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 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
The uncoupling protein (UCP) is a member of the mitochondrial membrane transporter family, which plays an important role in energy metabolism. In the present study, the UCP gene was considered as a candidate gene for ...The uncoupling protein (UCP) is a member of the mitochondrial membrane transporter family, which plays an important role in energy metabolism. In the present study, the UCP gene was considered as a candidate gene for chicken growth traits, and the association of UCP gene SNPs with growth rate was investigated in the eighth generation of NEAUHLF broiler lines. Two SNPs were found in chicken UCP gene, and the association analysis results showed that both the individual and combination of chicken UCPgene SNPs were significantly associated with body weight of 7 weeks (BW7) and carcass weight (CW) (P<0.05), and the combination had much significant effects than the single SNP. This research suggested that the UCP gene could be a candidate gene or linked to a major gene which affected growth traits in chicken.展开更多
Numerous growth and physiological variables of 3-week-old Populus simonii × P.nigra seedlings were assessed after treatment with either nitrate nitrogen(NO_(3)^(−)--N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) or ammon...Numerous growth and physiological variables of 3-week-old Populus simonii × P.nigra seedlings were assessed after treatment with either nitrate nitrogen(NO_(3)^(−)--N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) or ammonium nitrogen(NH_(4)^(+)+-N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) to determine the best nitrogen form and concentration to optimize growth,biomass allocation,pigment content,and photosynthetic capacity.The results of combining membership function and an evaluation index suggested that,5 mmol·L^(−1) nitrogen,regardless of the form,yielded the highest comprehensive evaluation index and good growth.In addition,a Pearson correlation analysis and network visualization revealed that the total mass,shoot mass,root mass,leaf dry mass,plant height,leaf area,chlorophyll a and total chlorophyll had a physiological index connectivity degree≥15 for both nitrogen forms.Net photosynthetic rate,stomatal conductance,transpiration rate,maximum photochemical efficiency of PSII,total nitrogen content,ground diameter,chlorophyll b,and carotenoid were unique indices for evaluating NH_(4)^(+)+-N-based nutrition,which could provide a theoretical basis for evaluating the effects of nitrogen fertilizer on seedlings,cultivation periods,and stress tolerance in P.simonii× P.nigra.展开更多
To select elite materials,the growth traits of 32 Betula platyphylla clones at three separated northern sites in Northeast China were investigated and analyzed.The results showed that there were significant difference...To select elite materials,the growth traits of 32 Betula platyphylla clones at three separated northern sites in Northeast China were investigated and analyzed.The results showed that there were significant differences among all variation sources in the different investigated traits(P<0.01).Except for the carbon contents,all the coeffi-cients of phenotypic variation of the other investigated traits were higher than 10%.The repeatability of different traits ranged from 0.760 to 0.998.Correlation analysis showed that tree height were significantly correlated with diameter at breast height,but neither was significantly correlated with leaf traits nor element contents.Additive main effects and multiplicative interaction analysis showed that genotype,environment and genotype×environment interactions were significantly different in diameter at breast height,which indicated that environment had a significant effect on genotype.Comprehensive assessment results showed that three clones with high and stable diameters at breast height were selected,and the genetic gains of diameter at breast height on sites Maoershan,Qingan,and Yongji were 21.24%,20.58%,and 38.65%,respectively.The results could provide a theoretical basis for elite clone selection in B.platyphylla and other broad leaved species.展开更多
To determine appropriate quantities of water and fertilizer required for early growth of hybrid poplar cuttings,we recorded the growth traits of four clones grown under four factors(irrigation and nitrogen,phosphorus,...To determine appropriate quantities of water and fertilizer required for early growth of hybrid poplar cuttings,we recorded the growth traits of four clones grown under four factors(irrigation and nitrogen,phosphorus,and potassium fertilizers),each with four levels,using an orthogonal experimental design.A logistic model was used to estimate growth in height.The growth curves for tree height were sigmoid,and the model R^2 values were greater than 0.9,which indicated that the fit was highly significant.ANOVA results for tree height and basal diameter indicated that all sources of variance showed significant differences(p<0.001).The average tree height and basal diameter for all the four clones under the different treatments ranged from 155.39 to 235.04 cm,and from 13.71 to 17.42 mm,respectively.A highly positive correlation between the extreme k value and tree height was observed,suggesting that the k value was an accurate estimation of tree height.For model parameters,the earliest average time point for the onset of the rapid growth period of poplar clones was 131 d,and the highest average increment in tree height during the rapid growth period was 138.78 cm.The highest average tree height for all clones under each factor was 219,210.51,200,and 201 cm when treated with either 1200 mL of water applied every third day,3 g of nitrogen,0 g of phosphorus,or 0 g of potassium,respectively.The most suitable treatment for the early growth of hybrid poplar cuttings,as suggested by the developed logistic model,was 1200 mL of water applied every third day and three applications of 1 g nitrogen(in the form of CH4N2O).展开更多
This study aimed to explore and improve the different economic values of Pinus koraiensis(Siebold and Zucc.)by examining the variations in 6 growth traits and 9 physicochemical wood properties among 53 P.koraiensis ha...This study aimed to explore and improve the different economic values of Pinus koraiensis(Siebold and Zucc.)by examining the variations in 6 growth traits and 9 physicochemical wood properties among 53 P.koraiensis half-sib families.Growth traits assessed included height,diameter at breast height,volume,degree of stem straight-ness,stem form,and branch number per node,while wood properties assessed included density,fiber length and width,fiber length to width ratio,and cellulose,hemicel-lulose,holocellulose,lignin,and ash contents.Except for degree of stem straightness and branch number per node,all other traits exhibited highly significant variations(P<0.01)among families.The coefficients of variation ranged from 5.3(stem form)to 66.7%(ash content),whereas,the herit-ability ranged from 0.136(degree of stem straightness)to 0.962(ash content).Significant correlations were observed among growth traits and wood physicochemical properties.Principal component analysis identified four distinct groups representing growth traits,wood chemical and physical properties,and stem form traits.Multi-trait comprehensive evaluation identified three groups of elite families based on breeding objectives,including rapid growth,improved timber production for building and furniture materials,and pulpwood production.These specific families should be used to establish new plantations.展开更多
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
We identified the FOXO gene and five single-nucleotide polymorphisms(SNPs)in its coding region in the Sanmen breeding population of the razor clam Sinonovacula constricta.The ScFOXO gene encodes a protein of 625 amino...We identified the FOXO gene and five single-nucleotide polymorphisms(SNPs)in its coding region in the Sanmen breeding population of the razor clam Sinonovacula constricta.The ScFOXO gene encodes a protein of 625 amino acids in length that contains a conserved DNA-binding domain.Real-time polymerase chain reaction analysis showed that ScFOXO mRNA is widely expressed in adult tissues,with higher expression in the siphons and gills.Of the SNPs,c.879G>C(Val293Val)and c.1725A>G(Ser575Ser)are synonymous mutations,and c.543C>T(Phe181Leu),c.848A>G(Tyr283Cys),and c.1625G>C(Gly542Phe)are non-synonymous mutations.The SNPs all show significant associations with total body weight,shell length,shell width,and shell height(SH)in this population.Polymorphic parameter analysis showed that all SNPs except c.848A>G(Tyr283Cys)exhibit complete linkage.The SNP c.1625G>C(Gly542Phe)was used for genetic linkage mapping and demonstrates the strongest linkage(logarithm of the odds[LOD]value:41.46)with the marker 96616(37.02 cM)in the linkage group 9.The LOD value of this marker in relation to growth traits ranges from 1.04 to 1.53;only markers with a LOD value3 were considered to be linked with growth traits in the razor clam linkage map.In summary,ScFOXO may be a growth trait-related gene and may represent a marker for Sanmen breeding group selection.展开更多
Seedling stage is an important period for forestry.The aim of this study was to estimate the growth trend of six local precious species and consider their implications for silviculture on forestry.We assessed height,d...Seedling stage is an important period for forestry.The aim of this study was to estimate the growth trend of six local precious species and consider their implications for silviculture on forestry.We assessed height,diameter near ground and crown width at 1,4,6 and 8-month.The variance analysis indicated that there were significant differences between species on all traits except diameter near ground and crown width at 8-month.There were no significant differences on height and crown width at all ages among replicates whereas there were significant differences on diameter near ground at 1 and 4 months,differences on diameter near ground at 6 months and no difference on diameter near ground at 8-month.The significant differences among interaction of species and replicates on diameter near ground at 1-months,4-month,6-month and crown width at 8-month were also found.Dalbergia odorifera had a higher growth period after 6-month.Aquilaria sinensis(Lour.)Spreng,Swietenia mahagoni(L.)Jacq.,Hopea hainanensis Merr.et Chun,Homalium hainanense Gagnep.and Cassia siamea Lam.had the same growth trend on all traits at the whole time.展开更多
In modern pig breeding programs,growth and fatness are vital economic traits that significantly influence porcine production.To identify underlying variants and candidate genes associated with growth and fatness trait...In modern pig breeding programs,growth and fatness are vital economic traits that significantly influence porcine production.To identify underlying variants and candidate genes associated with growth and fatness traits,a total of 1067 genotyped Duroc pigs with de-regressed estimated breeding values(DEBV)records were analyzed in a genome wide association study(GWAS)by using a single marker regression model.In total,28 potential single nucleotide polymorphisms(SNPs)were associated with these traits of interest.Moreover,VPS4 B,PHLPP1,and some other genes were highlighted as functionally plausible candidate genes that compose the underlying genetic architecture of porcine growth and fatness traits.Our findings contribute to a better understanding of the genetic architectures underlying swine growth and fatness traits that can be potentially used in pig breeding programs.展开更多
Bayesian and restricted maximum likelihood(REML) approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462progeni...Bayesian and restricted maximum likelihood(REML) approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462progenies(17 months old) from 28 families that were produced through artificial insemination using 39 parent fish. An animal model was applied to partition each weight value into a fixed effect, an additive genetic effect, and a residual effect. The average body weight of each family, which was measured at 110 days post-hatching, was considered as a covariate. For Bayesian analysis, heritability and breeding values were estimated using both the posterior mean and mode from the joint posterior conditional distribution. The results revealed that for additive genetic variance, the posterior mean estimate( δ_a^2=9 320) was highest but with the smallest residual variance,REML estimates( δ_a^2=8 088) came second and the posterior mode estimate( δ_a^2=7 849) was lowest. The corresponding three heritability estimates followed the same trend as additive genetic variance and they were all high. The Pearson correlations between each pair of the three estimates of breeding values were all high,particularly that between the posterior mean and REML estimates(0.996 9). These results reveal that the differences between Bayesian and REML methods in terms of estimation of heritability and breeding values were small. This study provides another feasible method of genetic parameter estimation in selective breeding programs of turbot.展开更多
[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples...[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples were extracted from the caudal fins of the hybrid grouper and its parents to amplify their MSTN genes.Then,MSTN gene sequences were analyzed using bioinformatics tools to predict their protein structures and functions.[Results]The hybrid grouper and its parents shared the same MSTN gene structure,consisting of three exons and two introns.Nucleotide sequence of the gene could be translated into 376 amino acids,including an N-terminal signal peptide,a proteolytic processing site(RXXR motif),and nine conserved cysteine residues at C-terminal,which were the typical features of transforming growth factor beta(TGF-β)superfamily proteins.Alignment of protein sequence showed that MSTN was highly conserved between the hybrid grouper and its parents.Especially,exon 3,an important functional domain,exhibited a sequence similarity of 100%among them.In addition,four variable amino acid residues were detected in exon 2 at positions 141,153,185 and 186 in the hybrid grouper,but they did not affect the secondary structure of the protein.[Conclusion]These results will provide molecular information for future investigation on the growth and heterosis of hybrid grouper species,and on the roles of MSTN gene in regulating the growth traits of the hybrid grouper.展开更多
Kumamoto oysters(Crassostrea sikamea)are important marine aquaculture shellfish because of their taste and round shell shape.Due to its small size,selective breeding is required to improve its market size,but there ar...Kumamoto oysters(Crassostrea sikamea)are important marine aquaculture shellfish because of their taste and round shell shape.Due to its small size,selective breeding is required to improve its market size,but there are no reports on traits suitable for direction selection and reproductive productivity of Kumamoto oysters of different ages.In this study,path analysis and one-way ANOVA were used to explore the influential indices of oyster body weight and fecundity.The results showed that shell height was the main factor affecting the body weight of Kumamoto oysters at one-year-old and two-year-old,followed by shell length.Body weight was the main factor influencing fecundity,and shell height showed a significant correlation with fecundity.Therefore,shell height should be considered the first parameter for selection when selecting Kumamoto oysters for body weight as the direct selection target.When one-year-old and two-year-old Kumamoto oysters were selected as parents from Xiangshan Bay,hatching parameters and growth parameters of F1 generation larvae were measured.The fecundity and egg diameters were 1.72×10^(6)and 46.60±3.62μm,respectively,which were significantly greater than one-aged oysters(5.86×10^(5),40.26±3.52μm).The hatching parameters(fertilized egg size,fertilization rate,and hatching rate)and larval growth performance(D-stage veliger and veliger)were similar and did not differ significantly(P>0.05),and after metamorphosis,there was also no significant difference in shell height size at 40 days of age(P>0.05).Therefore,there was no significant effect of age on reproduction,larval development,and the early growth of Kumamoto oysters.These results could provide a basis for parental sources and proper traits for Kumamoto oyster selection,which is beneficial to developing and utilizing this excellent germplasm resource.展开更多
The aim of this study was to evaluate genetic parameters of growth traits for improving selective breeding in olive flounder(Paralichthys olivaceus).A total of 82 full-sib families from 2 year-classes with complete pe...The aim of this study was to evaluate genetic parameters of growth traits for improving selective breeding in olive flounder(Paralichthys olivaceus).A total of 82 full-sib families from 2 year-classes with complete pedigree information were used to estimate heritabilities and genetic/phenotypic correlations for 4 growth performance traits(body weight BW,total length TL,body height BH and condition factor K)based on uni-trait and multi-trait linear mixed models,respectively.Data were analyzed by the restricted maximum likelihood(REML)method.The heritabilities of BW,TL and BH were 0.81,0.70 and 0.61,which are relatively high,however,heritability for K is low(0.11).For all growth traits,the common full-sib effects(c^(2))were at a low to moderate level(0.14–0.20);the maternal effects(m^(2))of the traits(except K)were also detected(0.15–0.19).The phenotypic and genetic correlations among BW,TL and BH were highly positive(0.70–0.91),however,the correlations between K and the other 3 traits was low or negligible(−0.22–0.26).According to our results,these traits(except K)could be selected and enhanced simultaneously.In addition,direct selection based on TL or BH,which is an easily measurable trait,will be more favorable than selection on BW.Moreover,our results indicated that growth parameters estimated in the juvenile stage could be used as a predictor of growth performance at later growth stages.展开更多
For important economic crops such as cucumbers,abiotic and biotic stress conditions have had an adverse effect.This study aimed to observe the effects of water stress and powdery mildew stress on cucumber plants.Bioti...For important economic crops such as cucumbers,abiotic and biotic stress conditions have had an adverse effect.This study aimed to observe the effects of water stress and powdery mildew stress on cucumber plants.Biotic stress at two levels,B0(no powdery mildew stress)and B1(powdery mildew stress)with three fertigation requirement levels(T1:Full fertigation,T2:Moderate nutrient solution deficit,T3:Severe nutrient solution deficit).Therefore,set up six treatments of B0T1,B1T2,B0T3,B1T1,B1T2,and B1T3.Leaf gas-exchange parameter first decreases and then increases under B1T1,B1T2,and B1T2.The leaf gas exchange parameter was significantly decreased under B0T2 and B0T3.Compared to the control experiment(CK,B0T1:no disease infestation and full irrigation),the plant height of cucumber decreased by 7.55%,10.62%,15.28%,23.27%,and 35.16%,respectively,under B0T2,B0T3,B1T1,B1T2 and B1T3;the stem diameter of cucumber decreased by 9.46%,15.74%,5.47%,13.45%,and 23.72%,respectively,under B0T2,B0T3,B1T1,B1T2,and B1T3;the leaf area of cucumber decreased by 13.76%,29.96%,13.43%,38.21%,and 66.83%,respectively,under B0T2,B0T3,B1T1,B1T2,and B1T3.The root-shoot ratio of cucumber was 3.92%,3.13%,3.63%,3.84%,4.41%,and 3.82%,respectively,under the B0T1,B0T2,B0T3,B1T1,B1T2,and B1T3.Therefore,this study can provide a basis for the research on greenhouse environmental control and cucumber cultivation management.展开更多
Grass carp has the highest production yield among all the farmed fish species around the world.But the molecular and genetic basis of growth traits is inadequately understood in this fish.In the present study,we apply...Grass carp has the highest production yield among all the farmed fish species around the world.But the molecular and genetic basis of growth traits is inadequately understood in this fish.In the present study,we apply whole-transcriptome sequencing to identify genes whose expression is different between fast and slow growing grass carp.We identified 1178 differentially expressed genes(DEGs),among which 270 were upregulated in the fast growing group and 908 upregulated in the slow growing group.The GO enrichment analysis revealed that DEGs was significantly enriched in protein synthesis and export machinery,cell division and development and metabolism,suggesting that cell division and metabolism may play key roles in development processes of fish.KEGG pathway analysis showed that MAPK signaling pathway may play a prominent role in growth difference.In addition,the majority of genes in immune responses related pathway were upregulated in the slow growing individuals.These results provide some valuable resources for understanding the molecular mechanisms of growth traits in fish.展开更多
Soil salinity diminishes soil health and reduces crop yield,which is becoming a major global concern.Salinity stress is one of the primary stresses,leading to several other secondary stresses that restrict plant growt...Soil salinity diminishes soil health and reduces crop yield,which is becoming a major global concern.Salinity stress is one of the primary stresses,leading to several other secondary stresses that restrict plant growth and soil fertility.The major secondary stresses induced in plants under saline-alkaline conditions include osmotic stress,nutrient limitation,and ionic stress,all of which negatively impact overall plant growth.Under stressed conditions,certain beneficial soil microflora are known to have evolved phytostimulating mechanisms,such as the synthesis of osmoprotectants,siderophores,1-aminocyclopropane-1-carboxylic acid(ACC)deaminase activity,phosphate solubilization,and hormone production,which enhance plant growth and development while mitigating nutrient stress.Beneficial soil-borne bacterial species such as Bacillus,Pseudomonas,and Klebsiella and fungal strains such as Trichoderma,Aspergillus,Penicillium,Alternaria,and Fusarium also aid in reducing salinity stress.Phosphate-solubilizing microorganisms also assist in nutrient acquisition via both enzymatic and non-enzymatic processes.In the case of enzymatic processes,they produce different enzymes such as alkaline phosphatases and phytases,whereas non-enzymatic processes produce organic acids such as gluconic,citric,malic,and oxalic acids.The native halotolerant/halophilic soil microbial gene pool with multifunctional traits and stress-induced gene expression can be developed as suitable bio-inoculants to enhance stress tolerance and optimize plant growth in saline soils.展开更多
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 the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-42)Program for Innovation Research Team in University of Heilongjiang Province (2010td02)
文摘The uncoupling protein (UCP) is a member of the mitochondrial membrane transporter family, which plays an important role in energy metabolism. In the present study, the UCP gene was considered as a candidate gene for chicken growth traits, and the association of UCP gene SNPs with growth rate was investigated in the eighth generation of NEAUHLF broiler lines. Two SNPs were found in chicken UCP gene, and the association analysis results showed that both the individual and combination of chicken UCPgene SNPs were significantly associated with body weight of 7 weeks (BW7) and carcass weight (CW) (P<0.05), and the combination had much significant effects than the single SNP. This research suggested that the UCP gene could be a candidate gene or linked to a major gene which affected growth traits in chicken.
基金This work was supported by the Science Fund Project of Heilongjiang Province of China(ZD2020C004)the Special Fund for Basic Scientifi c research operation Fee of Central University(2572019CT02)+1 种基金the Innovation Project of State Key Laboratory of Tree Genetics and Breeding(Northeast Forestry University)(2019A03)Heilongjiang Touyan Innovation Team Program(Tree Genetics and Breeding Innovation Team).
文摘Numerous growth and physiological variables of 3-week-old Populus simonii × P.nigra seedlings were assessed after treatment with either nitrate nitrogen(NO_(3)^(−)--N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) or ammonium nitrogen(NH_(4)^(+)+-N)(0.1,0.5,1,5,or 10 mmol·L^(−1)) to determine the best nitrogen form and concentration to optimize growth,biomass allocation,pigment content,and photosynthetic capacity.The results of combining membership function and an evaluation index suggested that,5 mmol·L^(−1) nitrogen,regardless of the form,yielded the highest comprehensive evaluation index and good growth.In addition,a Pearson correlation analysis and network visualization revealed that the total mass,shoot mass,root mass,leaf dry mass,plant height,leaf area,chlorophyll a and total chlorophyll had a physiological index connectivity degree≥15 for both nitrogen forms.Net photosynthetic rate,stomatal conductance,transpiration rate,maximum photochemical efficiency of PSII,total nitrogen content,ground diameter,chlorophyll b,and carotenoid were unique indices for evaluating NH_(4)^(+)+-N-based nutrition,which could provide a theoretical basis for evaluating the effects of nitrogen fertilizer on seedlings,cultivation periods,and stress tolerance in P.simonii× P.nigra.
基金the Fundamental Research Funds for the Central Universities(2572020DR01,2572020DY24).
文摘To select elite materials,the growth traits of 32 Betula platyphylla clones at three separated northern sites in Northeast China were investigated and analyzed.The results showed that there were significant differences among all variation sources in the different investigated traits(P<0.01).Except for the carbon contents,all the coeffi-cients of phenotypic variation of the other investigated traits were higher than 10%.The repeatability of different traits ranged from 0.760 to 0.998.Correlation analysis showed that tree height were significantly correlated with diameter at breast height,but neither was significantly correlated with leaf traits nor element contents.Additive main effects and multiplicative interaction analysis showed that genotype,environment and genotype×environment interactions were significantly different in diameter at breast height,which indicated that environment had a significant effect on genotype.Comprehensive assessment results showed that three clones with high and stable diameters at breast height were selected,and the genetic gains of diameter at breast height on sites Maoershan,Qingan,and Yongji were 21.24%,20.58%,and 38.65%,respectively.The results could provide a theoretical basis for elite clone selection in B.platyphylla and other broad leaved species.
基金financially supported by the National Key Research and Development Program of China(Grant No.2016YFD0600404)the Fundamental Research Funds for the Central Universities(2572017DA02)
文摘To determine appropriate quantities of water and fertilizer required for early growth of hybrid poplar cuttings,we recorded the growth traits of four clones grown under four factors(irrigation and nitrogen,phosphorus,and potassium fertilizers),each with four levels,using an orthogonal experimental design.A logistic model was used to estimate growth in height.The growth curves for tree height were sigmoid,and the model R^2 values were greater than 0.9,which indicated that the fit was highly significant.ANOVA results for tree height and basal diameter indicated that all sources of variance showed significant differences(p<0.001).The average tree height and basal diameter for all the four clones under the different treatments ranged from 155.39 to 235.04 cm,and from 13.71 to 17.42 mm,respectively.A highly positive correlation between the extreme k value and tree height was observed,suggesting that the k value was an accurate estimation of tree height.For model parameters,the earliest average time point for the onset of the rapid growth period of poplar clones was 131 d,and the highest average increment in tree height during the rapid growth period was 138.78 cm.The highest average tree height for all clones under each factor was 219,210.51,200,and 201 cm when treated with either 1200 mL of water applied every third day,3 g of nitrogen,0 g of phosphorus,or 0 g of potassium,respectively.The most suitable treatment for the early growth of hybrid poplar cuttings,as suggested by the developed logistic model,was 1200 mL of water applied every third day and three applications of 1 g nitrogen(in the form of CH4N2O).
基金This work was fi nancially supported by the fundamental Research Funds for the Central Universities(2572020DR01)HeilongjiangTouyan Innovation team program(Tree Genetics and Breeding Innovation Team).
文摘This study aimed to explore and improve the different economic values of Pinus koraiensis(Siebold and Zucc.)by examining the variations in 6 growth traits and 9 physicochemical wood properties among 53 P.koraiensis half-sib families.Growth traits assessed included height,diameter at breast height,volume,degree of stem straight-ness,stem form,and branch number per node,while wood properties assessed included density,fiber length and width,fiber length to width ratio,and cellulose,hemicel-lulose,holocellulose,lignin,and ash contents.Except for degree of stem straightness and branch number per node,all other traits exhibited highly significant variations(P<0.01)among families.The coefficients of variation ranged from 5.3(stem form)to 66.7%(ash content),whereas,the herit-ability ranged from 0.136(degree of stem straightness)to 0.962(ash content).Significant correlations were observed among growth traits and wood physicochemical properties.Principal component analysis identified four distinct groups representing growth traits,wood chemical and physical properties,and stem form traits.Multi-trait comprehensive evaluation identified three groups of elite families based on breeding objectives,including rapid growth,improved timber production for building and furniture materials,and pulpwood production.These specific families should be used to establish new plantations.
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This work was supported by the National Natural Science Foundation of China[grant number 31472278]the National High Technology Research and Development Program of China(863 Program)[grant number 2012AA10A400-3]the Shanghai Universities Knowledge Service Platform[grant number ZF1206].
文摘We identified the FOXO gene and five single-nucleotide polymorphisms(SNPs)in its coding region in the Sanmen breeding population of the razor clam Sinonovacula constricta.The ScFOXO gene encodes a protein of 625 amino acids in length that contains a conserved DNA-binding domain.Real-time polymerase chain reaction analysis showed that ScFOXO mRNA is widely expressed in adult tissues,with higher expression in the siphons and gills.Of the SNPs,c.879G>C(Val293Val)and c.1725A>G(Ser575Ser)are synonymous mutations,and c.543C>T(Phe181Leu),c.848A>G(Tyr283Cys),and c.1625G>C(Gly542Phe)are non-synonymous mutations.The SNPs all show significant associations with total body weight,shell length,shell width,and shell height(SH)in this population.Polymorphic parameter analysis showed that all SNPs except c.848A>G(Tyr283Cys)exhibit complete linkage.The SNP c.1625G>C(Gly542Phe)was used for genetic linkage mapping and demonstrates the strongest linkage(logarithm of the odds[LOD]value:41.46)with the marker 96616(37.02 cM)in the linkage group 9.The LOD value of this marker in relation to growth traits ranges from 1.04 to 1.53;only markers with a LOD value3 were considered to be linked with growth traits in the razor clam linkage map.In summary,ScFOXO may be a growth trait-related gene and may represent a marker for Sanmen breeding group selection.
文摘Seedling stage is an important period for forestry.The aim of this study was to estimate the growth trend of six local precious species and consider their implications for silviculture on forestry.We assessed height,diameter near ground and crown width at 1,4,6 and 8-month.The variance analysis indicated that there were significant differences between species on all traits except diameter near ground and crown width at 8-month.There were no significant differences on height and crown width at all ages among replicates whereas there were significant differences on diameter near ground at 1 and 4 months,differences on diameter near ground at 6 months and no difference on diameter near ground at 8-month.The significant differences among interaction of species and replicates on diameter near ground at 1-months,4-month,6-month and crown width at 8-month were also found.Dalbergia odorifera had a higher growth period after 6-month.Aquilaria sinensis(Lour.)Spreng,Swietenia mahagoni(L.)Jacq.,Hopea hainanensis Merr.et Chun,Homalium hainanense Gagnep.and Cassia siamea Lam.had the same growth trend on all traits at the whole time.
基金the earmarked fund for China Agriculture Research System(CARS-35)the National Natural Science Foundation of China(31772556)the Key R&D Program of Guangdong Province,China(2018B020203002)。
文摘In modern pig breeding programs,growth and fatness are vital economic traits that significantly influence porcine production.To identify underlying variants and candidate genes associated with growth and fatness traits,a total of 1067 genotyped Duroc pigs with de-regressed estimated breeding values(DEBV)records were analyzed in a genome wide association study(GWAS)by using a single marker regression model.In total,28 potential single nucleotide polymorphisms(SNPs)were associated with these traits of interest.Moreover,VPS4 B,PHLPP1,and some other genes were highlighted as functionally plausible candidate genes that compose the underlying genetic architecture of porcine growth and fatness traits.Our findings contribute to a better understanding of the genetic architectures underlying swine growth and fatness traits that can be potentially used in pig breeding programs.
基金The Taishan Scholar Program for Seed Industry under contract No.ZR2014CQ001the National High Technology Research and Development Program of China under contract No.2012AA10A408-7
文摘Bayesian and restricted maximum likelihood(REML) approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462progenies(17 months old) from 28 families that were produced through artificial insemination using 39 parent fish. An animal model was applied to partition each weight value into a fixed effect, an additive genetic effect, and a residual effect. The average body weight of each family, which was measured at 110 days post-hatching, was considered as a covariate. For Bayesian analysis, heritability and breeding values were estimated using both the posterior mean and mode from the joint posterior conditional distribution. The results revealed that for additive genetic variance, the posterior mean estimate( δ_a^2=9 320) was highest but with the smallest residual variance,REML estimates( δ_a^2=8 088) came second and the posterior mode estimate( δ_a^2=7 849) was lowest. The corresponding three heritability estimates followed the same trend as additive genetic variance and they were all high. The Pearson correlations between each pair of the three estimates of breeding values were all high,particularly that between the posterior mean and REML estimates(0.996 9). These results reveal that the differences between Bayesian and REML methods in terms of estimation of heritability and breeding values were small. This study provides another feasible method of genetic parameter estimation in selective breeding programs of turbot.
基金Supported by the Innovation Platform for Academicians of Hainan Province(YSPTZX202103)Hainan Provincial Natural Science Foundation of China(321QN263)+3 种基金National Natural Science Foundation of China(32160861)the Major Science and Technology Plan of Hainan Province(ZDKJ2021017)State Key Laboratory of Developmental Biology of Freshwater Fish(2020KF001)Scientific Research Foundation of Hainan Tropical Ocean University(RHDRC202010)。
文摘[Objectives]This study aimed to investigate the sequence structure and function of Myostatin(MSTN)gene in the hybrid grouper(Epinephelus fuscoguttatus,♀×Epinephelus polyphekadion,♂).[Methods]Genetic DNA samples were extracted from the caudal fins of the hybrid grouper and its parents to amplify their MSTN genes.Then,MSTN gene sequences were analyzed using bioinformatics tools to predict their protein structures and functions.[Results]The hybrid grouper and its parents shared the same MSTN gene structure,consisting of three exons and two introns.Nucleotide sequence of the gene could be translated into 376 amino acids,including an N-terminal signal peptide,a proteolytic processing site(RXXR motif),and nine conserved cysteine residues at C-terminal,which were the typical features of transforming growth factor beta(TGF-β)superfamily proteins.Alignment of protein sequence showed that MSTN was highly conserved between the hybrid grouper and its parents.Especially,exon 3,an important functional domain,exhibited a sequence similarity of 100%among them.In addition,four variable amino acid residues were detected in exon 2 at positions 141,153,185 and 186 in the hybrid grouper,but they did not affect the secondary structure of the protein.[Conclusion]These results will provide molecular information for future investigation on the growth and heterosis of hybrid grouper species,and on the roles of MSTN gene in regulating the growth traits of the hybrid grouper.
基金supported by grants from the“3315”Innovative Team of Ningbo City,the Science and Technology Planning Project of Ningbo City(2021S009).
文摘Kumamoto oysters(Crassostrea sikamea)are important marine aquaculture shellfish because of their taste and round shell shape.Due to its small size,selective breeding is required to improve its market size,but there are no reports on traits suitable for direction selection and reproductive productivity of Kumamoto oysters of different ages.In this study,path analysis and one-way ANOVA were used to explore the influential indices of oyster body weight and fecundity.The results showed that shell height was the main factor affecting the body weight of Kumamoto oysters at one-year-old and two-year-old,followed by shell length.Body weight was the main factor influencing fecundity,and shell height showed a significant correlation with fecundity.Therefore,shell height should be considered the first parameter for selection when selecting Kumamoto oysters for body weight as the direct selection target.When one-year-old and two-year-old Kumamoto oysters were selected as parents from Xiangshan Bay,hatching parameters and growth parameters of F1 generation larvae were measured.The fecundity and egg diameters were 1.72×10^(6)and 46.60±3.62μm,respectively,which were significantly greater than one-aged oysters(5.86×10^(5),40.26±3.52μm).The hatching parameters(fertilized egg size,fertilization rate,and hatching rate)and larval growth performance(D-stage veliger and veliger)were similar and did not differ significantly(P>0.05),and after metamorphosis,there was also no significant difference in shell height size at 40 days of age(P>0.05).Therefore,there was no significant effect of age on reproduction,larval development,and the early growth of Kumamoto oysters.These results could provide a basis for parental sources and proper traits for Kumamoto oyster selection,which is beneficial to developing and utilizing this excellent germplasm resource.
基金This work was supported by Central Public-interest Scientific Institution Basal Research Fund,CAFS,China(NO.2016HY-ZD0201)Taishan Scholar Project Fund of Shandong of China.
文摘The aim of this study was to evaluate genetic parameters of growth traits for improving selective breeding in olive flounder(Paralichthys olivaceus).A total of 82 full-sib families from 2 year-classes with complete pedigree information were used to estimate heritabilities and genetic/phenotypic correlations for 4 growth performance traits(body weight BW,total length TL,body height BH and condition factor K)based on uni-trait and multi-trait linear mixed models,respectively.Data were analyzed by the restricted maximum likelihood(REML)method.The heritabilities of BW,TL and BH were 0.81,0.70 and 0.61,which are relatively high,however,heritability for K is low(0.11).For all growth traits,the common full-sib effects(c^(2))were at a low to moderate level(0.14–0.20);the maternal effects(m^(2))of the traits(except K)were also detected(0.15–0.19).The phenotypic and genetic correlations among BW,TL and BH were highly positive(0.70–0.91),however,the correlations between K and the other 3 traits was low or negligible(−0.22–0.26).According to our results,these traits(except K)could be selected and enhanced simultaneously.In addition,direct selection based on TL or BH,which is an easily measurable trait,will be more favorable than selection on BW.Moreover,our results indicated that growth parameters estimated in the juvenile stage could be used as a predictor of growth performance at later growth stages.
基金This work was partially financially supported by the National Natural Science Foundation of China(Grant No.32071905,No.32171895,No.61771224)the Priority Academic Program Development of Jiangsu Higher Education Institutions(Grant No.PAPD-2018-87).
文摘For important economic crops such as cucumbers,abiotic and biotic stress conditions have had an adverse effect.This study aimed to observe the effects of water stress and powdery mildew stress on cucumber plants.Biotic stress at two levels,B0(no powdery mildew stress)and B1(powdery mildew stress)with three fertigation requirement levels(T1:Full fertigation,T2:Moderate nutrient solution deficit,T3:Severe nutrient solution deficit).Therefore,set up six treatments of B0T1,B1T2,B0T3,B1T1,B1T2,and B1T3.Leaf gas-exchange parameter first decreases and then increases under B1T1,B1T2,and B1T2.The leaf gas exchange parameter was significantly decreased under B0T2 and B0T3.Compared to the control experiment(CK,B0T1:no disease infestation and full irrigation),the plant height of cucumber decreased by 7.55%,10.62%,15.28%,23.27%,and 35.16%,respectively,under B0T2,B0T3,B1T1,B1T2 and B1T3;the stem diameter of cucumber decreased by 9.46%,15.74%,5.47%,13.45%,and 23.72%,respectively,under B0T2,B0T3,B1T1,B1T2,and B1T3;the leaf area of cucumber decreased by 13.76%,29.96%,13.43%,38.21%,and 66.83%,respectively,under B0T2,B0T3,B1T1,B1T2,and B1T3.The root-shoot ratio of cucumber was 3.92%,3.13%,3.63%,3.84%,4.41%,and 3.82%,respectively,under the B0T1,B0T2,B0T3,B1T1,B1T2,and B1T3.Therefore,this study can provide a basis for the research on greenhouse environmental control and cucumber cultivation management.
基金the Project of Shanghai Engineering and Technology Center for Promoting Ability(19DZ2284300)the Earmarked Fund for the China Agriculture Research System(CARS-45-03)。
文摘Grass carp has the highest production yield among all the farmed fish species around the world.But the molecular and genetic basis of growth traits is inadequately understood in this fish.In the present study,we apply whole-transcriptome sequencing to identify genes whose expression is different between fast and slow growing grass carp.We identified 1178 differentially expressed genes(DEGs),among which 270 were upregulated in the fast growing group and 908 upregulated in the slow growing group.The GO enrichment analysis revealed that DEGs was significantly enriched in protein synthesis and export machinery,cell division and development and metabolism,suggesting that cell division and metabolism may play key roles in development processes of fish.KEGG pathway analysis showed that MAPK signaling pathway may play a prominent role in growth difference.In addition,the majority of genes in immune responses related pathway were upregulated in the slow growing individuals.These results provide some valuable resources for understanding the molecular mechanisms of growth traits in fish.
文摘Soil salinity diminishes soil health and reduces crop yield,which is becoming a major global concern.Salinity stress is one of the primary stresses,leading to several other secondary stresses that restrict plant growth and soil fertility.The major secondary stresses induced in plants under saline-alkaline conditions include osmotic stress,nutrient limitation,and ionic stress,all of which negatively impact overall plant growth.Under stressed conditions,certain beneficial soil microflora are known to have evolved phytostimulating mechanisms,such as the synthesis of osmoprotectants,siderophores,1-aminocyclopropane-1-carboxylic acid(ACC)deaminase activity,phosphate solubilization,and hormone production,which enhance plant growth and development while mitigating nutrient stress.Beneficial soil-borne bacterial species such as Bacillus,Pseudomonas,and Klebsiella and fungal strains such as Trichoderma,Aspergillus,Penicillium,Alternaria,and Fusarium also aid in reducing salinity stress.Phosphate-solubilizing microorganisms also assist in nutrient acquisition via both enzymatic and non-enzymatic processes.In the case of enzymatic processes,they produce different enzymes such as alkaline phosphatases and phytases,whereas non-enzymatic processes produce organic acids such as gluconic,citric,malic,and oxalic acids.The native halotolerant/halophilic soil microbial gene pool with multifunctional traits and stress-induced gene expression can be developed as suitable bio-inoculants to enhance stress tolerance and optimize plant growth in saline soils.
