The giant freshwater prawn Macrobrachium rosenbergii distributed from tropical to subtropical regions,is a warm-water species,and its survival temperature is 14-35°C,which greatly limits its culture cycle and cul...The giant freshwater prawn Macrobrachium rosenbergii distributed from tropical to subtropical regions,is a warm-water species,and its survival temperature is 14-35°C,which greatly limits its culture cycle and culture area in China.Therefore,it is urgent to cultivate a new high quality,high yield variety with improved cold-resistance,but the genetic parameters for cold-resistance traits are unknown in M.rosenbergii.In this study,the cold-resistance of adult M.rosenbergii populations was tested using the indoor artificial cooling method.Individuals were selected from 139 families of Shufeng G3 generation and cultured for 200 days.A linear mixed model was constructed by ASReml-R to evaluate the genetic parameters of the cold-resistance trait(cooling degree hours,CDH)and growth traits(body weight,BW,and body length,BL)based on the restricted maximum likelihood(REML)method.The results show that the heritability of CDH was low(0.12±0.05),while the growth traits(BW and BL)had low to moderate heritability,with 0.20±0.06 for BW and 0.06±0.04 for BL.The phenotypic and genetic correlation between BW and BL was significantly positive,but significantly negative phenotypic and genetic correlations were detected between CDH and BW and between CDH and BL.Furthermore,the analysis of the differences between cold-resistance and phenotypic traits showed that the female reproductive status,exoskeleton hardness and claw number of adult prawns had a great influence on the cold-resistance of M.rosenbergii(P<0.05),indicating that adults with claws and hard exoskeletons are preferred as parents in subsequent breeding selection.The present results can be attributed to the selection and breeding of a new cold-resistant variety of M.rosenbergii.展开更多
The maintenance of sand-fixing vegetation is important for the stability of artificial sand-fixing systems in which seed dispersal plays a key role.Based on field wind tunnel experiments using 11 common plant species ...The maintenance of sand-fixing vegetation is important for the stability of artificial sand-fixing systems in which seed dispersal plays a key role.Based on field wind tunnel experiments using 11 common plant species on the southeastern edge of the Tengger Desert,China,we studied the secondary seed dispersal in the fixed and semi-fixed sand dunes as well as in the mobile dunes in order to understand the limitations of vegetation regeneration and the maintenance of its stability.Our results indicated that there were significant variations among the selected 11 plant species in the threshold of wind speed(TWS).The TWS of Caragana korshinskii was the highest among the 11 plant species,whereas that of Echinops gmelinii was the lowest.Seed morphological traits and underlying surface could generally explain the TWS.During the secondary seed dispersal processes,the proportions of seeds that did not disperse(no dispersal)and only dispersed over short distance(short-distance dispersal within the wind tunnel test section)were significantly higher than those of seeds that were buried(including lost seeds)and dispersed over long distance(long-distance dispersal beyond the wind tunnel test section).Compared with other habitats,the mobile dunes were the most difficult places for secondary seed dispersal.Buried seeds were the easiest to be found in the semi-fixed sand dunes,whereas fixed sand dunes were the best sites for seeds that dispersed over long distance.The results of linear mixed models showed that after controlling the dispersal distance,smaller and rounder seeds dispersed farther.Shape index and wind speed were the two significant influencing factors on the burial of seeds.The explanatory power of wind speed,underlying surface,and seed morphological traits on the seeds that did not disperse and dispersed over short distance was far greater than that on the seeds that were buried and dispersed over long distance,implying that the processes and mechanisms of burial and long-distance dispersal are more complex.In summary,most seeds in the study area either did not move,were buried,or dispersed over short distance,promoting local vegetation regeneration.展开更多
Many different factors,such as species traits,socio-economic factors,geographical and environmental factors,can lead to specimen collection preference.This study aims to determine whether grassland specimen collection...Many different factors,such as species traits,socio-economic factors,geographical and environmental factors,can lead to specimen collection preference.This study aims to determine whether grassland specimen collection in China is preferred by species traits(i.e.,plant height,flowering and fruiting period),environmental range(i.e.,the temperature and precipitation range)and geographical range(i.e.,distribution range and altitudinal range).Ordinary least squares models and phylogenetic generalized linear mixed models were used to analyze the relationships between specimen number and the explanatory variables.Random Forest models were then used to find the most parsimonious multivariate model.The results showed that interannual variation in specimen number between 1900 and 2020 was considerable.Specimen number of these species in southeast China was notably lower than that in northwest China.Environmental range and geographical range of species had significant positive correlations with specimen number.In addition,there were relatively weak but significant associations between specimen number and species trait(i.e.,plant height and flowering and fruiting period).Random Forest models indicated that distribution range was the most important variable,followed by flowering and fruiting period,and altitudinal range.These findings suggest that future floristic surveys should pay more attention to species with small geographical range,narrow environmental range,short plant height,and short flowering and fruiting period.The correction of specimen collection preference will also make the results of species distribution model,species evolution and other works based on specimen data more accurate.展开更多
Cereal is an essential source of calories and protein for the global population.Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and c...Cereal is an essential source of calories and protein for the global population.Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and categorised storage for enterprises,future trading prices,and policy planning.The use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality traits.Many studies have also proposed models and methods for predicting such traits based on multiplatform remote sensing data.In this paper,the key quality traits that are of interest to producers and consumers are introduced.The literature related to grain quality prediction was analyzed in detail,and a review was conducted on remote sensing platforms,commonly used methods,potential gaps,and future trends in crop quality prediction.This review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.展开更多
Soil salinization is the main factor that threatens the growth and development of plants and limits the increase of yield.It is of great significance to study the key soil environmental factors affecting plant root tr...Soil salinization is the main factor that threatens the growth and development of plants and limits the increase of yield.It is of great significance to study the key soil environmental factors affecting plant root traits to reveal the adaptation strategies of plants to saline-alkaline-stressed soil environments.In this study,the root biomass,root morphological parameters and root mineral nutrient content of two alfalfa cultivars with different sensitivities to alkaline stress were analyzed with black soil as the control group and the mixed saline-alkaline soil with a ratio of 7:3 between black soil and saline-alkaline soil as the saline-alkaline treatment group.At the same time,the correlation analysis of soil salinity indexes,soil nutrient indexes and the activities of key enzymes involved in soil carbon,nitrogen and phosphorus cycles was carried out.The results showed that compared with the control group,the pH,EC,and urease(URE)of the soil surrounding the roots of two alfalfa cultivars were significantly increased,while soil total nitrogen(TN),total phosphorus(TP),organic carbon(SOC),andα-glucosidase activity(AGC)were significantly decreased under saline-alkaline stress.There was no significant difference in root biomass and root morphological parameters of saline-alkaline tolerant cultivar GN under saline-alkaline stress.The number of root tips(RT),root surface area(RS)and root volume(RV)of AG were reduced by 61.16%,44.54%,and 45.31%,respectively,compared with control group.The ratios of K^(+)/Na^(+),Ca^(2+)/Na^(+)and Mg^(2+)/Na^(+)of GN were significantly higher than those of AG(p<0.05).The root fresh weight(RFW)and dry weight(RDW),root length(RL),RV and RT of alfalfa were positively regulated by soil SOC and TN,but negatively regulated by soil pH,EC,and URE(p<0.01).Root Ca^(2+)/Na+ratio was significantly positively correlated with soil TN,TP and SOC(p<0.01).The absorption of Mg and Ca ions in roots is significantly negatively regulated by soilβ-glucosidase activity(BGC)and acid phosphatase activity(APC)(p<0.05).This study improved knowledge of the relationship between root traits and soil environmental factors and offered a theoretical framework for elucidating how plant roots adapt to saline-alkaline stressed soil environments.展开更多
Investigating the role of Big Five personality traits in relation to various health outcomes has been extensively studied. The impact of “Big Five” on physical health is here explored for older Europeans with a focu...Investigating the role of Big Five personality traits in relation to various health outcomes has been extensively studied. The impact of “Big Five” on physical health is here explored for older Europeans with a focus on examining age groups differences. The study sample included 378,500 respondents derived from the seventh data wave of Survey of Health, Aging and Retirement in Europe (SHARE). The physical health status of older Europeans was estimated by constructing an index considering the combined effect of well-established health indicators such as the number of chronic diseases, mobility limitations, limitations with basic and instrumental activities of daily living, and self-perceived health. This index was used for an overall physical health assessment, for which the higher the score for an individual, the worst health level. Then, through a dichotomization process applied to the retrieved Principal Component Analysis scores, a two-group discrimination (good or bad health status) of SHARE participants was obtained as regards their physical health condition, allowing for further con-structing logistic regression models to assess the predictive significance of “Big Five” and their protective role for physical health. Results showed that neuroti-cism was the most significant predictor of physical health for all age groups un-der consideration, while extraversion, agreeableness and openness were not found to significantly affect the self-reported physical health levels of midlife adults aged 50 up to 64. Older adults aged 65 up to 79 were more prone to open-ness, whereas the oldest old individuals aged 80 up to 105 were mainly affected by openness and conscientiousness. .展开更多
A central goal of genetics is to understand the links between genetic variation and disease.Intuitively,one might expect diseasecausing variants to cluster into key pathways that drive disease etiology.But for complex...A central goal of genetics is to understand the links between genetic variation and disease.Intuitively,one might expect diseasecausing variants to cluster into key pathways that drive disease etiology.But for complex traits,association signals tend to be spread across most of the genome-including near many genes without an obvious connection to disease.展开更多
Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye ar...Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in pigs.However,the available genetic markers for these traits are limited.To uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.We performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,respectively.Variant annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in pigs.Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle development.Overall,this study provides new candidate loci and genes for the genetic improvement of pigs.展开更多
The variation and correlation of leaf economics and vein traits are crucial for predicting plant ecological strategies under different environmental changes.However,correlations between these two suites of traits and ...The variation and correlation of leaf economics and vein traits are crucial for predicting plant ecological strategies under different environmental changes.However,correlations between these two suites of traits and abiotic factors such as soil water and nitrogen content remain ambiguous.We measured leaf economics and vein traits as well as soil water and nitrogen content for two different shade-tolerant species(Betula platyphylla and Acer mono)in four mixed broadleaved-Korean pine(Pinus koraiensis)forests along a latitudinal gradient in Northeast China.We found that leaf economics traits and vein traits were decoupled in shade-intolerant species,Betula platphylla,but significantly coupled in a shadetolerant species,A.mono.We found stronger correlations among leaf traits in the shade tolerant species than in the shade intolerant species.Furthermore,leaf economic traits were positively correlated with the soil water gradient for both species,whereas vein traits were positively correlated with soil water gradient for the shade intolerant species but negatively correlated in the shade tolerant species.Although economic traits were positively correlated with soil nitrogen gradient in shade intolerant species but not correlated in shade tolerant species,vein traits were negatively correlated with soil nitrogen gradient in shade tolerant species but not correlated in shade intolerant species.Our study provides evidence for distinct correlations between leaf economics and vein traits and local abiotic factors of species differing in light demands.We recommend that the ecological significance of shade tolerance be considered for species when evaluating ecosystem functions and predicting plant responses to environmental changes.展开更多
Maintaining open flowers is critical for successful pollination and depends on long-term water and carbon balance.Yet the relationship between how flower hydraulic traits are coordinated in different habitats is poorl...Maintaining open flowers is critical for successful pollination and depends on long-term water and carbon balance.Yet the relationship between how flower hydraulic traits are coordinated in different habitats is poorly understood.Here,we hypothesize that the coordination and trade-offs between floral hydraulics and economics traits are independent of environmental conditions.To test this hypothesis,we investigated a total of 27 flower economics and hydraulic traits in six aquatic and six terrestrial herbaceous species grown in a tropical botanical garden.We found that although there were a few significant differences,most flower hydraulics and economics traits did not differ significantly between aquatic and terrestrial herbaceous plants.Both flower mass per area and floral longevity were significantly positively correlated with the time required for drying full-hydrated flowers to 70%relative water content.Flower dry matter content was strongly and positively related to drought tolerance of the flowers as indicated by flower water potential at the turgor loss point.In addition,there was a trade-off between hydraulic efficiency and the construction cost of a flower across species.Our results show that flowers of aquatic and terrestrial plants follow the same economics spectrum pattern.These results suggest a convergent flower economics design across terrestrial and aquatic plants,providing new insights into the mechanisms by which floral organs adapt to aquatic and terrestrial habitats.展开更多
Tree peony is a unique traditional f lower in China,with large,fragrant,and colorful f lowers.However,a relatively short and concentrated f lowering period limits the applications and production of tree peony.A genome...Tree peony is a unique traditional f lower in China,with large,fragrant,and colorful f lowers.However,a relatively short and concentrated f lowering period limits the applications and production of tree peony.A genome-wide association study(GWAS)was conducted to accelerate molecular breeding for the improvement of f lowering phenology traits and ornamental phenotypes in tree peony.A diverse panel of 451 tree peony accessions was phenotyped for 23 f lowering phenology traits and 4 f loral agronomic traits over 3 years.Genotyping by sequencing(GBS)was used to obtain a large number of genome-wide single-nucleotide polymorphisms(SNPs)(107050)for the panel genotypes,and 1047 candidate genes were identified by association mapping.Eighty-two related genes were observed during at least 2 years for f lowering,and seven SNPs repeatedly identified for multiple f lowering phenology traits over multiple years were highly significantly associated with five genes known to regulate f lowering time.We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of f lower bud differentiation and f lowering time in tree peony.This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony.The results expand our understanding of f lowering time control in perennial woody plants.Identification of markers closely related to these f lowering phenology traits can be used in tree peony breeding programs for important agronomic traits.展开更多
Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba pl...Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits,here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in Southern China and identified SNPs associated with five horticultural traits,based on 11704 SNPs derived from double-digest restriction-site associated DNA sequencing(ddRAD-seq).Clustering analysis revealed that these accessions were composed of three groups:C.speciosa group,C.insignis group,and hybrid group.The GWAS identified two,four,two,three,and four SNPs related to petal color,petal striation number,flowering time,trunk shape,and prickles on the trunk and branches,respectively.One to two candidate genes were found near the SNPs strongly associated with these traits.This study revealed the genetic relatedness in the Ceiba plants cultivated in Southern China and presented the first GWAS analysis for five horticultural traits for them,laying a foundation for phenotype-related marker selection and molecular breeding.展开更多
Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cu...Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cultivation.However,genome variation,population structure and genetic architecture of garlic agronomic traits were still not well elucidated.Here,1100258 single nucleotide polymorphisms(SNPs)were identified using genotyping-by-sequencing in 606 garlic accessions collected from43 countries.Population structure,principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations.Twenty agronomic traits,including above-ground growth traits,bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study.In total,542 SNPs were associated with these agronomic traits,among which 188 SNPs were repeatedly associated with more than two traits.One SNP(chr6:1896135972)was repeatedly associated with ten traits.These associated SNPs were located within or near 858 genes,56 of which were transcription factors.Interestingly,one non-synonymous SNP(Chr4:166524085)in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits.Additionally,gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in‘vegetative to reproductive phase transition of meristem’,‘shoot system development’,‘reproductive process’,etc.These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.展开更多
Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity,which limits gene mining for important agronomic traits.Here,314 sweetpotato germplasm resources were deeply resequenced,and 4599509 SN...Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity,which limits gene mining for important agronomic traits.Here,314 sweetpotato germplasm resources were deeply resequenced,and 4599509 SNPs and 846654 InDels were generated,among which 196124 SNPs were nonsynonymous and 9690 InDels were frameshifted.Based on the Indels,genome-wide marker primers were designed,and 3219 of 40366 primer pairs were selected to construct the core InDel marker set.The molecular ID of 104 sweetpotato samples verified the availability of these primers.The sweetpotato population structures were then assessed through multiple approaches using SNPs,and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources.As many as 20 important agronomic traits were evaluated,and a genome-wide association study was conducted on these traits.A total of 19 high-confidence loci were detected in both models.These loci included several candidate genes,such as IbMYB1,IbZEP1,and IbYABBY1,which might be involved in anthocyanin metabolism,carotenoid metabolism,and leaf morphogenesis,respectively.Among them,IbZEP1 and IbYABBY1 were first reported in sweetpotato.The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with f lesh color(orange or not orange)in sweetpotato.The expression levels of IbYABBY1 were also correlated with leaf shape.These results will assist in genetic and breeding studies in sweetpotato.展开更多
Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse env...Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.展开更多
The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic informat...The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described.The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing(ATAC-seq)samples across 11 tissues. An average of 50 ?796open chromatin regions were identified per sample,cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L(active in the duodenum), RCBTB1(muscle and liver), and novel long non-coding RNA ENSGALG00000053256(bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.展开更多
Background Carcass traits are crucial for broiler ducks,but carcass traits can only be measured postmortem.Genomic selection(GS)is an effective approach in animal breeding to improve selection and reduce costs.However...Background Carcass traits are crucial for broiler ducks,but carcass traits can only be measured postmortem.Genomic selection(GS)is an effective approach in animal breeding to improve selection and reduce costs.However,the performance of genomic prediction in duck carcass traits remains largely unknown.Results In this study,we estimated the genetic parameters,performed GS using different models and marker densi-ties,and compared the estimation performance between GS and conventional BLUP on 35 carcass traits in an F2 population of ducks.Most of the cut weight traits and intestine length traits were estimated to be high and moder-ate heritabilities,respectively,while the heritabilities of percentage slaughter traits were dynamic.The reliability of genome prediction using GBLUP increased by an average of 0.06 compared to the conventional BLUP method.The Permutation studies revealed that 50K markers had achieved ideal prediction reliability,while 3K markers still achieved 90.7%predictive capability would further reduce the cost for duck carcass traits.The genomic relationship matrix nor-malized by our true variance method instead of the widely used 2pi(1-pi)could achieve an increase in prediction reliability in most traits.We detected most of the bayesian models had a better performance,especially for BayesN.Compared to GBLUP,BayesN can further improve the predictive reliability with an average of 0.06 for duck carcass traits.Conclusion This study demonstrates genomic selection for duck carcass traits is promising.The genomic prediction can be further improved by modifying the genomic relationship matrix using our proposed true variance method and several Bayesian models.Permutation study provides a theoretical basis for the fact that low-density arrays can be used to reduce genotype costs in duck genome selection.展开更多
In petroleum-producing territories of West Siberia(Russia),oil well gas flares have a thermal effect on nearby plant communities.Such communities can be used as models for studying plant acclimation to global warming....In petroleum-producing territories of West Siberia(Russia),oil well gas flares have a thermal effect on nearby plant communities.Such communities can be used as models for studying plant acclimation to global warming.In the present study on the effect of the hydrothermal regime at the flare sites on mesophyll and stomatal functional traits of Betula pubescens,leaves were collected from trees at250 m(control site[CS]),200,150 and 100 m(maximum impact site[MIS])from a flare.From the CS to MIS site,the average annual air temperature increased by 0.5℃and bog water level decreased by 17 cm.On plants from the MIS,stomata were 16%smaller and density was 20%lower compared to those at the CS,resulting in lower maximum stomatal conductance in plants from the MIS(mean±SE:MIS 0.84±0.05 mol·m^(-2)s^(-1),CS 1.24±0.06 mol·m^(-2)s^(-1);F=12.6,P<0.01).Mesophyll cell volume was 1.9 times lower at MIS than at CS.Chloroplast numbers per cell also declined with distance from the flares,from 21(MIS)to18(CS;F=15.6,P<0.001),and chloroplast volume was 24%higher at the CS,whereas the number of mesophyll cells and chloroplasts numbers per unit leaf area were 1.9 and 1.8 times higher at the MIS than at the CS,respectively.As a result,leaves from the MIS had a large total mesophyll cell(Ames/A)and chloroplast(Achl/A)surface area per unit leaf area,resulting in a 46%increase in mesophyll conductance in plants from the MIS.Thus,structural changes in leaf epidermis consisted of a decrease in stomatal size and number,could lower transpiration losses with higher temperatures and less water.To compensate for the reduction in leaf conductance due to a decrease in stomatal conductance under these conditions,an increase in the number of mesophyll cells and chloroplasts per unit area provides a greater gas-exchange area and mesophyll conductance.展开更多
The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship bet...The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood. In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments. We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield. Using a genome-wide association study(GWAS)coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT. Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture. Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication-and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement. Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize. This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.展开更多
Background As pre-cut and pre-packaged chilled meat becomes increasingly popular,integrating the carcasscutting process into the pig industry chain has become a trend.Identifying quantitative trait loci(QTLs)of pork c...Background As pre-cut and pre-packaged chilled meat becomes increasingly popular,integrating the carcasscutting process into the pig industry chain has become a trend.Identifying quantitative trait loci(QTLs)of pork cuts would facilitate the selection of pigs with a higher overall value.However,previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts,neglecting the investigation of QTLs influencing these traits.This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips.Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values(GEBVs)for pork cuts.Results We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes,respectively.Specifically,we found that HMGA1,VRTN and BMP2 were associated with body length and weight.Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones,VRTN primarily affects the number of vertebrates,and BMP2 primarily affects the length of vertebrae and the size of hind leg bones.The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population,divided by the square root of the trait’s heritability.The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693.Notably,ribs,boneless picnic shoulder,tenderloin,hind leg bones,and scapula bones exhibited prediction accuracies exceeding 0.600.Employing better models,increasing marker density through genotype imputation,and pre-selecting markers significantly improved the prediction accuracy of GEBVs.Conclusions We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes.These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection.Additionally,we have constructed the first reference populations for genomic selection of pork cuts in pigs.展开更多
基金Supported by the Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural(Aquaculture)Varieties(No.2021C02069-4-3)the Major Research&Development Program(Modern Agriculture)of Jiangsu Province(No.BE2019352)+1 种基金the Earmarked Fund for the China Agriculture Research System(No.CARS-48)the Innovation Project of Postgraduate Scientific Research in Huzhou University in 2022(No.2022KYCX63)。
文摘The giant freshwater prawn Macrobrachium rosenbergii distributed from tropical to subtropical regions,is a warm-water species,and its survival temperature is 14-35°C,which greatly limits its culture cycle and culture area in China.Therefore,it is urgent to cultivate a new high quality,high yield variety with improved cold-resistance,but the genetic parameters for cold-resistance traits are unknown in M.rosenbergii.In this study,the cold-resistance of adult M.rosenbergii populations was tested using the indoor artificial cooling method.Individuals were selected from 139 families of Shufeng G3 generation and cultured for 200 days.A linear mixed model was constructed by ASReml-R to evaluate the genetic parameters of the cold-resistance trait(cooling degree hours,CDH)and growth traits(body weight,BW,and body length,BL)based on the restricted maximum likelihood(REML)method.The results show that the heritability of CDH was low(0.12±0.05),while the growth traits(BW and BL)had low to moderate heritability,with 0.20±0.06 for BW and 0.06±0.04 for BL.The phenotypic and genetic correlation between BW and BL was significantly positive,but significantly negative phenotypic and genetic correlations were detected between CDH and BW and between CDH and BL.Furthermore,the analysis of the differences between cold-resistance and phenotypic traits showed that the female reproductive status,exoskeleton hardness and claw number of adult prawns had a great influence on the cold-resistance of M.rosenbergii(P<0.05),indicating that adults with claws and hard exoskeletons are preferred as parents in subsequent breeding selection.The present results can be attributed to the selection and breeding of a new cold-resistant variety of M.rosenbergii.
基金supported by the Key R&D Program of Ningxia Hui Autonomous Region,China(2021BEG03008)the Natural Science Foundation of Ningxia Hui Autonomous Region,China(2021AAC03083).
文摘The maintenance of sand-fixing vegetation is important for the stability of artificial sand-fixing systems in which seed dispersal plays a key role.Based on field wind tunnel experiments using 11 common plant species on the southeastern edge of the Tengger Desert,China,we studied the secondary seed dispersal in the fixed and semi-fixed sand dunes as well as in the mobile dunes in order to understand the limitations of vegetation regeneration and the maintenance of its stability.Our results indicated that there were significant variations among the selected 11 plant species in the threshold of wind speed(TWS).The TWS of Caragana korshinskii was the highest among the 11 plant species,whereas that of Echinops gmelinii was the lowest.Seed morphological traits and underlying surface could generally explain the TWS.During the secondary seed dispersal processes,the proportions of seeds that did not disperse(no dispersal)and only dispersed over short distance(short-distance dispersal within the wind tunnel test section)were significantly higher than those of seeds that were buried(including lost seeds)and dispersed over long distance(long-distance dispersal beyond the wind tunnel test section).Compared with other habitats,the mobile dunes were the most difficult places for secondary seed dispersal.Buried seeds were the easiest to be found in the semi-fixed sand dunes,whereas fixed sand dunes were the best sites for seeds that dispersed over long distance.The results of linear mixed models showed that after controlling the dispersal distance,smaller and rounder seeds dispersed farther.Shape index and wind speed were the two significant influencing factors on the burial of seeds.The explanatory power of wind speed,underlying surface,and seed morphological traits on the seeds that did not disperse and dispersed over short distance was far greater than that on the seeds that were buried and dispersed over long distance,implying that the processes and mechanisms of burial and long-distance dispersal are more complex.In summary,most seeds in the study area either did not move,were buried,or dispersed over short distance,promoting local vegetation regeneration.
基金the Natural Science Foundation of Inner Mongolia,China(2023JQ01)the National Key R&D Program of China(2019YFA0607103)+2 种基金the Central Government Guides Local Science and Technology Development Fund Projects(2022ZY0224)the Open Project Program of Ministry of Education Key Laboratory of Ecology and Resources Use of the Mongolian Plateau,Hohhot,Inner Mongolia,China(KF2023003)Major Science and Technology Project of Inner Mongolia Autonomous Region:Monitoring,Assessment and Early Warning Technology Research of Biodiversity in Inner Mongolia(2021ZD0011)for financial support.
文摘Many different factors,such as species traits,socio-economic factors,geographical and environmental factors,can lead to specimen collection preference.This study aims to determine whether grassland specimen collection in China is preferred by species traits(i.e.,plant height,flowering and fruiting period),environmental range(i.e.,the temperature and precipitation range)and geographical range(i.e.,distribution range and altitudinal range).Ordinary least squares models and phylogenetic generalized linear mixed models were used to analyze the relationships between specimen number and the explanatory variables.Random Forest models were then used to find the most parsimonious multivariate model.The results showed that interannual variation in specimen number between 1900 and 2020 was considerable.Specimen number of these species in southeast China was notably lower than that in northwest China.Environmental range and geographical range of species had significant positive correlations with specimen number.In addition,there were relatively weak but significant associations between specimen number and species trait(i.e.,plant height and flowering and fruiting period).Random Forest models indicated that distribution range was the most important variable,followed by flowering and fruiting period,and altitudinal range.These findings suggest that future floristic surveys should pay more attention to species with small geographical range,narrow environmental range,short plant height,and short flowering and fruiting period.The correction of specimen collection preference will also make the results of species distribution model,species evolution and other works based on specimen data more accurate.
基金This study was supported by the National Natural Science Foundation of China(42271396)the Natural Science Foundation of Shandong Province(ZR2022MD017)+1 种基金the Key R&D Project of Hebei Province(22326406D)The European Space Agency(ESA)and Ministry of Science and Technology of China(MOST)Dragon(57457).
文摘Cereal is an essential source of calories and protein for the global population.Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and categorised storage for enterprises,future trading prices,and policy planning.The use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality traits.Many studies have also proposed models and methods for predicting such traits based on multiplatform remote sensing data.In this paper,the key quality traits that are of interest to producers and consumers are introduced.The literature related to grain quality prediction was analyzed in detail,and a review was conducted on remote sensing platforms,commonly used methods,potential gaps,and future trends in crop quality prediction.This review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.
基金the Agricultural Science and Technology Innovation Project of Jilin Province(Postdoctoral Fund Project)(CXGC2021RCB007)Agricultural Science and Technology Innovation Project of Jilin Province(Introduction of Doctor and High-Level Talents Project)(CXGC2022RCG008)+1 种基金Jilin Province Science and Technology Development Project(20200403014SF)Agricultural Science and Technology Innovation Project of Jilin Province(CXGC2021ZY036).
文摘Soil salinization is the main factor that threatens the growth and development of plants and limits the increase of yield.It is of great significance to study the key soil environmental factors affecting plant root traits to reveal the adaptation strategies of plants to saline-alkaline-stressed soil environments.In this study,the root biomass,root morphological parameters and root mineral nutrient content of two alfalfa cultivars with different sensitivities to alkaline stress were analyzed with black soil as the control group and the mixed saline-alkaline soil with a ratio of 7:3 between black soil and saline-alkaline soil as the saline-alkaline treatment group.At the same time,the correlation analysis of soil salinity indexes,soil nutrient indexes and the activities of key enzymes involved in soil carbon,nitrogen and phosphorus cycles was carried out.The results showed that compared with the control group,the pH,EC,and urease(URE)of the soil surrounding the roots of two alfalfa cultivars were significantly increased,while soil total nitrogen(TN),total phosphorus(TP),organic carbon(SOC),andα-glucosidase activity(AGC)were significantly decreased under saline-alkaline stress.There was no significant difference in root biomass and root morphological parameters of saline-alkaline tolerant cultivar GN under saline-alkaline stress.The number of root tips(RT),root surface area(RS)and root volume(RV)of AG were reduced by 61.16%,44.54%,and 45.31%,respectively,compared with control group.The ratios of K^(+)/Na^(+),Ca^(2+)/Na^(+)and Mg^(2+)/Na^(+)of GN were significantly higher than those of AG(p<0.05).The root fresh weight(RFW)and dry weight(RDW),root length(RL),RV and RT of alfalfa were positively regulated by soil SOC and TN,but negatively regulated by soil pH,EC,and URE(p<0.01).Root Ca^(2+)/Na+ratio was significantly positively correlated with soil TN,TP and SOC(p<0.01).The absorption of Mg and Ca ions in roots is significantly negatively regulated by soilβ-glucosidase activity(BGC)and acid phosphatase activity(APC)(p<0.05).This study improved knowledge of the relationship between root traits and soil environmental factors and offered a theoretical framework for elucidating how plant roots adapt to saline-alkaline stressed soil environments.
文摘Investigating the role of Big Five personality traits in relation to various health outcomes has been extensively studied. The impact of “Big Five” on physical health is here explored for older Europeans with a focus on examining age groups differences. The study sample included 378,500 respondents derived from the seventh data wave of Survey of Health, Aging and Retirement in Europe (SHARE). The physical health status of older Europeans was estimated by constructing an index considering the combined effect of well-established health indicators such as the number of chronic diseases, mobility limitations, limitations with basic and instrumental activities of daily living, and self-perceived health. This index was used for an overall physical health assessment, for which the higher the score for an individual, the worst health level. Then, through a dichotomization process applied to the retrieved Principal Component Analysis scores, a two-group discrimination (good or bad health status) of SHARE participants was obtained as regards their physical health condition, allowing for further con-structing logistic regression models to assess the predictive significance of “Big Five” and their protective role for physical health. Results showed that neuroti-cism was the most significant predictor of physical health for all age groups un-der consideration, while extraversion, agreeableness and openness were not found to significantly affect the self-reported physical health levels of midlife adults aged 50 up to 64. Older adults aged 65 up to 79 were more prone to open-ness, whereas the oldest old individuals aged 80 up to 105 were mainly affected by openness and conscientiousness. .
文摘A central goal of genetics is to understand the links between genetic variation and disease.Intuitively,one might expect diseasecausing variants to cluster into key pathways that drive disease etiology.But for complex traits,association signals tend to be spread across most of the genome-including near many genes without an obvious connection to disease.
基金supported by the National Natural Science Foundation of China(32172697,31830090,and 32002151)the Guangdong Provincial Natural Science Foundation,China(2021A1515011336)the Chinese Academy of Agricultural Sciences(CAAS-ZDRW202006)。
文摘Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in pigs.However,the available genetic markers for these traits are limited.To uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.We performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,respectively.Variant annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in pigs.Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle development.Overall,this study provides new candidate loci and genes for the genetic improvement of pigs.
基金This work was supported by the National Key R&D Program of China(2022YFD2201100)the National Natural Science Foundation of China(31971636)the Fundamental Research Funds for the Central Universities(2572022DS13).
文摘The variation and correlation of leaf economics and vein traits are crucial for predicting plant ecological strategies under different environmental changes.However,correlations between these two suites of traits and abiotic factors such as soil water and nitrogen content remain ambiguous.We measured leaf economics and vein traits as well as soil water and nitrogen content for two different shade-tolerant species(Betula platyphylla and Acer mono)in four mixed broadleaved-Korean pine(Pinus koraiensis)forests along a latitudinal gradient in Northeast China.We found that leaf economics traits and vein traits were decoupled in shade-intolerant species,Betula platphylla,but significantly coupled in a shadetolerant species,A.mono.We found stronger correlations among leaf traits in the shade tolerant species than in the shade intolerant species.Furthermore,leaf economic traits were positively correlated with the soil water gradient for both species,whereas vein traits were positively correlated with soil water gradient for the shade intolerant species but negatively correlated in the shade tolerant species.Although economic traits were positively correlated with soil nitrogen gradient in shade intolerant species but not correlated in shade tolerant species,vein traits were negatively correlated with soil nitrogen gradient in shade tolerant species but not correlated in shade intolerant species.Our study provides evidence for distinct correlations between leaf economics and vein traits and local abiotic factors of species differing in light demands.We recommend that the ecological significance of shade tolerance be considered for species when evaluating ecosystem functions and predicting plant responses to environmental changes.
基金supported by the National Natural Science Foundation of China(32171507,31870385,31901285)CAS"Light of West China"program。
文摘Maintaining open flowers is critical for successful pollination and depends on long-term water and carbon balance.Yet the relationship between how flower hydraulic traits are coordinated in different habitats is poorly understood.Here,we hypothesize that the coordination and trade-offs between floral hydraulics and economics traits are independent of environmental conditions.To test this hypothesis,we investigated a total of 27 flower economics and hydraulic traits in six aquatic and six terrestrial herbaceous species grown in a tropical botanical garden.We found that although there were a few significant differences,most flower hydraulics and economics traits did not differ significantly between aquatic and terrestrial herbaceous plants.Both flower mass per area and floral longevity were significantly positively correlated with the time required for drying full-hydrated flowers to 70%relative water content.Flower dry matter content was strongly and positively related to drought tolerance of the flowers as indicated by flower water potential at the turgor loss point.In addition,there was a trade-off between hydraulic efficiency and the construction cost of a flower across species.Our results show that flowers of aquatic and terrestrial plants follow the same economics spectrum pattern.These results suggest a convergent flower economics design across terrestrial and aquatic plants,providing new insights into the mechanisms by which floral organs adapt to aquatic and terrestrial habitats.
基金supported by the National Natural Science Foundation of China(U1804233)the Innovation Scientists and Technicians Troop Construction Projects of Henan Province(202101510003)the Outstanding Youth Fund of the Natural Science Foundation of Henan Province(202300410119).
文摘Tree peony is a unique traditional f lower in China,with large,fragrant,and colorful f lowers.However,a relatively short and concentrated f lowering period limits the applications and production of tree peony.A genome-wide association study(GWAS)was conducted to accelerate molecular breeding for the improvement of f lowering phenology traits and ornamental phenotypes in tree peony.A diverse panel of 451 tree peony accessions was phenotyped for 23 f lowering phenology traits and 4 f loral agronomic traits over 3 years.Genotyping by sequencing(GBS)was used to obtain a large number of genome-wide single-nucleotide polymorphisms(SNPs)(107050)for the panel genotypes,and 1047 candidate genes were identified by association mapping.Eighty-two related genes were observed during at least 2 years for f lowering,and seven SNPs repeatedly identified for multiple f lowering phenology traits over multiple years were highly significantly associated with five genes known to regulate f lowering time.We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of f lower bud differentiation and f lowering time in tree peony.This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony.The results expand our understanding of f lowering time control in perennial woody plants.Identification of markers closely related to these f lowering phenology traits can be used in tree peony breeding programs for important agronomic traits.
基金supported by the Guangzhou Landscaping Company(Grant No.2018–69).
文摘Ceiba species have high ornamental value and are widely cultivated in tropical regions.However,genetic background of cultivated Ceiba plants remains unclear.To understand the genetic relatedness of cultivated Ceiba plants and genetic basis of key horticultural traits,here we explored the genetic relatedness of 153 accessions of Ceiba plants cultivated in Southern China and identified SNPs associated with five horticultural traits,based on 11704 SNPs derived from double-digest restriction-site associated DNA sequencing(ddRAD-seq).Clustering analysis revealed that these accessions were composed of three groups:C.speciosa group,C.insignis group,and hybrid group.The GWAS identified two,four,two,three,and four SNPs related to petal color,petal striation number,flowering time,trunk shape,and prickles on the trunk and branches,respectively.One to two candidate genes were found near the SNPs strongly associated with these traits.This study revealed the genetic relatedness in the Ceiba plants cultivated in Southern China and presented the first GWAS analysis for five horticultural traits for them,laying a foundation for phenotype-related marker selection and molecular breeding.
基金supported by the Natural Science Foundation of China(31872946,32172566,and 32272731)National Key R&D Program of China(2021YFD1200201),China Agriculture Research System of MOF and MARA(CARS-24-A-01)+4 种基金Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-XTCX2018021)Youth Innovation Special Task of Chinese Academy of Agricultural Sciences(Y2023QC06)Agricultural Basic Long-Term Scientific and TechnologicalWork(NAES-GR-005)Safe Preservation Project of Crop Germplasm Resources of MOF(2022NWB037)National Hoticultural Gerplasm Centre Project(NHGRC2022-NH01).
文摘Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cultivation.However,genome variation,population structure and genetic architecture of garlic agronomic traits were still not well elucidated.Here,1100258 single nucleotide polymorphisms(SNPs)were identified using genotyping-by-sequencing in 606 garlic accessions collected from43 countries.Population structure,principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations.Twenty agronomic traits,including above-ground growth traits,bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study.In total,542 SNPs were associated with these agronomic traits,among which 188 SNPs were repeatedly associated with more than two traits.One SNP(chr6:1896135972)was repeatedly associated with ten traits.These associated SNPs were located within or near 858 genes,56 of which were transcription factors.Interestingly,one non-synonymous SNP(Chr4:166524085)in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits.Additionally,gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in‘vegetative to reproductive phase transition of meristem’,‘shoot system development’,‘reproductive process’,etc.These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.
基金This work was supported by the National Key Research&Development Program of China(2018YFD1000705/2018YFD1000700)the Natural Science Foundation of Jiangsu Province of China(BK20221213)the China Agriculture Research System(CARS-10-GW01).
文摘Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity,which limits gene mining for important agronomic traits.Here,314 sweetpotato germplasm resources were deeply resequenced,and 4599509 SNPs and 846654 InDels were generated,among which 196124 SNPs were nonsynonymous and 9690 InDels were frameshifted.Based on the Indels,genome-wide marker primers were designed,and 3219 of 40366 primer pairs were selected to construct the core InDel marker set.The molecular ID of 104 sweetpotato samples verified the availability of these primers.The sweetpotato population structures were then assessed through multiple approaches using SNPs,and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources.As many as 20 important agronomic traits were evaluated,and a genome-wide association study was conducted on these traits.A total of 19 high-confidence loci were detected in both models.These loci included several candidate genes,such as IbMYB1,IbZEP1,and IbYABBY1,which might be involved in anthocyanin metabolism,carotenoid metabolism,and leaf morphogenesis,respectively.Among them,IbZEP1 and IbYABBY1 were first reported in sweetpotato.The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with f lesh color(orange or not orange)in sweetpotato.The expression levels of IbYABBY1 were also correlated with leaf shape.These results will assist in genetic and breeding studies in sweetpotato.
基金supported by the Russian Science Foundation within the Project No.21-66-00007support of the Russian Ministry of Science and Higher Education。
文摘Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.
基金supported by the National Natural Science Foundation of China(U2002205,32272862)。
文摘The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described.The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing(ATAC-seq)samples across 11 tissues. An average of 50 ?796open chromatin regions were identified per sample,cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L(active in the duodenum), RCBTB1(muscle and liver), and novel long non-coding RNA ENSGALG00000053256(bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.
基金supported by grants from the Key Technologies Research on New Breed of Broiler Poultry by Integration of Breeding,Reproduction and Promotion(2021CXGC010805-02)Taishan Industry Leadership Talent Project of Shandong province in China(TSCY20190108)+1 种基金China Agriculture Research System of MOF and MARA(CARS-42)the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences(CXGC-IAS-09).
文摘Background Carcass traits are crucial for broiler ducks,but carcass traits can only be measured postmortem.Genomic selection(GS)is an effective approach in animal breeding to improve selection and reduce costs.However,the performance of genomic prediction in duck carcass traits remains largely unknown.Results In this study,we estimated the genetic parameters,performed GS using different models and marker densi-ties,and compared the estimation performance between GS and conventional BLUP on 35 carcass traits in an F2 population of ducks.Most of the cut weight traits and intestine length traits were estimated to be high and moder-ate heritabilities,respectively,while the heritabilities of percentage slaughter traits were dynamic.The reliability of genome prediction using GBLUP increased by an average of 0.06 compared to the conventional BLUP method.The Permutation studies revealed that 50K markers had achieved ideal prediction reliability,while 3K markers still achieved 90.7%predictive capability would further reduce the cost for duck carcass traits.The genomic relationship matrix nor-malized by our true variance method instead of the widely used 2pi(1-pi)could achieve an increase in prediction reliability in most traits.We detected most of the bayesian models had a better performance,especially for BayesN.Compared to GBLUP,BayesN can further improve the predictive reliability with an average of 0.06 for duck carcass traits.Conclusion This study demonstrates genomic selection for duck carcass traits is promising.The genomic prediction can be further improved by modifying the genomic relationship matrix using our proposed true variance method and several Bayesian models.Permutation study provides a theoretical basis for the fact that low-density arrays can be used to reduce genotype costs in duck genome selection.
基金performed within the budget themes of the Institute Botanic Garden UB RASthe framework of the state assignment FEWZ-2020–0009 from the Ministry of Education and Science of the Russian Federation。
文摘In petroleum-producing territories of West Siberia(Russia),oil well gas flares have a thermal effect on nearby plant communities.Such communities can be used as models for studying plant acclimation to global warming.In the present study on the effect of the hydrothermal regime at the flare sites on mesophyll and stomatal functional traits of Betula pubescens,leaves were collected from trees at250 m(control site[CS]),200,150 and 100 m(maximum impact site[MIS])from a flare.From the CS to MIS site,the average annual air temperature increased by 0.5℃and bog water level decreased by 17 cm.On plants from the MIS,stomata were 16%smaller and density was 20%lower compared to those at the CS,resulting in lower maximum stomatal conductance in plants from the MIS(mean±SE:MIS 0.84±0.05 mol·m^(-2)s^(-1),CS 1.24±0.06 mol·m^(-2)s^(-1);F=12.6,P<0.01).Mesophyll cell volume was 1.9 times lower at MIS than at CS.Chloroplast numbers per cell also declined with distance from the flares,from 21(MIS)to18(CS;F=15.6,P<0.001),and chloroplast volume was 24%higher at the CS,whereas the number of mesophyll cells and chloroplasts numbers per unit leaf area were 1.9 and 1.8 times higher at the MIS than at the CS,respectively.As a result,leaves from the MIS had a large total mesophyll cell(Ames/A)and chloroplast(Achl/A)surface area per unit leaf area,resulting in a 46%increase in mesophyll conductance in plants from the MIS.Thus,structural changes in leaf epidermis consisted of a decrease in stomatal size and number,could lower transpiration losses with higher temperatures and less water.To compensate for the reduction in leaf conductance due to a decrease in stomatal conductance under these conditions,an increase in the number of mesophyll cells and chloroplasts per unit area provides a greater gas-exchange area and mesophyll conductance.
基金supported by grants from the National Natural Science Foundation of China (31971891)the Guangxi Key Research and Development Projects, China (GuikeAB21238004)+1 种基金the Scientific Innovation 2030 Project, China (2022ZD0401703)the Modern AgroIndustry Technology Research System of Maize, China (CARS-02-03)。
文摘The crown root system is the most important root component in maize at both the vegetative and reproductive stages. However, the genetic basis of maize crown root traits(CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood. In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments. We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield. Using a genome-wide association study(GWAS)coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT. Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture. Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication-and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement. Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize. This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.
基金National Natural Science Foundation of China[grant number 32160782].
文摘Background As pre-cut and pre-packaged chilled meat becomes increasingly popular,integrating the carcasscutting process into the pig industry chain has become a trend.Identifying quantitative trait loci(QTLs)of pork cuts would facilitate the selection of pigs with a higher overall value.However,previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts,neglecting the investigation of QTLs influencing these traits.This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips.Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values(GEBVs)for pork cuts.Results We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes,respectively.Specifically,we found that HMGA1,VRTN and BMP2 were associated with body length and weight.Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones,VRTN primarily affects the number of vertebrates,and BMP2 primarily affects the length of vertebrae and the size of hind leg bones.The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population,divided by the square root of the trait’s heritability.The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693.Notably,ribs,boneless picnic shoulder,tenderloin,hind leg bones,and scapula bones exhibited prediction accuracies exceeding 0.600.Employing better models,increasing marker density through genotype imputation,and pre-selecting markers significantly improved the prediction accuracy of GEBVs.Conclusions We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes.These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection.Additionally,we have constructed the first reference populations for genomic selection of pork cuts in pigs.
