Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

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.

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

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.

Correlation and Path Analysis for Growth Traits in F_1 Population of Pearl Oyster Pinctada martensii

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.

Estimates of Heritability and Genetic Correlations for Growth Traits in Chinese Shrimp Fenneropenaeus chinensis

[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.

Study on the Variation in Growth Traits of Cupressus funebris

[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.

Genetic parameter estimates for growth traits at early stage of Pacific abalone,Haliotis discus hannai Ino

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.

Predictive ability of genomic selection models for breeding value estimation on growth traits of Pacific white shrimp Litopenaeus vannamei

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.

Effects of different nitrogen forms and concentrations on seedling growth traits and physiological characteristics of Populus simonii × P. nigra

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.

Relationship Between Combined Genotypes of UCP Gene and Growth Traits in Chickens

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

Polymorphisms in the Myostatin-1 gene and their association with growth traits in Ancherythroculter nigrocauda

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.

G×E Analysis of Growth Traits of Betula platyphylla Clones at Three Separated Sites in Northeastern China

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.

Expression Pattern of IGF-I Gene and Correlation between Its SNPs and Growth Traits in Sheep

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.

Single nucleotide polymorphisms in intron 1 and intron 2 of Larimichthys crocea growth hormone gene are correlated with growth traits

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.

Estimated reproductive success of brooders and heritability of growth traits for large yellow croaker (Larimichthys crocea) using microsatellites

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.

Variation analysis of growth traits of four poplar clones under different water and fertilizer management

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).

Association of myostatin Variants with Growth Traits of Zhikong Scallop(Chlamys farreri)

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.

Variations in growth traits and wood physicochemical properties among Pinus koraiensis families in Northeast China

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.

SNP Genotyping of Myostatin (MSTN) Gene through Taq Man Probe Assay and Association Study between MSTN Genotypes and Growth Traits of Tan Sheep

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.

Genetic parameter evaluation for growth and cold resistance traits of the giant freshwater prawn Macrobrachium rosenbergii

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.

Polymorphisms of the IGF1 gene and their association with growth traits, serum concentration and expression rate of IGF1 and IGF1R in buffalo

The insulin-like growth factor 1（IGF1） gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffalo IGF1 and found two novel single nucleotide polymorphisms（SNPs）, G64 A and G280A, in the noncoding sequences of exon 1 and exon 4, respectively. Statistical analysis of different genotypes showed that the individuals with GG genotypes had significantly（P〈0.05） higher body weight（BW） and average daily gain（ADG） than those with other genotypes at ages of 3–6 months in G64A SNP and 6–9 months in G280A SNP. The combined genotypes of these two SNPs produced three haplotypes, GG/GG, AG/AG, and AA/AA, which were significantly associated（P〈0.0001） with BW and ADG at an age from 3 to 12 months. Buffaloes with the homozygous GG/GG haplotype showed higher growth performance than other buffaloes. The two SNPs were correlated with m RNA levels of IGF1 and IGF1 receptor（IGF1 R） in semitendinosus muscle as well as with the serum concentration level of IGF1. Also, buffaloes with GG/GG haplotype showed higher m RNA and serum concentration levels. The data revealed that these two SNPs could be valuable genetic markers for selection of Egyptian buffaloes for better performance in the population.