Increasing the oil content is a key objective in peanut breeding programs.Accurate identification of quantitative trait loci(QTLs)with linked markers for oil content can facilitate marker-assisted selection for high-o...Increasing the oil content is a key objective in peanut breeding programs.Accurate identification of quantitative trait loci(QTLs)with linked markers for oil content can facilitate marker-assisted selection for high-oil breeding.In this study,a highdensity bin map was constructed by resequencing a recombinant inbred line(RIL)population(ZH16×J11)consisting of 295 lines.The bin map contained 4,212 loci and had a total length of 1,162.3 c M.Ten QTLs for oil content were identified in six linkage groups.Notably,two of these QTLs,qOCB03.1 and qOCB06.1,were consistently detected in a minimum of three environments and explained up to 13.62%of the phenotypic variation.They have not been reported in previous studies and thus are novel QTLs.The combination of favorable alleles from qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%.Two insertions/deletions(In Dels)markers linked to qOCB03.1 and qOCB06.1 were developed,and their association with oil content was validated in another RIL population(ZH10×ICG12625)with diverse phenotypes.In addition,the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb interval on chromosome B03 and a 1.51 Mb interval on chromosome B06,respectively.The annotation of genomic variants,analysis of transcriptome sequencing,and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs.The candidate genes identified in this study can enable the map-based cloning of key genes controlling oil content in peanut.Furthermore,these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for greater oil content in peanut.展开更多
Tea,originating in China over 3,000 years ago,has transitioned from a medicinal herb to a widely consumed beverage.Despite considerable research focusing on tea plants in southwestern China,little attention has been p...Tea,originating in China over 3,000 years ago,has transitioned from a medicinal herb to a widely consumed beverage.Despite considerable research focusing on tea plants in southwestern China,little attention has been paid to those on Hainan Island.The notable resemblance between Hainan tea and C.sinensis var.assamica,alongside the unique geographical and climatic conditions of Hainan Island,has presented significant challenges for taxonomic and genetic investigations concerning Hainan tea.Our study bridged this gap by collecting 500 samples from Hainan Province and employing whole-genome resequencing to examine interspecific differences between Hainan tea and cultivated varieties.The findings confirmed the distinct taxonomic position of Hainan tea within Camellia sinensis,providing valuable insights for resource conservation and molecular breeding.Furthermore,our methodology offers a framework for investigating the origin,domestication,and genetic diversity of other species native to Hainan Island.展开更多
Limosilactobacillus reuteri is a resident probiotic in the intestines of animals with strong environmental adaptability.In the current study,to elucidate the adaptation strategies of L.reuteri to the intestine of mice...Limosilactobacillus reuteri is a resident probiotic in the intestines of animals with strong environmental adaptability.In the current study,to elucidate the adaptation strategies of L.reuteri to the intestine of mice supplemented with three dietary components(oil,peptide and cellulose),whole genome resequencing and determination of intracellular metabolites were carried out.The resequencing results showed that L.reuteri TO60(LR-TO)from the intestines of mice supplemented with high docosahexaenoic acid(DHA)tuna oil,or fermented Benincasa hispida culture(L.reuteri FB151,abbreviated as LR-FB)had relatively consistent single nucleotide polymorphisms(SNPs)and insertions and deletions(InDels),and those of L.reuteri from the intestines of mice supplemented with Rhopilema esculentum polypeptides(L.reuteri RE225,abbreviated as LR-RE)were quite different from them.The KEGG functional annotation of resequencing and the intracellular metabolites suggested that in all of the L.reuteri adapted to the intestinal environment mainly by regulating carbohydrate metabolism and membrane transport metabolic pathways.However,there were still some differences in their genes and metabolites,which may be related to the changes in the intestinal environment caused by three different types of dietary interventions.Our study analyzed the adaptation mechanism of L.reuteri to different isolated sources at the genetic level and metabolic level,which is helpful to clarify the adaptation strategies of probiotics to the intestinal environment,and provide supplementary information for the use of dietary nutritional supplements.展开更多
Lactiplantibacillus plantarum is known to be widely accepted as starter culture with antibacterial and biogenic amines(BAs)degrading abilities,but its salt tolerance is a crucial factor limiting its effectiveness as a...Lactiplantibacillus plantarum is known to be widely accepted as starter culture with antibacterial and biogenic amines(BAs)degrading abilities,but its salt tolerance is a crucial factor limiting its effectiveness as a starter for fermentation.In the present study,the adaptive laboratory evolution(ALE)approach was used to enhance the salt tolerance of the parental strain Lpb.plantarum His6-WS.Sixteen salt-tolerant strains were obtained by selection on MRS medium containing 10%NaCl.Compared to the parental strain,the evolved strain Lpb.plantarum H11-ES exhibited excellent genetic stability,a shorter lag period and a higher maximum population density in the MRS containing 8%NaCl.Additionally,the evolved strain Lpb.plantarum H11-ES improved its BAs-degrading ability in high-concentration NaCl environments.Characterization of cell morphology showed that the evolved strain Lpb.plantarum H11-ES had significantly strengthened the integrity and length of cell membrane and cell wall compared to its parent.Furthermore,whole genome resequencing revealed that the mutations in the poly(glycerol-phosphate)alpha-glucosyltransferase(TagE)and the ATP-binding cassette(ABC)transporters likely contributed to the evolution of salt-tolerant by altering cell morphology and participating in membrane transport.Collectively,this study successfully isolated Lpb.plantarum strain with enhanced salt tolerance and aminedegrading abilities,while also highlighting the importance of the cell wall in increasing the salt tolerance.This provides a theoretical basis for future regulation and selection of salt-tolerant LAB.展开更多
Dear Editor,Recently,Liang et al.(2024)conducted comprehensive genome resequencing and metabolomic analyses of 299 representative accessions from extant citrus species,offering an extensive overview of genetic diversi...Dear Editor,Recently,Liang et al.(2024)conducted comprehensive genome resequencing and metabolomic analyses of 299 representative accessions from extant citrus species,offering an extensive overview of genetic diversity and metabolic profiles across citrus populations.Their study included a correlation analysis that assessed the relationship between metabolite content and bioactivities,resulting in the selection of the top 100 annotated metabolites exhibiting the highest correlation coefficients(Pearson’s r)across various chemical assays,cell lines,and CYP450 enzymes(Liang et al.,2024).展开更多
Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance.The purpose of this study was to comprehensively analyze the genetic b...Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance.The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments,clarify the impact of environmental factors on genome diversity,and lay the foundation for breeding goat breeds to adapt to climate change.A total of 240 dairy goats were subjected to genome resequencing,and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated.By integrating multiple approaches such as phylogenetic analysis,population structure analysis,gene flow and population history exploration,selection signal analysis,and genome-environment association analysis,an in-depth investigation was carried out.Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds.Through signal analysis(θπ,FST,XP-CLR),we identified numerous candidate genes associated with cold adaptation in dairy goats(STRIP1,ALX3,HTR4,NTRK2,MRPL11,PELI3,DPP3,BBS1)and cashmere goats(MED12L,MARC2,MARC1,DSG3,C6H4orf22,CHD7,MYPN,KIAA0825,MITF).Genomeenvironment association(GEA)analysis confirmed the link between these genes and environmental factors.Moreover,a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds.This study contributes to understanding the genetic basis of cold adaptation,providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles,thereby ensuring sustainable animal husbandry.展开更多
基金supported by the National Key Research and Development Program of China(2022YFD1200400)the National Natural Science Foundation of China(32161143006 and 31971903)+4 种基金the National Peanut Industry Technology System Construction,China(CARS13)the National Crop Germplasm Resources Center,China(NCGRC-2022-036)the National Program for Crop Germplasm Protection of China(19210163)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2021-OCRI)the Guangdong Provincial Key Research and Development Program-Modern Seed Industry,China(2022B0202060004)。
文摘Increasing the oil content is a key objective in peanut breeding programs.Accurate identification of quantitative trait loci(QTLs)with linked markers for oil content can facilitate marker-assisted selection for high-oil breeding.In this study,a highdensity bin map was constructed by resequencing a recombinant inbred line(RIL)population(ZH16×J11)consisting of 295 lines.The bin map contained 4,212 loci and had a total length of 1,162.3 c M.Ten QTLs for oil content were identified in six linkage groups.Notably,two of these QTLs,qOCB03.1 and qOCB06.1,were consistently detected in a minimum of three environments and explained up to 13.62%of the phenotypic variation.They have not been reported in previous studies and thus are novel QTLs.The combination of favorable alleles from qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%.Two insertions/deletions(In Dels)markers linked to qOCB03.1 and qOCB06.1 were developed,and their association with oil content was validated in another RIL population(ZH10×ICG12625)with diverse phenotypes.In addition,the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb interval on chromosome B03 and a 1.51 Mb interval on chromosome B06,respectively.The annotation of genomic variants,analysis of transcriptome sequencing,and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs.The candidate genes identified in this study can enable the map-based cloning of key genes controlling oil content in peanut.Furthermore,these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for greater oil content in peanut.
基金supported by the Hainan Academy of Agricultural Sciences Research Project(HAAS2022KJCX03)Research and Demonstration on Key Technologies of Germplasm Resource Bank Construction and Resource Innovation Utilization of Wuzhishan Big Leaf Tea(ZDYF2024XDNY245)Monitoring and Analysis of Key Quality Components of Hainan Big Leaf Black Tea and Development and Demonstration of New Standardized Processing Technology(WZSKTPXM202202).
文摘Tea,originating in China over 3,000 years ago,has transitioned from a medicinal herb to a widely consumed beverage.Despite considerable research focusing on tea plants in southwestern China,little attention has been paid to those on Hainan Island.The notable resemblance between Hainan tea and C.sinensis var.assamica,alongside the unique geographical and climatic conditions of Hainan Island,has presented significant challenges for taxonomic and genetic investigations concerning Hainan tea.Our study bridged this gap by collecting 500 samples from Hainan Province and employing whole-genome resequencing to examine interspecific differences between Hainan tea and cultivated varieties.The findings confirmed the distinct taxonomic position of Hainan tea within Camellia sinensis,providing valuable insights for resource conservation and molecular breeding.Furthermore,our methodology offers a framework for investigating the origin,domestication,and genetic diversity of other species native to Hainan Island.
基金sponsored by the Natural Science Foundation of Zhejiang Province(LY19C010003)the Natural Science Foundation of Zhejiang Province(LQ22D060002)+1 种基金the Fund of State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products(ZS20190105)the K.C.Wong Magna Fund of Ningbo University.
文摘Limosilactobacillus reuteri is a resident probiotic in the intestines of animals with strong environmental adaptability.In the current study,to elucidate the adaptation strategies of L.reuteri to the intestine of mice supplemented with three dietary components(oil,peptide and cellulose),whole genome resequencing and determination of intracellular metabolites were carried out.The resequencing results showed that L.reuteri TO60(LR-TO)from the intestines of mice supplemented with high docosahexaenoic acid(DHA)tuna oil,or fermented Benincasa hispida culture(L.reuteri FB151,abbreviated as LR-FB)had relatively consistent single nucleotide polymorphisms(SNPs)and insertions and deletions(InDels),and those of L.reuteri from the intestines of mice supplemented with Rhopilema esculentum polypeptides(L.reuteri RE225,abbreviated as LR-RE)were quite different from them.The KEGG functional annotation of resequencing and the intracellular metabolites suggested that in all of the L.reuteri adapted to the intestinal environment mainly by regulating carbohydrate metabolism and membrane transport metabolic pathways.However,there were still some differences in their genes and metabolites,which may be related to the changes in the intestinal environment caused by three different types of dietary interventions.Our study analyzed the adaptation mechanism of L.reuteri to different isolated sources at the genetic level and metabolic level,which is helpful to clarify the adaptation strategies of probiotics to the intestinal environment,and provide supplementary information for the use of dietary nutritional supplements.
基金supported by the National Key Research and Development Project of China(2022YFD2100905)the Key Scientific Research Project of Universities in Henan Province(25A550009).
文摘Lactiplantibacillus plantarum is known to be widely accepted as starter culture with antibacterial and biogenic amines(BAs)degrading abilities,but its salt tolerance is a crucial factor limiting its effectiveness as a starter for fermentation.In the present study,the adaptive laboratory evolution(ALE)approach was used to enhance the salt tolerance of the parental strain Lpb.plantarum His6-WS.Sixteen salt-tolerant strains were obtained by selection on MRS medium containing 10%NaCl.Compared to the parental strain,the evolved strain Lpb.plantarum H11-ES exhibited excellent genetic stability,a shorter lag period and a higher maximum population density in the MRS containing 8%NaCl.Additionally,the evolved strain Lpb.plantarum H11-ES improved its BAs-degrading ability in high-concentration NaCl environments.Characterization of cell morphology showed that the evolved strain Lpb.plantarum H11-ES had significantly strengthened the integrity and length of cell membrane and cell wall compared to its parent.Furthermore,whole genome resequencing revealed that the mutations in the poly(glycerol-phosphate)alpha-glucosyltransferase(TagE)and the ATP-binding cassette(ABC)transporters likely contributed to the evolution of salt-tolerant by altering cell morphology and participating in membrane transport.Collectively,this study successfully isolated Lpb.plantarum strain with enhanced salt tolerance and aminedegrading abilities,while also highlighting the importance of the cell wall in increasing the salt tolerance.This provides a theoretical basis for future regulation and selection of salt-tolerant LAB.
文摘Dear Editor,Recently,Liang et al.(2024)conducted comprehensive genome resequencing and metabolomic analyses of 299 representative accessions from extant citrus species,offering an extensive overview of genetic diversity and metabolic profiles across citrus populations.Their study included a correlation analysis that assessed the relationship between metabolite content and bioactivities,resulting in the selection of the top 100 annotated metabolites exhibiting the highest correlation coefficients(Pearson’s r)across various chemical assays,cell lines,and CYP450 enzymes(Liang et al.,2024).
基金supported by the Genome Sequence Archiv in National Genomics Data Center,China National Center for Bioinformation/Beijing Institute of Genomics(CRA017705)supported the discovers could been obtained from the corresponding authors.
文摘Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance.The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments,clarify the impact of environmental factors on genome diversity,and lay the foundation for breeding goat breeds to adapt to climate change.A total of 240 dairy goats were subjected to genome resequencing,and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated.By integrating multiple approaches such as phylogenetic analysis,population structure analysis,gene flow and population history exploration,selection signal analysis,and genome-environment association analysis,an in-depth investigation was carried out.Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds.Through signal analysis(θπ,FST,XP-CLR),we identified numerous candidate genes associated with cold adaptation in dairy goats(STRIP1,ALX3,HTR4,NTRK2,MRPL11,PELI3,DPP3,BBS1)and cashmere goats(MED12L,MARC2,MARC1,DSG3,C6H4orf22,CHD7,MYPN,KIAA0825,MITF).Genomeenvironment association(GEA)analysis confirmed the link between these genes and environmental factors.Moreover,a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds.This study contributes to understanding the genetic basis of cold adaptation,providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles,thereby ensuring sustainable animal husbandry.
