(DS),which is vital for sustainable agriculture and global food security.Uncovering DS adaptation and tolerance mechanisms in crops is necessary to alleviate climate challenges.Innovative plant breeding demands revolutionary approaches to develop stress-smart plants.Metabolomics,a promising field in plant breeding,offers a predictive tool to identify metabolic markers associated with plant performance under DS,enabling accelerated crop improvement.Central to DS adaptation is metabolomics-driven metabolic regulation,which is critical for maintaining cell osmotic potential in crops.Recent innovations allow rapid mapping of specific metabolites to their genetic pathways,providing a valuable resource for plant scientists.Metabolomics-driven molecular breeding,integrating techniques such as mQTL and mGWAS,enhances our ability to discover key genetic elements linked to stress-responsive metabolites.This integration offers a beneficial platform for plant scientists,yielding significant insights into the complex metabolic networks underlying DS tolerance.Therefore,this review discusses(1)insights into metabolic regulation for DS adaptation,(2)the multifaceted role of metabolites in DS tolerance and nutritional/yield trait improvement,(3)the potential of single-cell metabolomics and imaging,(4)metabolomics-driven molecular breeding,and(5)the application of metabolic and genetic engineering for DS-tolerant crops.We finally propose that the metabolomics-driven approach positions drought-smart crops as key contributors to future food production,supporting the vital goal of achieving“zero hunger”.展开更多
植物代谢物是人类食物和营养物质的重要来源。代谢组学是对生物体内代谢物进行定量和定性分析,研究代谢物合成和调控机制的一门新兴学科。基于代谢组的全基因组关联分析(metabolome-based genome-wide association study,mGWAS)是将代...植物代谢物是人类食物和营养物质的重要来源。代谢组学是对生物体内代谢物进行定量和定性分析,研究代谢物合成和调控机制的一门新兴学科。基于代谢组的全基因组关联分析(metabolome-based genome-wide association study,mGWAS)是将代谢组数据作为表型,与基因型数据进行关联分析的一种方法。概述了近几年利用mGWAS技术在植物代谢调控网络研究、初生和次生代谢物的形成机制、代谢物在植物生长发育和胁迫应答中的作用,同时综述了mGWAS在代谢物相关候选基因的定位和调控营养、品质相关代谢通路的挖掘,为深入了解植物代谢物合成调控的遗传机制奠定基础。展开更多
Background Chickens provide globally important livestock products.Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding.Influenced by...Background Chickens provide globally important livestock products.Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding.Influenced by a combination of genetic and environmental factors,metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits.However,the serum metabolite profile and genetic archi-tecture of the metabolome in chickens have not been well studied.Results Here,comprehensive metabolome detection was performed using non-targeted LC–MS/MS on serum from a chicken advanced intercross line(AIL).In total,7,191 metabolites were used to construct a chicken serum metabo-lomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population.Regula-tory loci affecting metabolites were identified in a metabolome genome-wide association study(mGWAS).There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome.Many functional genes affect metabolite synthesis,metabolism,and regulation.We highlight the key roles of TDH and AASS in amino acids,and ABCB1 and CD36 in lipids.Conclusions We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a refer-ence for future chicken metabolome characterization work.Meanwhile,we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.展开更多
Potato is an important crop for ensuring global food and nutritional security.The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not full...Potato is an important crop for ensuring global food and nutritional security.The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not fully understood.In this study,we used a multi-omics approach to decipher its domestication footprint.The metabolomic remodeling of potato tubers featured a decrease in diversity and content of bitter steroidal glycoalkaloids(SGAs)and an increase in nutritional flavonoid content.Two biosynthesis genes affecting the structural divergence of SGAs and two transcription factors that regulate SGA content in potato were characterized.Two tandem MYB transcription factors were shown to modulate the phenylpropanoid flux between phenolic acids and flavonoids.Furthermore,we uncovered that selection of coding and cis-regulatory variations has substantially reshaped tuber metabolite diversity and content,respectively.Through dissection of the genetic architecture of 2046 loci for 568 metabolites,we identified 2745 epistatic interactions and 268 pleiotropic effects,providing a roadmap for metabolic manipulation in tubers.Taken together,these findings deepen our understanding of potato domestication and offer genetic strategies for developing cultivars with improved quality.展开更多
Metabolites in skeletal muscles play an important role in their growth,development,immunity and other physiological activities.However,the genetic basis of metabolites in skeletal muscle remains poorly understood.Here...Metabolites in skeletal muscles play an important role in their growth,development,immunity and other physiological activities.However,the genetic basis of metabolites in skeletal muscle remains poorly understood.Here,we identified 247 candidate divergent regions containing 905 protein-coding genes closely related to metabolic pathways,including lysine degradation and fatty acid biosynthesis.We then profiled 3,060 metabolites in 246 skeletal muscle samples from F_2 segregating population generated by mallard×Pekin duck crosses using metabolomic approaches.We identified 2,044 significant metabolome-based GWAS signals and 21 candidate genes potentially modulating metabolite contents in skeletal muscle.Among them,the levels of 2-aminoadipic acid in skeletal muscle were significantly correlated with body weight and intramuscular fat content,determined by a 939-bp CR1 LINE insertion in AADAT.We further found that the CR1 LINE insertion most possibly led to a splice mutation in AADAT,resulting in the downregulation of the lysine degradation pathway in skeletal muscle.Moreover,intramuscular fat content and fatty acids biosynthesis pathway was significantly increased in individuals with CR1 LINE insertion.This study enhances our understanding of the genetic basis of skeletal muscle metabolic traits and promotes the efficient utilization of metabolite traits in the genetic improvement of animals.展开更多
Tocopherols(vitamin E)play essential roles in human health because of their antioxidant activity,and plantderived oils are the richest sources of tocopherols in the human diet.Although soybean(Glycinemax)is one of the...Tocopherols(vitamin E)play essential roles in human health because of their antioxidant activity,and plantderived oils are the richest sources of tocopherols in the human diet.Although soybean(Glycinemax)is one of themain sources of plant-derived oil and tocopherol in the world,the relationship between tocopherol and oil in soybean seeds remains unclear.Here,we focus on dissecting tocopherol metabolism with the longterm goal of increasing a-tocopherol content and soybean oil quality.We first collected tocopherol and fatty acid profiles in a soybean population(>800 soybean accessions)and found that tocopherol content increased during soybean domestication.A strong positive correlation between tocopherol and oil content was also detected.Five tocopherol pathway–related lociwere identified using a metabolite genome-wide association study strategy.Genetic variations in three tocopherol pathway genes were responsible for total tocopherol content and composition in the soybean population through effects on enzyme activity,mainly caused by non-conserved amino acid substitution or changes in gene transcription level.Moreover,the fatty acid regulatory transcription factor GmZF351 directly activated tocopherol pathway gene expression,increasing both fatty acid and tocopherol contents in soybean seeds.Our study reveals the functional differentiation of tocopherol pathway genes in soybean populations and provides a framework for development of new soybean varieties with high a-tocopherol content and oil quality in seeds.展开更多
As well as being a popular vegetable crop worldwide,waxy corn represents an important amylopectin source,but little is known about its breeding history and flavor characteristics.In this study,through comparative-omic...As well as being a popular vegetable crop worldwide,waxy corn represents an important amylopectin source,but little is known about its breeding history and flavor characteristics.In this study,through comparative-omic analyses between 318 diverse waxy corn and 507 representative field corn inbred lines we revealed that many metabolic pathways and genes exhibited selection characteristics during the breeding history of waxy corn,contributing to the divergence between waxy and field corn.We showed that waxy corn is not only altered in its glutinous property but also its sweetness,aroma,and palatability are all significantly affected.A substantial proportion(43%)of flavor-related metabolites have pleiotropic effects,affecting both flavor and yield characteristics,and 27%of these metabolites are related to antagonistic outcomes on yield and flavor.Furthermore,through multiple concrete examples,we demonstrated how yield and quality are coordinately or antagonistically regulated at the genetic level.In particular,some sweet molecules,such as DIMBOA and raffinose,which do not participate in the starch biosynthesis pathway,were identified as potential targets for breeding a new type of“sweet-waxy”corn.Taken together,our findings shed light on the historical selection of waxy corn and demonstrate the genetic and metabolic basis of waxy corn flavor,collectively providing valuable resources and knowledge for future crop breeding for improved nutritional quality.展开更多
Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of majo...Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution.The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication.Interestingly,fruit malic acid and citric acid showed the opposite selection trends during the improvement.We identified a novel gene cluster(CGC1,cucurbitacin gene cluster on chromosome 1)containing both regulatory and structural genes involved in cucurbitacin biosynthesis,which revealed a cascade of transcriptional regulation operating mechanisms.In the CGC1,an allele caused a single nucleotide change in Cl ERF1 binding sites(GCC-box)in the promoter of Cl Bh1,which resulted in reduced expression of Cl Bh1 and inhibition of cucurbitacin synthesis in cultivated watermelon.Functional analysis revealed that a rare insertion of 244 amino acids,which arose in C.amarus and became fixed in sweet watermelon,in Cl OSC(oxidosqualene cyclase)was critical for the negative selection of cucurbitacins during watermelon evolution.This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.展开更多
DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,a...DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,and metabolic profiling on a population comprising wild tomatoes,landraces,and cultivars.A total of 8,375 differentially methylated regions(DMRs)were identified,with methylation levels progressively decreasing from domestication to improvement.We found that over 20%of DMRs overlapped with selective sweeps.Moreover,more than 80%of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms(SNPs),and DMRs had strong linkages with adjacent SNPs.We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs.We detected 971 and 711 large-effect loci via SNP and DMR markers,respectively.Combined with multi-omics,we identified 13 candidate genes and updated the polyphenol biosynthetic pathway.Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity.Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.展开更多
Understanding the intricate relationship between genetics,metabolites,and microbiota is paramount for unraveling the complexities that define buffalo milk composition.In this study,we employed a multi-omics approach t...Understanding the intricate relationship between genetics,metabolites,and microbiota is paramount for unraveling the complexities that define buffalo milk composition.In this study,we employed a multi-omics approach to dissect the genetic and metabolic determinants of buffalo milk traits.Metabolomics analysis of 100 buffalo milk samples revealed a rich profile of 446 metabolites,with a particular emphasis on those associated with amino acid biosynthesis.Metabolite-based Genome-Wide Association Studies(mGWAS)uncovered 13 significant genetic variants,with a pronounced focus on L-Proline.Notably,single nucleotide polymorphisms(SNPs)within the ATG16L1 gene implicated its role in proline production.Concurrently,an in-depth exploration of milk microbiota dynamics highlighted marked differences between buffaloes with high and low proline groups.High proline abundance correlated with increased microbial diversity,dominated by Firmicutes and Proteobacteria.Distinct genera,such as Acinetobacter and Corynebacterium,characterized low and high proline groups,respectively.Functional changes in milk microbiota,especially in amino acid biosynthesis pathways,underscored proline’s pivotal role in shaping microbial functions.Correlations between milk microbiota abundance and proline levels emphasized the intricate relationship between host physiology and microbial composition.These findings not only advance our understanding of the genetic basis of metabolic traits in buffalo milk but also present potential biomarkers for targeted breeding strategies.This integrated approach provides a nuanced perspective on milk composition,offering implications for dairy quality and nutritional enhancement.展开更多
基金supported by the National Natural Science Foundation of China(91935304,31770328,and 32001541)the Huazhong Agricultural University Scientific&Technological Self-Innovation Foundation(2017RC006)+1 种基金the China Postdoctoral Science Foundation(2018M642866 and 2021T140246)the Hubei Provincial Natural Science Foundation(2020CFB149).
文摘Common wheat(Triticum aestivum L.)is a leading cereal crop,but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize.The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets.Meanwhile,the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals.One such productive avenue is combining metabolomics approaches with genetic designs.However,this trial is not as widespread as that for sequencing technologies,especially when the acquisition,understanding,and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized.In this review,we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes.Considerable progress has been made in delivering improved varieties,suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and,as such,this procedure could serve as an-omics-informed roadmap for executing similar improvement strategies in wheat and other species.
基金supported by Chinese National Key R&DProject for Synthetic Biology(2018YFA0902500)National Natural Science Foundation of China(32273118)+3 种基金The Guangdong Key R&D Project(2022B1111070005)Shenzhen Special Fund for Sustainable Development(KCXFZ20211020164013021)Shenzhen University 2035 Program for Excellent Research(2022B010)supported by a startup grant from the Food Futures Institute of Murdoch University,Australia.
文摘Global crop productivity faces a significant threat from climate change-induced drought stress(DS),which is vital for sustainable agriculture and global food security.Uncovering DS adaptation and tolerance mechanisms in crops is necessary to alleviate climate challenges.Innovative plant breeding demands revolutionary approaches to develop stress-smart plants.Metabolomics,a promising field in plant breeding,offers a predictive tool to identify metabolic markers associated with plant performance under DS,enabling accelerated crop improvement.Central to DS adaptation is metabolomics-driven metabolic regulation,which is critical for maintaining cell osmotic potential in crops.Recent innovations allow rapid mapping of specific metabolites to their genetic pathways,providing a valuable resource for plant scientists.Metabolomics-driven molecular breeding,integrating techniques such as mQTL and mGWAS,enhances our ability to discover key genetic elements linked to stress-responsive metabolites.This integration offers a beneficial platform for plant scientists,yielding significant insights into the complex metabolic networks underlying DS tolerance.Therefore,this review discusses(1)insights into metabolic regulation for DS adaptation,(2)the multifaceted role of metabolites in DS tolerance and nutritional/yield trait improvement,(3)the potential of single-cell metabolomics and imaging,(4)metabolomics-driven molecular breeding,and(5)the application of metabolic and genetic engineering for DS-tolerant crops.We finally propose that the metabolomics-driven approach positions drought-smart crops as key contributors to future food production,supporting the vital goal of achieving“zero hunger”.
文摘植物代谢物是人类食物和营养物质的重要来源。代谢组学是对生物体内代谢物进行定量和定性分析,研究代谢物合成和调控机制的一门新兴学科。基于代谢组的全基因组关联分析(metabolome-based genome-wide association study,mGWAS)是将代谢组数据作为表型,与基因型数据进行关联分析的一种方法。概述了近几年利用mGWAS技术在植物代谢调控网络研究、初生和次生代谢物的形成机制、代谢物在植物生长发育和胁迫应答中的作用,同时综述了mGWAS在代谢物相关候选基因的定位和调控营养、品质相关代谢通路的挖掘,为深入了解植物代谢物合成调控的遗传机制奠定基础。
基金supported by National Natural Science Foundation of China(No.32172719,U2002205,32272862).
文摘Background Chickens provide globally important livestock products.Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding.Influenced by a combination of genetic and environmental factors,metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits.However,the serum metabolite profile and genetic archi-tecture of the metabolome in chickens have not been well studied.Results Here,comprehensive metabolome detection was performed using non-targeted LC–MS/MS on serum from a chicken advanced intercross line(AIL).In total,7,191 metabolites were used to construct a chicken serum metabo-lomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population.Regula-tory loci affecting metabolites were identified in a metabolome genome-wide association study(mGWAS).There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome.Many functional genes affect metabolite synthesis,metabolism,and regulation.We highlight the key roles of TDH and AASS in amino acids,and ABCB1 and CD36 in lipids.Conclusions We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a refer-ence for future chicken metabolome characterization work.Meanwhile,we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding.
基金funded by the National Key Research and Development Program of China(2022YFF1002500)the National Natural Science Foundation of China(32272725 and 32488302)+1 种基金the Guangdong Major Project of Basic and Applied Basic Research(2021B0301030004)the China Postdoctoral Science Foundation(2022M723463).
文摘Potato is an important crop for ensuring global food and nutritional security.The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not fully understood.In this study,we used a multi-omics approach to decipher its domestication footprint.The metabolomic remodeling of potato tubers featured a decrease in diversity and content of bitter steroidal glycoalkaloids(SGAs)and an increase in nutritional flavonoid content.Two biosynthesis genes affecting the structural divergence of SGAs and two transcription factors that regulate SGA content in potato were characterized.Two tandem MYB transcription factors were shown to modulate the phenylpropanoid flux between phenolic acids and flavonoids.Furthermore,we uncovered that selection of coding and cis-regulatory variations has substantially reshaped tuber metabolite diversity and content,respectively.Through dissection of the genetic architecture of 2046 loci for 568 metabolites,we identified 2745 epistatic interactions and 268 pleiotropic effects,providing a roadmap for metabolic manipulation in tubers.Taken together,these findings deepen our understanding of potato domestication and offer genetic strategies for developing cultivars with improved quality.
基金supported by grants from the National Science Fund for Distinguished Young Scholars (32325047)the Innovation Program of Chinese Academy of Agricultural Sciences (CAAS-CS-202201)+1 种基金the China Agriculture Research System of MOF and MARA (CARS-42-05)the National Key R&D Program of China (2023YFD1300300,2022YFF1000100)。
文摘Metabolites in skeletal muscles play an important role in their growth,development,immunity and other physiological activities.However,the genetic basis of metabolites in skeletal muscle remains poorly understood.Here,we identified 247 candidate divergent regions containing 905 protein-coding genes closely related to metabolic pathways,including lysine degradation and fatty acid biosynthesis.We then profiled 3,060 metabolites in 246 skeletal muscle samples from F_2 segregating population generated by mallard×Pekin duck crosses using metabolomic approaches.We identified 2,044 significant metabolome-based GWAS signals and 21 candidate genes potentially modulating metabolite contents in skeletal muscle.Among them,the levels of 2-aminoadipic acid in skeletal muscle were significantly correlated with body weight and intramuscular fat content,determined by a 939-bp CR1 LINE insertion in AADAT.We further found that the CR1 LINE insertion most possibly led to a splice mutation in AADAT,resulting in the downregulation of the lysine degradation pathway in skeletal muscle.Moreover,intramuscular fat content and fatty acids biosynthesis pathway was significantly increased in individuals with CR1 LINE insertion.This study enhances our understanding of the genetic basis of skeletal muscle metabolic traits and promotes the efficient utilization of metabolite traits in the genetic improvement of animals.
基金financially supported by the National Key Research and Development Program of China(2021YFF1001200 and 2018YFA0900600)the Chinese Academy of Science(XDA24040202)the State Key Laboratory of Plant Genomics of China(grant no.SKLPG2016A-13).
文摘Tocopherols(vitamin E)play essential roles in human health because of their antioxidant activity,and plantderived oils are the richest sources of tocopherols in the human diet.Although soybean(Glycinemax)is one of themain sources of plant-derived oil and tocopherol in the world,the relationship between tocopherol and oil in soybean seeds remains unclear.Here,we focus on dissecting tocopherol metabolism with the longterm goal of increasing a-tocopherol content and soybean oil quality.We first collected tocopherol and fatty acid profiles in a soybean population(>800 soybean accessions)and found that tocopherol content increased during soybean domestication.A strong positive correlation between tocopherol and oil content was also detected.Five tocopherol pathway–related lociwere identified using a metabolite genome-wide association study strategy.Genetic variations in three tocopherol pathway genes were responsible for total tocopherol content and composition in the soybean population through effects on enzyme activity,mainly caused by non-conserved amino acid substitution or changes in gene transcription level.Moreover,the fatty acid regulatory transcription factor GmZF351 directly activated tocopherol pathway gene expression,increasing both fatty acid and tocopherol contents in soybean seeds.Our study reveals the functional differentiation of tocopherol pathway genes in soybean populations and provides a framework for development of new soybean varieties with high a-tocopherol content and oil quality in seeds.
基金Biological Breeding-National Science and Technology Major Project(2023ZD04073)National Natural Science Foundation of China(32321005,32101773,31971964)+1 种基金China Postdoctoral Science Foundation(2022M711280)Science and Technology Program of Guangdong Province(2023A0505090005).
文摘As well as being a popular vegetable crop worldwide,waxy corn represents an important amylopectin source,but little is known about its breeding history and flavor characteristics.In this study,through comparative-omic analyses between 318 diverse waxy corn and 507 representative field corn inbred lines we revealed that many metabolic pathways and genes exhibited selection characteristics during the breeding history of waxy corn,contributing to the divergence between waxy and field corn.We showed that waxy corn is not only altered in its glutinous property but also its sweetness,aroma,and palatability are all significantly affected.A substantial proportion(43%)of flavor-related metabolites have pleiotropic effects,affecting both flavor and yield characteristics,and 27%of these metabolites are related to antagonistic outcomes on yield and flavor.Furthermore,through multiple concrete examples,we demonstrated how yield and quality are coordinately or antagonistically regulated at the genetic level.In particular,some sweet molecules,such as DIMBOA and raffinose,which do not participate in the starch biosynthesis pathway,were identified as potential targets for breeding a new type of“sweet-waxy”corn.Taken together,our findings shed light on the historical selection of waxy corn and demonstrate the genetic and metabolic basis of waxy corn flavor,collectively providing valuable resources and knowledge for future crop breeding for improved nutritional quality.
基金supported by the Agricultural Science and Technology Innovation Program(CAAS-ASTIP-ZFRI-07)the National Key R&D Program of China(2018YFD0100704)+5 种基金the China Agriculture Research System(CARS-25-03)the National Natural Science Fund for Distinguished Young Scholars(31625021)the National Natural Science Foundation of China(31672178,31471893)the Hainan University Startup Fund KYQD(ZR)1866Project supported by Hainan Yazhou Bay Seed Laboratory(B21Y10901)the Natural Science Foundation of Hainan Province(322RC574)。
文摘Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution.The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication.Interestingly,fruit malic acid and citric acid showed the opposite selection trends during the improvement.We identified a novel gene cluster(CGC1,cucurbitacin gene cluster on chromosome 1)containing both regulatory and structural genes involved in cucurbitacin biosynthesis,which revealed a cascade of transcriptional regulation operating mechanisms.In the CGC1,an allele caused a single nucleotide change in Cl ERF1 binding sites(GCC-box)in the promoter of Cl Bh1,which resulted in reduced expression of Cl Bh1 and inhibition of cucurbitacin synthesis in cultivated watermelon.Functional analysis revealed that a rare insertion of 244 amino acids,which arose in C.amarus and became fixed in sweet watermelon,in Cl OSC(oxidosqualene cyclase)was critical for the negative selection of cucurbitacins during watermelon evolution.This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.
基金supported by the Hainan Province Science and Technology Special Fund(ZDYF2022XDNY144)the National Natural Science Foundation of China(32100212)+3 种基金the National Key Research and Development Program of China(2021YFA0909600,2022YFF1001900)the Young Elite Scientists Sponsorship Program by CAST(2019QNRC001)the Hainan Provincial Academician Innovation Platform Project(HD-YSZX-202003,HD-YSZX-202004)the Hainan University Startup Fund(KYQD(ZR)1916,KYQD(ZR)21025)。
文摘DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,and metabolic profiling on a population comprising wild tomatoes,landraces,and cultivars.A total of 8,375 differentially methylated regions(DMRs)were identified,with methylation levels progressively decreasing from domestication to improvement.We found that over 20%of DMRs overlapped with selective sweeps.Moreover,more than 80%of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms(SNPs),and DMRs had strong linkages with adjacent SNPs.We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs.We detected 971 and 711 large-effect loci via SNP and DMR markers,respectively.Combined with multi-omics,we identified 13 candidate genes and updated the polyphenol biosynthetic pathway.Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity.Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.
基金financially supported by the National Natural Science Foundation of China(32160779)the Natural Science Foundation of Guangxi Zhuang Autonomous Region(2020GXNSFDA297032).
文摘Understanding the intricate relationship between genetics,metabolites,and microbiota is paramount for unraveling the complexities that define buffalo milk composition.In this study,we employed a multi-omics approach to dissect the genetic and metabolic determinants of buffalo milk traits.Metabolomics analysis of 100 buffalo milk samples revealed a rich profile of 446 metabolites,with a particular emphasis on those associated with amino acid biosynthesis.Metabolite-based Genome-Wide Association Studies(mGWAS)uncovered 13 significant genetic variants,with a pronounced focus on L-Proline.Notably,single nucleotide polymorphisms(SNPs)within the ATG16L1 gene implicated its role in proline production.Concurrently,an in-depth exploration of milk microbiota dynamics highlighted marked differences between buffaloes with high and low proline groups.High proline abundance correlated with increased microbial diversity,dominated by Firmicutes and Proteobacteria.Distinct genera,such as Acinetobacter and Corynebacterium,characterized low and high proline groups,respectively.Functional changes in milk microbiota,especially in amino acid biosynthesis pathways,underscored proline’s pivotal role in shaping microbial functions.Correlations between milk microbiota abundance and proline levels emphasized the intricate relationship between host physiology and microbial composition.These findings not only advance our understanding of the genetic basis of metabolic traits in buffalo milk but also present potential biomarkers for targeted breeding strategies.This integrated approach provides a nuanced perspective on milk composition,offering implications for dairy quality and nutritional enhancement.
