Background Lactate is a classical byproduct of glucose metabolism,and the main lactate production pathway depends on glycolysis.Lactate stabilized HIF1αby inhibiting PHD activity,leading to hypoxic stress response an...Background Lactate is a classical byproduct of glucose metabolism,and the main lactate production pathway depends on glycolysis.Lactate stabilized HIF1αby inhibiting PHD activity,leading to hypoxic stress response and exacerbating glycolysis in multiple tissues.However,the redox induction mechanism of lactate in mammary gland has not been understood yet.Herein,we describe a lactate-responsive HIF1α/circadian control mechanism in oxidative stress in the mammary glands of dairy cows.Results The in vivo study showed that dairy cows with high lactate concentrations are associated with reduced milk yield and more ROS accumulation in mammary gland.Western blot results in MAC-T cells showed positive correlation between lactate concentrations,expression of HIF1αand oxidative stress indicators,but not circadian core components.To test how lactate-mediated HIF1αdysfunction leads to cell protection process,we investigated altered expression of circadian core related genes following HIF1αstabilization.We found that stabilized HIF1αby lactate inhibited stimulated expression of circadian core components due to the similarity of HRE and E-box transcription elements.Furthermore,we found that lactate treatment strengthened the binding of HIF1αwith BMAL1,HMOX1 and FOXO3 in MAC-T cells.Moreover,HIF1αknockdown altered expression of circadian rhythm related genes and reduced oxidative stress state.Conclusion In summary,our study highlights the central role of competitive transcriptional element occupancy in lactate-mediated oxidative stress of mammary gland,which is caused by HIF1αstabilization and circadian rhythm dysfunction.Our findings introduce a novel nutritional strategy with potential applications in dairy farming for optimizing milk production and maintaining mammary gland health.展开更多
Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure precisely.Examples include time-dependent traits such as reproductive statu...Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure precisely.Examples include time-dependent traits such as reproductive status,or lifespan.Incomplete measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound respectively.Here we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example trait.Methods We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×Jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New Zealand.We used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three visits.Three methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation approach.Results Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was reduced.For sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to 0.95.The estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring increased.Conclusion Our results indicate that using some methods,phenotypes derived from one observation per offspring for a time-dependent trait such as AGEP4 may provide comparable sire rankings to three observations per offspring.This has implications for the design of large-scale phenotyping initiatives where animal breeders aim to estimate variance parameters and estimated breeding values(EBVs)for phenotypes that are challenging to measure or prohibitively expensive.展开更多
Strongly acidic soils （pH 〈 5.0） are detrimental to tea （Camellia sinensis） production and quality. Little information exists on the ability of surface amendments to ameliorate subsoil acidity in the tea garden s...Strongly acidic soils （pH 〈 5.0） are detrimental to tea （Camellia sinensis） production and quality. Little information exists on the ability of surface amendments to ameliorate subsoil acidity in the tea garden soils. A 120-d glasshouse column leaching experiment was conducted using commonly available soil ameliorants. Alkaline slag （AS） and organic residues, pig manure （PM） and rapeseed cake （RC） differing in ash alkalinity and C/N ratio were incorporated alone and in combination into the surface （0-15 cm） of soil columns （10 cm internal diameter x 50 cm long） packed with soil from the acidic soil layer （15-30 cm） of an Ultisol （initial pH -- 4.4）. During the 120-d experiment, the soil columns were watered （about 127 mm over 9 applications） according to the long-term mean annual rainfall （1 143 mm） and the leachates were collected and analyzed. At the end of the experiment, soil columns were partitioned into various depths and the chemical properties of soil were measured. The PM with a higher C/N ratio increased subsoil pH, whereas the RC with a lower C/N ratio decreased subsoil pH. However, combined amendments had a greater ability to reduce subsoil acidity than either of the amendments alone. The increases in pH of the subsoil were mainly ascribed to decreased base cation concentrations and the decomposition of organic anions present in dissolved organic carbon （DOC） and immobilization of nitrate that had been leached down from the amended layer. A significant （P 〈 0.05） correlation between alkalinity production （reduced exchangeable acidity - N-cycle alkalinity） and alkalinity balance （net alkalinity production - N-cycle alkalinity） was observed at the end of the experiment. Additionally, combined amendments significantly increased （P ~ 0.05） subsoil cation concentrations and decreased subsoil A1 saturation （P 〈 0.05）. Combined applications of AS with organic amendments to surface soils are effective in reducing subsoil acidity in high-rainfall areas. Further investigations under field conditions and over longer timeframes are needed to fully understand their practical effectiveness in ameliorating acidity of deeper soil layers under naturally occurring leaching regimes.展开更多
Electrical conductivity(EC)of soil-water extracts is commonly used to assess soil salinity.However,its conversion to the EC of saturated soil paste extracts(ECe),the standard measure of soil salinity,is currently requ...Electrical conductivity(EC)of soil-water extracts is commonly used to assess soil salinity.However,its conversion to the EC of saturated soil paste extracts(ECe),the standard measure of soil salinity,is currently required for practical applications.Although many regression models can be used to obtain ECe from the EC of soil-water extracts,the application of a site-specific model to different sites is not straightforward due to confounding soil factors such as soil texture.This study was conducted to develop a universal regression model to estimate a conversion factor(CF)for predicting EC_(e) from EC of soil-water extracts at a 1:5 ratio(EC_(1:5)),by employing a site-specific soil texture(i.e.,sand content).A regression model,CF=8.9105e^(0.0106sand)/1.2984(r^(2)=0.97,P<0.001),was developed based on the results of coastal saline soil surveys(n=173)and laboratory experiments using artificial saline soils with different textures(n=6,sand content=10%-65%)and salinity levels(n=7,salinity=1-24 dS m^(-1)).Model performance was validated using an independent dataset and demonstrated that EC_(e) prediction using the developed model is more suitable for highly saline soils than for low saline soils.The feasibility of the regression model should be tested at other sites.Other soil factors affecting EC conversion factor also need to be explored to revise and improve the model through further studies.展开更多
Background:Cotton seed fibres are long single-celled epidermal trichomes that first appear on the surface of the ovule at anthesis and then elongate rapidly over a period of 15-25 days until a secondary cell wall(SCW)...Background:Cotton seed fibres are long single-celled epidermal trichomes that first appear on the surface of the ovule at anthesis and then elongate rapidly over a period of 15-25 days until a secondary cell wall(SCW)begins to develop through a rapid increase in the deposition of microfibrillar cellulose between the plasma membrane and the primary cell wall that eventually terminates elongation.Quantitative measurements of the different polysaccharide components in both wall types over time and how they influence fibre quality can direct studies involved in enhanc-ing fibre properties for yarn quality through cell wall manipulation or molecular breeding.Results:A detailed chemical analysis of cell wall composition by differential solvent fractionation was used to identify the range of polysaccharides present in mature cotton fibres and used to validate a simpler total cell wall monosaccharide linkage analysis protocol for wall compositional analysis.Analysis of fibres from 5 days post-anthesis through maturity for three cultivated species,Gossypium hirsutum,G.barbadense,and G.arboreum,showed the dynamic nature of cell wall polysaccharide composition through fibre development and that it progressed differently for each species.Plants grown in the glasshouse during either autumn to winter or spring to summer and within each species had fibre qualities and temporal aspects of cell wall development that were different for each season.Notably,the timing of the deposition of the SCW was delayed in winter grown plants and appeared to influence key fibre qual-ity properties.Conclusions:These results suggest that the temporal aspects of cell wall polysaccharide biogenesis during fibre development influence final fibre quality,and this timing is determined by both genetic and environmental factors.The onset of SCW synthesis appears to be a critical factor coinciding with termination of fibre elongation and specify-ing the duration of wall thickening that then affects fibre length and other wall-associated quality parameters that ultimately determine yarn quality.展开更多
Cultivated Triticeae members,including wheat,barley,and rye,are at the center of attention of plant biologists due to their significant contribution to global food security.The completion of the first reference genome...Cultivated Triticeae members,including wheat,barley,and rye,are at the center of attention of plant biologists due to their significant contribution to global food security.The completion of the first reference genome sequence of bread wheat(IWGSC,2018)was a major leap forward for the wheat scientific community.展开更多
Sheep(Ovis aries)represent one of the most important livestock species for global animal protein and wool production.However,little is known about the genetic and biological basis of ovine phenotypes,particularly thos...Sheep(Ovis aries)represent one of the most important livestock species for global animal protein and wool production.However,little is known about the genetic and biological basis of ovine phenotypes,particularly those with high economic value and environmental impact.Here,by integrat-ing 1413 RNA sequencing(RNA-seq)samples from 51 distinct tissues across 14 developmental time points,representing early-prenatal,late-prenatal,neonatal,lamb,juvenile,adult,and elderly stages,we constructed a high-resolution Developmental Gene Expression Atlas(dGEA)in sheep.We ob-served dynamic patterns of gene expression and regulatory networks across tissues and developmental stages.Leveraging this resource to interpret genetic associations for 48 monogenic and 12 complex traits in sheep,we found that genes upregulated at prenatal developmental stages played more important roles in shaping these phenotypes than those upregulated at postnatal stages.For instance,genetic associations of crimp number,mean staple length(MSL),and individual birthweight were significantly enriched in the prenatal rather than postnatal skin and immune tissues.By comprehensively integrating genome-wide association study(GWAS)fine-mapping results with the sheep dGEA,we identified several candidate genes for complex traits in sheep,such as SOX9 for MSL,GNRHR for litter size at birth,and PRKDC for live weight.These results provide novel insights into the developmental and molecular architecture of ovine phenotypes.The dGEA(https://sheepdgea.njau.edu.cn/)will serve as an invalu-able resource for sheep developmental biology,genetics,genomics,and selective breeding.展开更多
Bactrocera tryoni and Bactrocera neohumeralis are morphologically similar sibling pest fruit fly species that possess different biological attributes,geographic distributions,and host ranges.The need to differentiate ...Bactrocera tryoni and Bactrocera neohumeralis are morphologically similar sibling pest fruit fly species that possess different biological attributes,geographic distributions,and host ranges.The need to differentiate between the two species is critical for accurate pest status assessment,management,biosecurity,and maintenance of reference colonies.While morphologically similar,adults may be separated based on subtle characters;however,some characters exhibit intraspecific variability,creating overlap between the two species.Additionally,there is currently no single molecular marker or rapid diagnostic assay that can reliably distinguish between B.neohumeralis and B.tryoni;therefore,ambiguous samples remain undiagnosed.Here we report the first molecular marker that can consistently distinguish between B.tryoni and B.neohumeralis.Our diagnostic region consists of two adjacent single nucleotide polymorphisms(SNPs)within the pangolin(pan)gene region.We confirmed the genotypes of each species are consistent across their distributional range,then developed a tetra-primer amplification refractory mutation system(ARMS)PCR assay for rapid diagnosis of the species.The assay utilizes four primers in multiplex,with two outer universal primers,and two internal primers:one designed to target two adjacent SNPs(AA)present in B.tryoni and the other targeting adjacent SNPs present in B.neohumeralis(GG).The assay accurately discriminates between the two species,but their SNP genotypes are shared with other nontarget tephritid fruit fly species.Therefore,this assay is most suited to adult diagnostics where species confirmation is necessary in determining ambiguous surveillance trap catches;maintaining pure colony lines;and in Sterile Insect Technique management responses.展开更多
Carbon dioxide （CO2） is the main anthropogenic gas which has drastically increased since the industrial revolution, and current concentrations are projected to double by the end of this century. As a consequence, el...Carbon dioxide （CO2） is the main anthropogenic gas which has drastically increased since the industrial revolution, and current concentrations are projected to double by the end of this century. As a consequence, elevated CO2 is expected to alter the earths＇ climate, increase global temperatures and change weather patterns. This is likely to have both direct and indirect impacts on plants, insect pests, plant pathogens and their distribution, and is therefore problematic for the security of future food production. This review summarizes the latest findings and highlights current knowledge gaps regarding the influence of climate change on insect, plant and pathogen interactions with an emphasis on agriculture and food production. Direct effects of climate change, including increased CO2 concentration, temperature, patterns of rainfall and severe weather events that impact insects （namely vectors of plant pathogens） are discussed. Elevated CO2 and temperature, together with plant pathogen infection, can considerably change plant biochemistry and therefore plant defense responses. This can have substantial consequences on insect fecun- dity, feeding rates, survival, population size, and dispersal. Generally, changes in host plant quality due to elevated CO2 （e.g., carbon to nitrogen ratios in C3 plants） negatively affect insect pests. However, compensatory feeding, increased population size and distribution have also been reported for some agricultural insect pests. This underlines the importance of additional research on more targeted, individual insect-plant scenarios at specific locations to fully understand the impact of a changing climate on insect-plant-pathogen interactions.展开更多
Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes.More than 3000 wheat cultivars have be...Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes.More than 3000 wheat cultivars have been registered,released,and documented since 1949 in China.In this study,a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced.A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94x for each cultivar,and more than 60.92 million SNPs and 2.54 million InDels were captured,based on the Chinese Spring RefSeq genome v1.0.Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes,with distinct genomic regions and phenotypes tar-geted by different breeders across the decades.There are very clear instances illustrating how introduced Italian and otherforeign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars.Importantly,the resequencing data also highlighted significant asymmetric breeding selec-tion among the three sub-genomes:this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes.Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding.Conserved and extended sharing of linkage disequilibrium(LD)blocks was highlighted among pedigree-related cultivars,in which fewer haplotype differences were detected.Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value.Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars,we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation(pyramiding)of bene-ficial haplotypes.Collectively,our study demonstrates the influence of "founder genotypes" on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dy-namic when applied in the context of modern genomics-informed breeding.展开更多
scCloudMine is a cloud-based application for visualization,comparison,and exploration of single-cell transcriptome data.It does not require an on-site,high-power computing server,installation,or associated expertise a...scCloudMine is a cloud-based application for visualization,comparison,and exploration of single-cell transcriptome data.It does not require an on-site,high-power computing server,installation,or associated expertise and expense.Users upload their own or publicly available scRNA-seq datasets after preprocessing for visualization using a web browser.The data can be viewed in two color modes—Cluster,representing cell identity,and Values,showing levels of expression—and data can be queried using keywords or gene identification number(s).Using the app to compare studies,we determined that some genes frequently used as cell-type markers are in fact study specific.The apparent cell-specific expression of PHO1;H3 differed between GFP-tagging and scRNA-seq studies.Some phosphate transporter genes were induced by protoplasting,but they retained cell specificity,suggesting that cell-specific responses to stress(i.e.,protoplasting)can occur.Examination of the cell specificity of hormone response genes revealed that 132 hormone-responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells,in contrast to previous reports.It also appears that JAZ repressors have cell-type-specific functions.These features identified using scCloudMine highlight the need for resources to enable biological researchers to compare their datasets of interest under a variety of parameters.scCloudMine enables researchers to form new hypotheses and perform comparative studies and allows for the easy re-use of data from this emerging technology by a wide variety of users who may not have access or funding for high-performance on-site computing and support.展开更多
Good culturing methods play an important role in the study of insect behavior and its application to pest management. Here, we describe and validate a new method for rearing the parasitoid wasp, Diachasmirnorpha kraus...Good culturing methods play an important role in the study of insect behavior and its application to pest management. Here, we describe and validate a new method for rearing the parasitoid wasp, Diachasmirnorpha kraussii, which attacks some of the world＇s worst fruit fly pests and is an internationally used biological control agent. Our method differs from standard culturing approaches by presenting adult wasps with host- infested artificial media within a ＂culturing bag,＂ which mimics a natural （fruit） oviposition substrate. In laboratory trials using wild collected D. kraussii, the culturing bag method was compared to the use of host-infested nectarines, and a commonly used laboratory method of presenting host-infested artificial media within Petri dishes. The culturing bag method proved to be a significant improvement on both methods, combining the advantages of high host survival in artificial media with parasitism levels that were the equivalent to those recorded using host-infested fruits. In our field study, culturing bags infested with the Queensland fruit fly, Bactrocera tryoni, and hung in a mixed peach and nectarine orchard proved to be effective ＂artificial fruits＂ attracting wild D. kraussii for oviposition. Significantly more adult wasps were reared from the culturing bags compared to field collected fruits. This was shown to be due to higher fruit fly larval density in the bags, as similar percentage parasitism rates were found between the culturing bags and ripe fruits. We discuss how this cheap, time-efficient method could be applied to collecting and monitoring wild D. kraussii populations in orchards, and assist in maintaining genetic variability in parasitoid laboratory cultures.展开更多
Secondary cell walls(SCWs)in stem cells provide mechanical strength and structural support for growth.SCW thickening varies under different light conditions.Our previous study revealed that blue light enhances SCW thi...Secondary cell walls(SCWs)in stem cells provide mechanical strength and structural support for growth.SCW thickening varies under different light conditions.Our previous study revealed that blue light enhances SCW thickening through the redundant function of MYC2 and MYC4 directed by CRYPTOCHROME1(CRY1)signaling in fiber cells of the Arabidopsis inflorescence stem.In this study,we find that the Arabidopsis PHYTOCHROME B mutant phyB displays thinner SCWs in stem fibers,but thicker SCWs are deposited in the PHYTOCHROME INTERACTING FACTOR(PIF)quadruple mutant pif1pif3pif4pif5(pifq).The shaded light condition with a low ratio of red to far-red light inhibits stem SCW thickening.PIF4 interacts with MYC2 and MYC4 to affect their localization in nuclei,and this interaction results in inhibition of the MYCs’transactivation activity on the NST1 promoter.Genetic evidence shows that regulation of SCW thickening by PIFs is dependent on MYC2/MYC4 function.Together,the results of this study reveal a PHYB-PIF4-MYC2/MYC4 module that inhibits SCW thickening in fiber cells of the Arabidopsis stem.展开更多
The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy fo...The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.展开更多
hole-grain cereals,including wheat,barley,oat,rye,corn,rice,millet,and triticale,are a rich source of calories,essential vitamins,minerals,and phytochemicals that both nourish and protect humans and animals from disea...hole-grain cereals,including wheat,barley,oat,rye,corn,rice,millet,and triticale,are a rich source of calories,essential vitamins,minerals,and phytochemicals that both nourish and protect humans and animals from diseases such as heart attack and cancer[1].However,susceptibility to foliar diseases caused by necrotrophic or biotrophic fungal pathogens continues to reduce yield potential or lead to total crop failure and famine in developing nations[2].Historically,foliar diseases of cereals have been controlled using either fungicide treatment[3]or plant breeding[4].展开更多
基金supported by National Nature Science Foundation of China(32102552 and 32172741).
文摘Background Lactate is a classical byproduct of glucose metabolism,and the main lactate production pathway depends on glycolysis.Lactate stabilized HIF1αby inhibiting PHD activity,leading to hypoxic stress response and exacerbating glycolysis in multiple tissues.However,the redox induction mechanism of lactate in mammary gland has not been understood yet.Herein,we describe a lactate-responsive HIF1α/circadian control mechanism in oxidative stress in the mammary glands of dairy cows.Results The in vivo study showed that dairy cows with high lactate concentrations are associated with reduced milk yield and more ROS accumulation in mammary gland.Western blot results in MAC-T cells showed positive correlation between lactate concentrations,expression of HIF1αand oxidative stress indicators,but not circadian core components.To test how lactate-mediated HIF1αdysfunction leads to cell protection process,we investigated altered expression of circadian core related genes following HIF1αstabilization.We found that stabilized HIF1αby lactate inhibited stimulated expression of circadian core components due to the similarity of HRE and E-box transcription elements.Furthermore,we found that lactate treatment strengthened the binding of HIF1αwith BMAL1,HMOX1 and FOXO3 in MAC-T cells.Moreover,HIF1αknockdown altered expression of circadian rhythm related genes and reduced oxidative stress state.Conclusion In summary,our study highlights the central role of competitive transcriptional element occupancy in lactate-mediated oxidative stress of mammary gland,which is caused by HIF1αstabilization and circadian rhythm dysfunction.Our findings introduce a novel nutritional strategy with potential applications in dairy farming for optimizing milk production and maintaining mammary gland health.
基金funded by New Zealand dairy farmers through Dairy NZ Inc. and by the New Zealand Ministry of Business,Innovation and Employment (DRCX1302)support was kindly received from LIC and CRV
文摘Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure precisely.Examples include time-dependent traits such as reproductive status,or lifespan.Incomplete measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound respectively.Here we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example trait.Methods We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×Jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New Zealand.We used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three visits.Three methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation approach.Results Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was reduced.For sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to 0.95.The estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring increased.Conclusion Our results indicate that using some methods,phenotypes derived from one observation per offspring for a time-dependent trait such as AGEP4 may provide comparable sire rankings to three observations per offspring.This has implications for the design of large-scale phenotyping initiatives where animal breeders aim to estimate variance parameters and estimated breeding values(EBVs)for phenotypes that are challenging to measure or prohibitively expensive.
基金This study was supported by the National Natural Science Foundation of China （No. 41401336）, the Na- tural Science Foundation of Jiangsu Province, China （No. BK20130105）, the State Key Laboratory of Soil and Sustainable Agriculture, Chinese Academy of Sci-ence （No. Y412201452）, and the Environmental Pro- tection Public Benefit Research Foundation of China （No. 201309036）. We thank the three anonymous refe- rees for their helpful comments.
文摘Strongly acidic soils （pH 〈 5.0） are detrimental to tea （Camellia sinensis） production and quality. Little information exists on the ability of surface amendments to ameliorate subsoil acidity in the tea garden soils. A 120-d glasshouse column leaching experiment was conducted using commonly available soil ameliorants. Alkaline slag （AS） and organic residues, pig manure （PM） and rapeseed cake （RC） differing in ash alkalinity and C/N ratio were incorporated alone and in combination into the surface （0-15 cm） of soil columns （10 cm internal diameter x 50 cm long） packed with soil from the acidic soil layer （15-30 cm） of an Ultisol （initial pH -- 4.4）. During the 120-d experiment, the soil columns were watered （about 127 mm over 9 applications） according to the long-term mean annual rainfall （1 143 mm） and the leachates were collected and analyzed. At the end of the experiment, soil columns were partitioned into various depths and the chemical properties of soil were measured. The PM with a higher C/N ratio increased subsoil pH, whereas the RC with a lower C/N ratio decreased subsoil pH. However, combined amendments had a greater ability to reduce subsoil acidity than either of the amendments alone. The increases in pH of the subsoil were mainly ascribed to decreased base cation concentrations and the decomposition of organic anions present in dissolved organic carbon （DOC） and immobilization of nitrate that had been leached down from the amended layer. A significant （P 〈 0.05） correlation between alkalinity production （reduced exchangeable acidity - N-cycle alkalinity） and alkalinity balance （net alkalinity production - N-cycle alkalinity） was observed at the end of the experiment. Additionally, combined amendments significantly increased （P ~ 0.05） subsoil cation concentrations and decreased subsoil A1 saturation （P 〈 0.05）. Combined applications of AS with organic amendments to surface soils are effective in reducing subsoil acidity in high-rainfall areas. Further investigations under field conditions and over longer timeframes are needed to fully understand their practical effectiveness in ameliorating acidity of deeper soil layers under naturally occurring leaching regimes.
基金support of the Cooperative Research Program of Agriculture Science and Technology Development,Rural Development Administration,Republic of Korea(No.PJ0138732021)。
文摘Electrical conductivity(EC)of soil-water extracts is commonly used to assess soil salinity.However,its conversion to the EC of saturated soil paste extracts(ECe),the standard measure of soil salinity,is currently required for practical applications.Although many regression models can be used to obtain ECe from the EC of soil-water extracts,the application of a site-specific model to different sites is not straightforward due to confounding soil factors such as soil texture.This study was conducted to develop a universal regression model to estimate a conversion factor(CF)for predicting EC_(e) from EC of soil-water extracts at a 1:5 ratio(EC_(1:5)),by employing a site-specific soil texture(i.e.,sand content).A regression model,CF=8.9105e^(0.0106sand)/1.2984(r^(2)=0.97,P<0.001),was developed based on the results of coastal saline soil surveys(n=173)and laboratory experiments using artificial saline soils with different textures(n=6,sand content=10%-65%)and salinity levels(n=7,salinity=1-24 dS m^(-1)).Model performance was validated using an independent dataset and demonstrated that EC_(e) prediction using the developed model is more suitable for highly saline soils than for low saline soils.The feasibility of the regression model should be tested at other sites.Other soil factors affecting EC conversion factor also need to be explored to revise and improve the model through further studies.
基金Pettolino FA,Yulia D and Llewellyn DJ were supported by Cotton Breeding Australia and Bacic A by the ARC Centre of Excellence in Plant Cell Walls(CE1101007).The funding bodies had no role in the design of the study and collection,analysis,and interpretation of data or in writing the manuscript.
文摘Background:Cotton seed fibres are long single-celled epidermal trichomes that first appear on the surface of the ovule at anthesis and then elongate rapidly over a period of 15-25 days until a secondary cell wall(SCW)begins to develop through a rapid increase in the deposition of microfibrillar cellulose between the plasma membrane and the primary cell wall that eventually terminates elongation.Quantitative measurements of the different polysaccharide components in both wall types over time and how they influence fibre quality can direct studies involved in enhanc-ing fibre properties for yarn quality through cell wall manipulation or molecular breeding.Results:A detailed chemical analysis of cell wall composition by differential solvent fractionation was used to identify the range of polysaccharides present in mature cotton fibres and used to validate a simpler total cell wall monosaccharide linkage analysis protocol for wall compositional analysis.Analysis of fibres from 5 days post-anthesis through maturity for three cultivated species,Gossypium hirsutum,G.barbadense,and G.arboreum,showed the dynamic nature of cell wall polysaccharide composition through fibre development and that it progressed differently for each species.Plants grown in the glasshouse during either autumn to winter or spring to summer and within each species had fibre qualities and temporal aspects of cell wall development that were different for each season.Notably,the timing of the deposition of the SCW was delayed in winter grown plants and appeared to influence key fibre qual-ity properties.Conclusions:These results suggest that the temporal aspects of cell wall polysaccharide biogenesis during fibre development influence final fibre quality,and this timing is determined by both genetic and environmental factors.The onset of SCW synthesis appears to be a critical factor coinciding with termination of fibre elongation and specify-ing the duration of wall thickening that then affects fibre length and other wall-associated quality parameters that ultimately determine yarn quality.
基金the National Natural Science Foundation of China(32361143512)the State Key Laboratory of Crop Gene Resource and Breedingthe National Key R&D Program of China(no.2024YFF1000600).
文摘Cultivated Triticeae members,including wheat,barley,and rye,are at the center of attention of plant biologists due to their significant contribution to global food security.The completion of the first reference genome sequence of bread wheat(IWGSC,2018)was a major leap forward for the wheat scientific community.
基金supported by grants from the National Key R&D Program of China(Grant No.2021YFF1000702)the National Natural Science Foundation of China(Grant No.32402755)+7 种基金the Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(Grant No.CXGC2023F10)the Project of Seed Industry Revitalization in Jiangsu Province,China(Grant No.JBGS[2021]113)the 2023 Excellent Postdoctoral Program in Jiangsu Province,China(Grant No.2023ZB584)the Australian Research Council's Discovery Projects(Grant Nos.DP200100499 and DP160101056)the Department of Agriculture,Fisheries and Forestry of the Commonwealth of Australia(Grant No.DAFF 1193857-31)the Flling the Research Gap(2013-2016)‘Host Control of Methane Emissions from Sheep,Australia(Grant No.DP160101056)the Institute Strategic Programme grants(Grant Nos.BBS/E/D/10002070 and BB/X010945/1)awarded to the Roslin Institute by the Biotechnology and Biological Sciences Research Council,UKthe high-performance computing platform of Bioinformatics Center,Nanjing Agricultural University,China.We would like to express our deep gratitude to the late Professor Shengli Zhang for his invaluable support and guidance.
文摘Sheep(Ovis aries)represent one of the most important livestock species for global animal protein and wool production.However,little is known about the genetic and biological basis of ovine phenotypes,particularly those with high economic value and environmental impact.Here,by integrat-ing 1413 RNA sequencing(RNA-seq)samples from 51 distinct tissues across 14 developmental time points,representing early-prenatal,late-prenatal,neonatal,lamb,juvenile,adult,and elderly stages,we constructed a high-resolution Developmental Gene Expression Atlas(dGEA)in sheep.We ob-served dynamic patterns of gene expression and regulatory networks across tissues and developmental stages.Leveraging this resource to interpret genetic associations for 48 monogenic and 12 complex traits in sheep,we found that genes upregulated at prenatal developmental stages played more important roles in shaping these phenotypes than those upregulated at postnatal stages.For instance,genetic associations of crimp number,mean staple length(MSL),and individual birthweight were significantly enriched in the prenatal rather than postnatal skin and immune tissues.By comprehensively integrating genome-wide association study(GWAS)fine-mapping results with the sheep dGEA,we identified several candidate genes for complex traits in sheep,such as SOX9 for MSL,GNRHR for litter size at birth,and PRKDC for live weight.These results provide novel insights into the developmental and molecular architecture of ovine phenotypes.The dGEA(https://sheepdgea.njau.edu.cn/)will serve as an invalu-able resource for sheep developmental biology,genetics,genomics,and selective breeding.
基金We thank the Tertiary Education Commission of New Zealand for funding to H.J.P.Stuart Gilchrist for enabling GBS alignments to the prepublication B.tryoni reference genome.This study was conducted as part of the"Phenology,demography,and distribution of Australia's fruit flies"project,funded through the Strengthening Australia's Fruit Fly System Research ProgramFunding for the program is provided by the Australian Government,with contributions matched from state and territory governments.
文摘Bactrocera tryoni and Bactrocera neohumeralis are morphologically similar sibling pest fruit fly species that possess different biological attributes,geographic distributions,and host ranges.The need to differentiate between the two species is critical for accurate pest status assessment,management,biosecurity,and maintenance of reference colonies.While morphologically similar,adults may be separated based on subtle characters;however,some characters exhibit intraspecific variability,creating overlap between the two species.Additionally,there is currently no single molecular marker or rapid diagnostic assay that can reliably distinguish between B.neohumeralis and B.tryoni;therefore,ambiguous samples remain undiagnosed.Here we report the first molecular marker that can consistently distinguish between B.tryoni and B.neohumeralis.Our diagnostic region consists of two adjacent single nucleotide polymorphisms(SNPs)within the pangolin(pan)gene region.We confirmed the genotypes of each species are consistent across their distributional range,then developed a tetra-primer amplification refractory mutation system(ARMS)PCR assay for rapid diagnosis of the species.The assay utilizes four primers in multiplex,with two outer universal primers,and two internal primers:one designed to target two adjacent SNPs(AA)present in B.tryoni and the other targeting adjacent SNPs present in B.neohumeralis(GG).The assay accurately discriminates between the two species,but their SNP genotypes are shared with other nontarget tephritid fruit fly species.Therefore,this assay is most suited to adult diagnostics where species confirmation is necessary in determining ambiguous surveillance trap catches;maintaining pure colony lines;and in Sterile Insect Technique management responses.
文摘Carbon dioxide （CO2） is the main anthropogenic gas which has drastically increased since the industrial revolution, and current concentrations are projected to double by the end of this century. As a consequence, elevated CO2 is expected to alter the earths＇ climate, increase global temperatures and change weather patterns. This is likely to have both direct and indirect impacts on plants, insect pests, plant pathogens and their distribution, and is therefore problematic for the security of future food production. This review summarizes the latest findings and highlights current knowledge gaps regarding the influence of climate change on insect, plant and pathogen interactions with an emphasis on agriculture and food production. Direct effects of climate change, including increased CO2 concentration, temperature, patterns of rainfall and severe weather events that impact insects （namely vectors of plant pathogens） are discussed. Elevated CO2 and temperature, together with plant pathogen infection, can considerably change plant biochemistry and therefore plant defense responses. This can have substantial consequences on insect fecun- dity, feeding rates, survival, population size, and dispersal. Generally, changes in host plant quality due to elevated CO2 （e.g., carbon to nitrogen ratios in C3 plants） negatively affect insect pests. However, compensatory feeding, increased population size and distribution have also been reported for some agricultural insect pests. This underlines the importance of additional research on more targeted, individual insect-plant scenarios at specific locations to fully understand the impact of a changing climate on insect-plant-pathogen interactions.
基金the Key Research and Development Program of China(2016YFD0100302)the Central Public-interest Scientific Institution Basal Research Fund(Y2017PT39)the CAAS-Innovation Team Program(CAAS-XTCX2018020).
文摘Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes.More than 3000 wheat cultivars have been registered,released,and documented since 1949 in China.In this study,a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced.A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94x for each cultivar,and more than 60.92 million SNPs and 2.54 million InDels were captured,based on the Chinese Spring RefSeq genome v1.0.Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes,with distinct genomic regions and phenotypes tar-geted by different breeders across the decades.There are very clear instances illustrating how introduced Italian and otherforeign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars.Importantly,the resequencing data also highlighted significant asymmetric breeding selec-tion among the three sub-genomes:this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes.Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding.Conserved and extended sharing of linkage disequilibrium(LD)blocks was highlighted among pedigree-related cultivars,in which fewer haplotype differences were detected.Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value.Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars,we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation(pyramiding)of bene-ficial haplotypes.Collectively,our study demonstrates the influence of "founder genotypes" on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dy-namic when applied in the context of modern genomics-informed breeding.
基金supported by grants from the Australian Research Council Discovery to J.W.(DP210103258)the Australian Research Council Industrial Transformation Research Hub in Medicinal Agriculture(IT180100006)to J.W.and M.G.L.
文摘scCloudMine is a cloud-based application for visualization,comparison,and exploration of single-cell transcriptome data.It does not require an on-site,high-power computing server,installation,or associated expertise and expense.Users upload their own or publicly available scRNA-seq datasets after preprocessing for visualization using a web browser.The data can be viewed in two color modes—Cluster,representing cell identity,and Values,showing levels of expression—and data can be queried using keywords or gene identification number(s).Using the app to compare studies,we determined that some genes frequently used as cell-type markers are in fact study specific.The apparent cell-specific expression of PHO1;H3 differed between GFP-tagging and scRNA-seq studies.Some phosphate transporter genes were induced by protoplasting,but they retained cell specificity,suggesting that cell-specific responses to stress(i.e.,protoplasting)can occur.Examination of the cell specificity of hormone response genes revealed that 132 hormone-responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells,in contrast to previous reports.It also appears that JAZ repressors have cell-type-specific functions.These features identified using scCloudMine highlight the need for resources to enable biological researchers to compare their datasets of interest under a variety of parameters.scCloudMine enables researchers to form new hypotheses and perform comparative studies and allows for the easy re-use of data from this emerging technology by a wide variety of users who may not have access or funding for high-performance on-site computing and support.
文摘Good culturing methods play an important role in the study of insect behavior and its application to pest management. Here, we describe and validate a new method for rearing the parasitoid wasp, Diachasmirnorpha kraussii, which attacks some of the world＇s worst fruit fly pests and is an internationally used biological control agent. Our method differs from standard culturing approaches by presenting adult wasps with host- infested artificial media within a ＂culturing bag,＂ which mimics a natural （fruit） oviposition substrate. In laboratory trials using wild collected D. kraussii, the culturing bag method was compared to the use of host-infested nectarines, and a commonly used laboratory method of presenting host-infested artificial media within Petri dishes. The culturing bag method proved to be a significant improvement on both methods, combining the advantages of high host survival in artificial media with parasitism levels that were the equivalent to those recorded using host-infested fruits. In our field study, culturing bags infested with the Queensland fruit fly, Bactrocera tryoni, and hung in a mixed peach and nectarine orchard proved to be effective ＂artificial fruits＂ attracting wild D. kraussii for oviposition. Significantly more adult wasps were reared from the culturing bags compared to field collected fruits. This was shown to be due to higher fruit fly larval density in the bags, as similar percentage parasitism rates were found between the culturing bags and ripe fruits. We discuss how this cheap, time-efficient method could be applied to collecting and monitoring wild D. kraussii populations in orchards, and assist in maintaining genetic variability in parasitoid laboratory cultures.
基金supported by the National Natural Science Foundation of China(grant no.32130072,31630014)the Chinese Academy of Sciences(grant no.XDB27020104).
文摘Secondary cell walls(SCWs)in stem cells provide mechanical strength and structural support for growth.SCW thickening varies under different light conditions.Our previous study revealed that blue light enhances SCW thickening through the redundant function of MYC2 and MYC4 directed by CRYPTOCHROME1(CRY1)signaling in fiber cells of the Arabidopsis inflorescence stem.In this study,we find that the Arabidopsis PHYTOCHROME B mutant phyB displays thinner SCWs in stem fibers,but thicker SCWs are deposited in the PHYTOCHROME INTERACTING FACTOR(PIF)quadruple mutant pif1pif3pif4pif5(pifq).The shaded light condition with a low ratio of red to far-red light inhibits stem SCW thickening.PIF4 interacts with MYC2 and MYC4 to affect their localization in nuclei,and this interaction results in inhibition of the MYCs’transactivation activity on the NST1 promoter.Genetic evidence shows that regulation of SCW thickening by PIFs is dependent on MYC2/MYC4 function.Together,the results of this study reveal a PHYB-PIF4-MYC2/MYC4 module that inhibits SCW thickening in fiber cells of the Arabidopsis stem.
基金supported by funding from the National Key Research and Development Program of China(2022YFF1003402)the China Natural Science Foundation(31371622)the CAAS Innovation Program.
文摘The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.
基金the Alexander von Humboldt Foundation for supporting P.M.D.during his fellow-ship programthe host institution Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)Gatersleben+1 种基金the German Federal Ministry of Education and Research(BMBF)[grant numbers FKZ 031A053(DPPN)and FKZ 031B0184(GeneBank 2.0)]the Deutsche Forschungsgemeinschaft(DFG,German Research Foundation)(grant HE 9114/1-1)for supporting D.K.D.and S.L.
文摘hole-grain cereals,including wheat,barley,oat,rye,corn,rice,millet,and triticale,are a rich source of calories,essential vitamins,minerals,and phytochemicals that both nourish and protect humans and animals from diseases such as heart attack and cancer[1].However,susceptibility to foliar diseases caused by necrotrophic or biotrophic fungal pathogens continues to reduce yield potential or lead to total crop failure and famine in developing nations[2].Historically,foliar diseases of cereals have been controlled using either fungicide treatment[3]or plant breeding[4].
