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
120 pearl oysters （Pinctada martensii） were randomly sampled from F1 population, and shell length, shell width, shell height, shell weight and total weight of each sample were measured. Correlation and path analysis...120 pearl oysters （Pinctada martensii） were randomly sampled from F1 population, and shell length, shell width, shell height, shell weight and total weight of each sample were measured. Correlation and path analysis were conducted on the basis of measurement data. The results showed that shell length, shell width, shell height, shell weight and total weight were significantly correlated （P 〈 0.05）. Total weight was significantly and positively correlated with shell weight （r = 0.8970）, shell height （r = 0.6974）, shell width （r = 0.6521） and shell length （r = 0.5486）. Shell weight, shell height, shell width and shell length had positive and direct effects on total wet weight, with the values of 0.6356, 0.1872, 0.1814 and 0.0599, respectively. The results indicated that growth traits （shell length, shell width, shell height, shell weight and total wet weigh） of the F1 population could be improved by direct or indirect selection.展开更多
[Objective] The aim was to estimate the heritability and genetic correlations of growth traits of Chinese shrimp Fenneropenaeus chinensis so as to provide basis and technical parameters for the breeding and selecting ...[Objective] The aim was to estimate the heritability and genetic correlations of growth traits of Chinese shrimp Fenneropenaeus chinensis so as to provide basis and technical parameters for the breeding and selecting of Chinese shrimp.[Method] 51 full-sib families（including 35 half-sib families）of the Chinese shrimp F.chinensis were obtained by artificial insemination.Four growth traits of these families were measured,including body length,cephalothorax length,abdorminal segment length and body weight.According to quantitative genetics theory,the heritability of each growth trait,genetic and phenotypic correlation among these traits was statistically studied.[Result] The heritability was 0.36-0.51 for body length,0.14-0.24 for cephalothorax length,0.25-0.50 for abdominal segment length,and 0.04-0.29 for body weight.High and positive genetic correlations were obtained among growth traits.The genetic correlation between body weight and abdominal segment length was the highest（0.92）,followed by body length and abdominal segment length（0.91）,body length and body weight（0.88）,body weight and cephalothorax length（0.87）,abdominal segment length and cephalothorax length（0.86）,while the genetic correlation between body length and cephalothorax length was the lowest（0.83）.[Conclusion] The phenotypic correlation of body length,cephalothorax length,abdorminal segment length and body weight of Chinese shrimp F.chinensis were from 0.80 to 0.90 with extremely significant difference（P0.01）among the four growth traits by t-test.展开更多
[Objective] This study aimed to investigate the variation in growth traits of Cupressus funebris in Chongqing Municipality, thus laying the foundation for further breeding and improvement of fine varieties. [Method] G...[Objective] This study aimed to investigate the variation in growth traits of Cupressus funebris in Chongqing Municipality, thus laying the foundation for further breeding and improvement of fine varieties. [Method] Growth traits of three fine stands of C. funebris in Qijiang, Pengshui and Youyang of Chongqing Municipality were investigated. [Result] The results showed that C. funebris stand in Pengshui exhibited the best growth performance, followed by C. funebris stand in Qijiang; C. funebris stand in Youyang exhibited the poorest growth performance. The average volume growth of C. funebris in Pengshui, Qijiang and Youyang was 0.14, 0.11 and 0.06 m^3, respectively. Among different stands, variation coefficients of major growth traits were above 11.31%, and the maximum variation coefficient of the volume was 39.11%; within the stands, variation coefficients of plant height were basically the same （about 20%）. The variation coefficient of diameter at breast height in Qijiang reached the maximum of 42.42%, followed by that in Youyang. The variation coeffi- cients of volume and diameter at breast height were consistent; seed bearing coefficient （SBC） of C. funebris stand in Pengshui exhibited the maximum variation, which indicated that C. funebris stand in Pengshui was conducive to establishing seed stands and constructing seed orchard by using the selected stands. [Conclusion] It is necessary to conduct provenance selection.展开更多
Heritability and genetic and phenotypic correlations were estimated for juvenile growth traits of Pacific abalone Haliotis discus hannai Ino. The estimates were calculated from shell length and shell width measurement...Heritability and genetic and phenotypic correlations were estimated for juvenile growth traits of Pacific abalone Haliotis discus hannai Ino. The estimates were calculated from shell length and shell width measurements on progeny resulting from 12 half-sib families and 36 full-sib families obtained using artificial fertilization of mating three females to each male. The measurements were taken at 10, 20 and 30 d after fertilization. It was found that heritability estimates based on sire component ranged from 0.23 to 0.36 for shell length and 0.21 to 0.32 for shell width. Heritability estimates from dam component were larger than those from sire component at three ages, indicating presence of maternal effects, non-additive genetic effects and common environmental effects. Phenotypic correlations were significant at three ages （P 〈 0.05）, with values of 0.92, 0.93 and 0.92, respectively. Genetic correlations from the paternal half-sib correlation analysis were highly positive at three ages, with values of 0.50, 0.78 and 0.81, respectively. The results suggest that selective breeding is an effective approach to improving growth traits of Pacific abalone stocks.展开更多
The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron re...The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.展开更多
We estimated the reproductive success of adult brood fish and the heritability of growthrelated traits for large yellow croaker （Larimichthys crocea）. We created two independent full-factorial cross groups （1 and 2...We estimated the reproductive success of adult brood fish and the heritability of growthrelated traits for large yellow croaker （Larimichthys crocea）. We created two independent full-factorial cross groups （1 and 2） by crossing 4 malesx4 females and 4 males^3 females, respectively. We measured the body weight （BW）, body length （BL）, and body height （BH） of 281 individuals from group 1 and 318 individuals from group 2 at 20 months post hatch （harvest age）. We also collected a tissue sample from each individual. The parents and offspring were genotyped using six polymorphic mierosatellites. Of the 599 offspring, 99.2% were assigned to a single pair of parents. In both groups, some parent pairs produced a large number of offsprings while other pairs did not produce any offspring. The genetic diversity and putative No were lower in the offsprings than in the parents in both groups. The heritability estimates at 20-month age were 0.13±0.10 for BW, 0.19±0.13 for BL, and 0.09±0.06 for BH. The genetic and phenotype correlation between BW, BL, and BH was close to 1. The results provide basic information for selective breeding and further genetic characterization of large yellow croaker.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
Genomic selection(GS)can be used to accelerate genetic improvement by shortening the selection interval.The successful application of GS depends largely on the accuracy of the prediction of genomic estimated breeding ...Genomic selection(GS)can be used to accelerate genetic improvement by shortening the selection interval.The successful application of GS depends largely on the accuracy of the prediction of genomic estimated breeding value(GEBV).This study is a fi rst attempt to understand the practicality of GS in Litopenaeus vannamei and aims to evaluate models for GS on growth traits.The performance of GS models in L.vannamei was evaluated in a population consisting of 205 individuals,which were genotyped for 6 359 single nucleotide polymorphism(SNP)markers by specifi c length amplifi ed fragment sequencing(SLAF-seq)and phenotyped for body length and body weight.Three GS models(RR-BLUP,Bayes A,and Bayesian LASSO)were used to obtain the GEBV,and their predictive ability was assessed by the reliability of the GEBV and the bias of the predicted phenotypes.The mean reliability of the GEBVs for body length and body weight predicted by the dif ferent models was 0.296 and 0.411,respectively.For each trait,the performances of the three models were very similar to each other with respect to predictability.The regression coeffi cients estimated by the three models were close to one,suggesting near to zero bias for the predictions.Therefore,when GS was applied in a L.vannamei population for the studied scenarios,all three models appeared practicable.Further analyses suggested that improved estimation of the genomic prediction could be realized by increasing the size of the training population as well as the density of SNPs.展开更多
Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservati...Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservative regulator of muscle growth,and has become one of the most important target genes for genetic improvement of the production of farmed animals.In this study,four single nucleotide polymorphisms(SNPs) were identified in the 5' flanking region of MSTN gene(Cf MSTN) in Zhikong scallop(Chlamys farreri).The association of these SNPs with scallop growth traits,including shell length,shell height,body weight and striated muscle weight was analyzed.The SNP g-1162G>T was found to associate with shell length,shell height,and striated muscle weight.The TT type scallops showed significantly higher trait values than those of GT type,and the GG type individuals exhibited median values.On the contrary,significantly more Cf MSTN transcripts were detected in the striated muscle of GT type scallops than in those of TT and GG type ones.Our results suggested that Cf MSTN might regulate the scallop muscle growth negatively,and SNP g-1162G>T can be used as a candidate marker for the selective breeding of high-yielding scallop.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 fo...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
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 2 462 pro...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 2 462 progenies （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 （σa^2 =9 320） was highest but with the smallest residual variance, REML estimates （σa^28 088） came second and the posterior mode estimate （σa^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
Myostatin （MSTN） is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1 （M...Myostatin （MSTN） is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1 （MSTN-1） in two commercial hatchery populations of Ancherythroculter nigrocauda, an economically important freshwater fish, were screened for single nucleotide polymorphisms （SNPs） and then genotyped by direct sequencing of PCR products. Five SNPs were identified in intron 1 and exon 2, including a non-synonymous mutation causing an amino acid change （Val to Ile） at position 180. Association analyses based on 300 individuals revealed that the g. 1129T〉C SNP locus was significantly associated with total length （TL）, body length （BL）, body height （BH） and body weight （BW） in 6- and 18-month-old populations, while the g. 1289G〉A locus was significantly associated with BH and BW in the 6-month-old population. Haplotype analyses revealed that fish with the genotype combinations TC/TC or TC/GA showed better growth performance. Our results suggest that g.l129T〉C and g.1289G〉A have positive effects on growth traits and may be candidate gene markers for marker-assisted selection in A. nigrocauda.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 establish a rapid, accurate and economical real-time PCR assay system based on TaqMan probe technology for the detection of genetic variations of single nucleotide polymorphisms （SNPs） in myestatin （MSTN） gene,...To establish a rapid, accurate and economical real-time PCR assay system based on TaqMan probe technology for the detection of genetic variations of single nucleotide polymorphisms （SNPs） in myestatin （MSTN） gene, a pair of TaqMan probes were designed on the polymorphism loci of MSTN gene and used in PCR reaction system for SNP genotyping. Meanwhile, an association study was performed between MSTN genotypes and growth traits of Tan sheep, including birth weight, weaning weight, 3-month weight, and 6-month weight. The results showed that rs417816017 locus of MSTN gene in Tan sheep had two genotypes ： YY and XY. The individuals with genotype XY had a growth advantage over the ones with genotype YY. The results indicate that TaqMan probe-based real-time PCR assay can be used to detect the genotype of MSTN gene, which will provide candidate genes for breeding of Tan sheep.展开更多
This study was to investigate the expression pattern of IGF-I gene and correlation between its SNPs and growth traits in sheep.The expression patterns of IGF-I gene in brain,muscle,skin,liver and heart of Liangshan se...This study was to investigate the expression pattern of IGF-I gene and correlation between its SNPs and growth traits in sheep.The expression patterns of IGF-I gene in brain,muscle,skin,liver and heart of Liangshan semi-wool sheep were detected at six growth stages（15,60,105,195,240 days） by employing qRT-PCR approach,and the correlation between SNPs of IGF-I gene and growth traits via SSCP method.The first inflection point of IGF-I gene expression was observed at day 105 in all five tissues.From 15-105 days IGF-I gene gave a decline-ascending trend in muscle,brain and liver,while it did not vary significantly during day 15-day 60 and was up-regulated in heart and liver at day 105.Whenafter,the expression level was down-regulated in liver,while that in muscle,heart,brain and skin assumed the second inflection point.The expression levels of IGF-I gene in brain and skin at day 195 were significantly higher than that at day 150 and day 240.These suggest the synchronous expression of IGF-I gene in all five tissues.Two SNPs located at the leader region and exon 3 of IGF-I gene were middle or low polymorphic.The SNP locus detected with primer P-1 was significantly correlated with birth weight of Liangshan semi-wool sheep（P 〈0.05）,while that detected with primer P-2 was significantly correlated with weaning weight and the weaning daily gain（P 〈 0.05）.The expression of IGF-I in all tissues had the similar developmental patterns,and strong correlation of the SNPs of IGF-I gene was confirmed with the eary growth traits to provide theoretical basis for the growth regulation and applying to assisted selective breeding with the SNPs in liangshan semi-wool sheep.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
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grants of the Guangdong Marine and Fishery Bureau(No.B02068)Guangdong Ocean University(No.E06031).
文摘120 pearl oysters （Pinctada martensii） were randomly sampled from F1 population, and shell length, shell width, shell height, shell weight and total weight of each sample were measured. Correlation and path analysis were conducted on the basis of measurement data. The results showed that shell length, shell width, shell height, shell weight and total weight were significantly correlated （P 〈 0.05）. Total weight was significantly and positively correlated with shell weight （r = 0.8970）, shell height （r = 0.6974）, shell width （r = 0.6521） and shell length （r = 0.5486）. Shell weight, shell height, shell width and shell length had positive and direct effects on total wet weight, with the values of 0.6356, 0.1872, 0.1814 and 0.0599, respectively. The results indicated that growth traits （shell length, shell width, shell height, shell weight and total wet weigh） of the F1 population could be improved by direct or indirect selection.
基金Supported by National Natural Science Foundation of China(40706052)China Agriculture Research System(CARS-47)~~
文摘[Objective] The aim was to estimate the heritability and genetic correlations of growth traits of Chinese shrimp Fenneropenaeus chinensis so as to provide basis and technical parameters for the breeding and selecting of Chinese shrimp.[Method] 51 full-sib families（including 35 half-sib families）of the Chinese shrimp F.chinensis were obtained by artificial insemination.Four growth traits of these families were measured,including body length,cephalothorax length,abdorminal segment length and body weight.According to quantitative genetics theory,the heritability of each growth trait,genetic and phenotypic correlation among these traits was statistically studied.[Result] The heritability was 0.36-0.51 for body length,0.14-0.24 for cephalothorax length,0.25-0.50 for abdominal segment length,and 0.04-0.29 for body weight.High and positive genetic correlations were obtained among growth traits.The genetic correlation between body weight and abdominal segment length was the highest（0.92）,followed by body length and abdominal segment length（0.91）,body length and body weight（0.88）,body weight and cephalothorax length（0.87）,abdominal segment length and cephalothorax length（0.86）,while the genetic correlation between body length and cephalothorax length was the lowest（0.83）.[Conclusion] The phenotypic correlation of body length,cephalothorax length,abdorminal segment length and body weight of Chinese shrimp F.chinensis were from 0.80 to 0.90 with extremely significant difference（P0.01）among the four growth traits by t-test.
文摘[Objective] This study aimed to investigate the variation in growth traits of Cupressus funebris in Chongqing Municipality, thus laying the foundation for further breeding and improvement of fine varieties. [Method] Growth traits of three fine stands of C. funebris in Qijiang, Pengshui and Youyang of Chongqing Municipality were investigated. [Result] The results showed that C. funebris stand in Pengshui exhibited the best growth performance, followed by C. funebris stand in Qijiang; C. funebris stand in Youyang exhibited the poorest growth performance. The average volume growth of C. funebris in Pengshui, Qijiang and Youyang was 0.14, 0.11 and 0.06 m^3, respectively. Among different stands, variation coefficients of major growth traits were above 11.31%, and the maximum variation coefficient of the volume was 39.11%; within the stands, variation coefficients of plant height were basically the same （about 20%）. The variation coefficient of diameter at breast height in Qijiang reached the maximum of 42.42%, followed by that in Youyang. The variation coeffi- cients of volume and diameter at breast height were consistent; seed bearing coefficient （SBC） of C. funebris stand in Pengshui exhibited the maximum variation, which indicated that C. funebris stand in Pengshui was conducive to establishing seed stands and constructing seed orchard by using the selected stands. [Conclusion] It is necessary to conduct provenance selection.
基金The study was supported by the National High Technology Development Project of China under contract No.2006AA10A407the National Natural Science Foundation of China under contract No.30371117.
文摘Heritability and genetic and phenotypic correlations were estimated for juvenile growth traits of Pacific abalone Haliotis discus hannai Ino. The estimates were calculated from shell length and shell width measurements on progeny resulting from 12 half-sib families and 36 full-sib families obtained using artificial fertilization of mating three females to each male. The measurements were taken at 10, 20 and 30 d after fertilization. It was found that heritability estimates based on sire component ranged from 0.23 to 0.36 for shell length and 0.21 to 0.32 for shell width. Heritability estimates from dam component were larger than those from sire component at three ages, indicating presence of maternal effects, non-additive genetic effects and common environmental effects. Phenotypic correlations were significant at three ages （P 〈 0.05）, with values of 0.92, 0.93 and 0.92, respectively. Genetic correlations from the paternal half-sib correlation analysis were highly positive at three ages, with values of 0.50, 0.78 and 0.81, respectively. The results suggest that selective breeding is an effective approach to improving growth traits of Pacific abalone stocks.
基金Supported by the National Basic Research Program of China(973Program)(No.2010CB126304)the Special Fund for Agro-scientific Research in the Public Interest(No.200903046)the Project from the Ministry of Science and Technology of China(No.2006DKA30470017)
文摘The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.
基金Supported by the Special Fund for Agro-Scientific Research in the Public Interest (No. 200903029-4)Key Project of Science and Technology Department of Fujian Province (No. 2010N0021)the Foundation for Young Professors of Jimei University (No. 2009C002)
文摘We estimated the reproductive success of adult brood fish and the heritability of growthrelated traits for large yellow croaker （Larimichthys crocea）. We created two independent full-factorial cross groups （1 and 2） by crossing 4 malesx4 females and 4 males^3 females, respectively. We measured the body weight （BW）, body length （BL）, and body height （BH） of 281 individuals from group 1 and 318 individuals from group 2 at 20 months post hatch （harvest age）. We also collected a tissue sample from each individual. The parents and offspring were genotyped using six polymorphic mierosatellites. Of the 599 offspring, 99.2% were assigned to a single pair of parents. In both groups, some parent pairs produced a large number of offsprings while other pairs did not produce any offspring. The genetic diversity and putative No were lower in the offsprings than in the parents in both groups. The heritability estimates at 20-month age were 0.13±0.10 for BW, 0.19±0.13 for BL, and 0.09±0.06 for BH. The genetic and phenotype correlation between BW, BL, and BH was close to 1. The results provide basic information for selective breeding and further genetic characterization of large yellow croaker.
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Supported by the National High Technology Research and Development Program of China(863 Program)(No.2012AA10A404)the National Natural Science Foundation of China(No.31502161)Financially Supported by Qingdao National Laboratory for Marine Science and Technology(No.2015ASKJ02)
文摘Genomic selection(GS)can be used to accelerate genetic improvement by shortening the selection interval.The successful application of GS depends largely on the accuracy of the prediction of genomic estimated breeding value(GEBV).This study is a fi rst attempt to understand the practicality of GS in Litopenaeus vannamei and aims to evaluate models for GS on growth traits.The performance of GS models in L.vannamei was evaluated in a population consisting of 205 individuals,which were genotyped for 6 359 single nucleotide polymorphism(SNP)markers by specifi c length amplifi ed fragment sequencing(SLAF-seq)and phenotyped for body length and body weight.Three GS models(RR-BLUP,Bayes A,and Bayesian LASSO)were used to obtain the GEBV,and their predictive ability was assessed by the reliability of the GEBV and the bias of the predicted phenotypes.The mean reliability of the GEBVs for body length and body weight predicted by the dif ferent models was 0.296 and 0.411,respectively.For each trait,the performances of the three models were very similar to each other with respect to predictability.The regression coeffi cients estimated by the three models were close to one,suggesting near to zero bias for the predictions.Therefore,when GS was applied in a L.vannamei population for the studied scenarios,all three models appeared practicable.Further analyses suggested that improved estimation of the genomic prediction could be realized by increasing the size of the training population as well as the density of SNPs.
基金supported by the National High-Tech R&D Program (863 Program,2012AA10A402)Doctoral Fund of Ministry of Education of China (20120132130 002)the National Key Technology R&D Program of China (2011BAD13B06)
文摘Scallop is a popular sea food and an important aquaculture shellfish.Identification of genes and genetic variants relating to scallop growth could benefit high-yielding scallop breeding.Myostatin(MSTN) is a conservative regulator of muscle growth,and has become one of the most important target genes for genetic improvement of the production of farmed animals.In this study,four single nucleotide polymorphisms(SNPs) were identified in the 5' flanking region of MSTN gene(Cf MSTN) in Zhikong scallop(Chlamys farreri).The association of these SNPs with scallop growth traits,including shell length,shell height,body weight and striated muscle weight was analyzed.The SNP g-1162G>T was found to associate with shell length,shell height,and striated muscle weight.The TT type scallops showed significantly higher trait values than those of GT type,and the GG type individuals exhibited median values.On the contrary,significantly more Cf MSTN transcripts were detected in the striated muscle of GT type scallops than in those of TT and GG type ones.Our results suggested that Cf MSTN might regulate the scallop muscle growth negatively,and SNP g-1162G>T can be used as a candidate marker for the selective breeding of high-yielding scallop.
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 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 2 462 progenies （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 （σa^2 =9 320） was highest but with the smallest residual variance, REML estimates （σa^28 088） came second and the posterior mode estimate （σa^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 National Science Foundation for Young Scientists of China(No.31402296)the National Science Foundation for Post-Doctoral Scientists of China(No.2014M562077)the Wuhan Chenguang Project for Young Scholars(No.201372304010832)
文摘Myostatin （MSTN） is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1 （MSTN-1） in two commercial hatchery populations of Ancherythroculter nigrocauda, an economically important freshwater fish, were screened for single nucleotide polymorphisms （SNPs） and then genotyped by direct sequencing of PCR products. Five SNPs were identified in intron 1 and exon 2, including a non-synonymous mutation causing an amino acid change （Val to Ile） at position 180. Association analyses based on 300 individuals revealed that the g. 1129T〉C SNP locus was significantly associated with total length （TL）, body length （BL）, body height （BH） and body weight （BW） in 6- and 18-month-old populations, while the g. 1289G〉A locus was significantly associated with BH and BW in the 6-month-old population. Haplotype analyses revealed that fish with the genotype combinations TC/TC or TC/GA showed better growth performance. Our results suggest that g.l129T〉C and g.1289G〉A have positive effects on growth traits and may be candidate gene markers for marker-assisted selection in A. nigrocauda.
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Supported by Special Fund for Science and Technology Development of Ningxia Hui Autonomous Region(2012ZDN1001)Domestic Animal Germplasm Resources Sharing Platform Project(2005DKA21101)
文摘To establish a rapid, accurate and economical real-time PCR assay system based on TaqMan probe technology for the detection of genetic variations of single nucleotide polymorphisms （SNPs） in myestatin （MSTN） gene, a pair of TaqMan probes were designed on the polymorphism loci of MSTN gene and used in PCR reaction system for SNP genotyping. Meanwhile, an association study was performed between MSTN genotypes and growth traits of Tan sheep, including birth weight, weaning weight, 3-month weight, and 6-month weight. The results showed that rs417816017 locus of MSTN gene in Tan sheep had two genotypes ： YY and XY. The individuals with genotype XY had a growth advantage over the ones with genotype YY. The results indicate that TaqMan probe-based real-time PCR assay can be used to detect the genotype of MSTN gene, which will provide candidate genes for breeding of Tan sheep.
基金Supported by Genetic Diversity and Phylogenetic Analysis of Tibetan Sheep(2012JY0126)
文摘This study was to investigate the expression pattern of IGF-I gene and correlation between its SNPs and growth traits in sheep.The expression patterns of IGF-I gene in brain,muscle,skin,liver and heart of Liangshan semi-wool sheep were detected at six growth stages（15,60,105,195,240 days） by employing qRT-PCR approach,and the correlation between SNPs of IGF-I gene and growth traits via SSCP method.The first inflection point of IGF-I gene expression was observed at day 105 in all five tissues.From 15-105 days IGF-I gene gave a decline-ascending trend in muscle,brain and liver,while it did not vary significantly during day 15-day 60 and was up-regulated in heart and liver at day 105.Whenafter,the expression level was down-regulated in liver,while that in muscle,heart,brain and skin assumed the second inflection point.The expression levels of IGF-I gene in brain and skin at day 195 were significantly higher than that at day 150 and day 240.These suggest the synchronous expression of IGF-I gene in all five tissues.Two SNPs located at the leader region and exon 3 of IGF-I gene were middle or low polymorphic.The SNP locus detected with primer P-1 was significantly correlated with birth weight of Liangshan semi-wool sheep（P 〈0.05）,while that detected with primer P-2 was significantly correlated with weaning weight and the weaning daily gain（P 〈 0.05）.The expression of IGF-I in all tissues had the similar developmental patterns,and strong correlation of the SNPs of IGF-I gene was confirmed with the eary growth traits to provide theoretical basis for the growth regulation and applying to assisted selective breeding with the SNPs in liangshan semi-wool sheep.
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.
