scholarly journals Identification and Expression Characterization of the Smad3 Gene and SNPs Associated with Growth Traits in the Hard Clam (Meretrix meretrix)

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 83
Author(s):  
Lulu Fu ◽  
Qiudie Chi ◽  
Yongbo Bao ◽  
Hanhan Yao ◽  
Zhihua Lin ◽  
...  
Keyword(s):  
Growth And Development ◽  
Time Course ◽  
Growth Traits ◽  
Expression Profiles ◽  
Promoter Sequence ◽  
Expression Level ◽  
Hard Clam ◽  
Meretrix Meretrix ◽  
Nucleotide Polymorphisms ◽  
Expression Characterization

It has been demonstrated that the sekelsky mothers against decapentaplegic homolog 3 (Smad3) plays an important role in the growth and development of vertebrates. However, little is known about the association between the Smad3 gene and the growth traits of mollusks. In this study, Smad3 from the hard clam Meretrix meretrix (Mm-Smad3) was cloned, characterized, and screened for growth-related single nucleotide polymorphisms (SNPs) in its exons. The full-length cDNA of Mm-Smad3 was 1938 bp, encoding a protein with 428 amino acid residues. The protein sequence included an MH1 (27–135 aa) and MH2 domain (233–404 aa). Promoter analysis showed that the promoter sequence of Mm-Smad3 was 2548 bp, and the binding sites of Pit-1a, Antp, Hb, and other transcription factors are related to the growth and development of hard clams. The phylogenetic tree was divided into two major clusters, including mollusks and vertebrate. The expression level of Mm-Smad3 was predominantly detected in the mantle and foot, while extremely less expression was observed in the digestive gland. The low expression level of Mm-Smad3 was detected at the stages of unfertilized mature eggs, fertilized eggs, four-cell embryos, blastula, gastrulae, trochophore, and D-shaped larvae, whereas an opposite trend was observed regarding the highest expression at the umbo larvae stage (p < 0.05). In the mantle repair experiment, the time-course expression profiles showed that compared to the expression level at 0 h, Mm-Smad3 significantly decreased at 6 h (p < 0.05) but increased at 12 and 48 h. Further, the association analysis identified 11 SNPs in the exons of Mm-Smad3, of which three loci (c.597 C > T, c.660 C > T, c.792 A > T) were significantly related to the growth traits of clam (p < 0.05). Overall, our findings indicated that Mm-Smad3 is a growth-related gene and the detected SNP sites provide growth-related markers for molecular marker-assisted breeding of this species.

scholarly journals Function of the Porcine TRPC1 Gene in Myogenesis and Muscle Growth

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 147
Author(s):  
Yu Fu ◽  
Peng Shang ◽  
Bo Zhang ◽  
Xiaolong Tian ◽  
Ruixue Nie ◽  
...  
Keyword(s):  
Transient Receptor Potential ◽  
Growth Traits ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Receptor Potential ◽  
Transient Receptor Potential Channel ◽  
Nucleotide Polymorphisms ◽  
Pig Breeds ◽  
Muscle Tissues ◽  
Transient Receptor

In animals, muscle growth is a quantitative trait controlled by multiple genes. Previously, we showed that the transient receptor potential channel 1 (TRPC1) gene was differentially expressed in muscle tissues between pig breeds with divergent growth traits base on RNA-seq. Here, we characterized TRPC1 expression profiles in different tissues and pig breeds and showed that TRPC1 was highly expressed in the muscle. We found two single nucleotide polymorphisms (SNPs) (C-1763T and C-1604T) in TRPC1 that could affect the promoter region activity and regulate pig growth rate. Functionally, we used RNAi and overexpression to illustrate that TRPC1 promotes myoblast proliferation, migration, differentiation, fusion, and muscle hypertrophy while inhibiting muscle degradation. These processes may be mediated by the activation of Wnt signaling pathways. Altogether, our results revealed that TRPC1 might promote muscle growth and development and plays a key role in Wnt-mediated myogenesis.

Mining single nucleotide polymorphisms from EST data of hard clam Meretrix meretrix

2010 ◽  
Vol 2 (S1) ◽  
pp. 69-72 ◽  
Author(s):  
Hongjun Li ◽  
Dan Zhu ◽  
Xianggang Gao ◽  
Yun-feng Li ◽  
Jian Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Hard Clam ◽  
Meretrix Meretrix ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Association of IGF1R Polymorphisms with Growth Traits and its Expression Profiles in Different Pig Breeds

2020 ◽  
Author(s):  
Ying Bai ◽  
Xin Zhang ◽  
Qingyang Zhang ◽  
Yufang Liu ◽  
Xinxing Dong
Keyword(s):  
Growth Factor ◽  
Growth Traits ◽  
Expression Profiles ◽  
Average Daily Gain ◽  
Kinase Domain ◽  
Tyrosine Kinase Domain ◽  
Growth Stages ◽  
Insulin Like Growth Factor ◽  
Nucleotide Polymorphisms ◽  
Pig Breeds

Insulin-like growth factor 1 receptor (IGF1R) is one component of insulin-like growth factor system, which has biological functions of growth traits. The aim of this study is to investigate the entire exons of IGF1R in the three commercial pig breeds, Duroc, Yorkshire and Landrace, to identify novel single nucleotide polymorphisms and their correlation with growth traits. One novel SNP (c.3678C>T) in the exon 20 was detected. This SNP caused the change of amino acid (Ser1217Phe), a portion of cytoplasmic tyrosine kinase domain of IGF1R. At the c.3678C>T site, three genotypes were significantly associated with average daily gain at different growth stage in Yorkshire and Landrace breeds. Meanwhile, we identified the differently expressed pattern of IGF1R in muscle of Yorkshire and Jinhua pigs at different growth stages. Our results provide useful information on understanding the effect of porcine IGF1R gene on growth. The novel IGF1R polymorphism may be useful as molecular markers in pig selection but future studies are required.

scholarly journals Expression profiles and polymorphic identification of the <i>ACSL1</i> gene and their association with body size traits in Dezhou donkeys

2020 ◽  
Vol 63 (2) ◽  
pp. 377-386
Author(s):  
Zhenyu Lai ◽  
Fei Wu ◽  
Zihui Zhou ◽  
Mei Li ◽  
Yuan Gao ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Body Size ◽  
Association Analysis ◽  
Growth And Development ◽  
Growth Traits ◽  
Expression Profiles ◽  
Wild Genotype ◽  
Mutant Genotype ◽  
Polymorphic Loci ◽  
Genotype Ii

Abstract. Finding out the genetic mechanism of growth and development traits and the development of related molecular markers can help improve the breeding of livestock. The long-chain acyl coenzyme A synthase 1 (ACSL1) gene plays a major role in lipid synthesis and fatty acid catabolism. However, there are few studies on the ACSL1 gene polymorphism of Dezhou donkeys. This study analyzed the expression level of the ACSL1 gene in different tissues of young and adult Dezhou donkeys, as well as association analysis of four gene polymorphic loci in 450 individuals. The results showed that expression levels of the ACSL1 gene are higher in heart, liver, spleen, lung, renal, gastric and muscle tissues of adult donkeys than in those of young donkeys. In the association analysis between genotype and body size traits, the wild genotype DD at the ACSL1-1 locus in female and male donkeys was greater than the mutant genotype II (P<0.05); genotype II of ACSL1-2 was significantly higher than that of DD in withers height, body length, rump width and body weight of male donkeys (P<0.05); and ACSL1-3 showed a tendency for the wild genotype II to be greater than the mutant genotype DD in female and male donkeys (P<0.05). In addition, among the five haplotype combinations constructed, Hap3Hap3 (II-II-DD-DD) and Hap6Hap6 (DD-II-II-II) haplotype combinations were superior to other haplotype combinations in growth traits, which also indicated that the results of haplotype combination association analysis and genotype association analysis tended to be the same. In conclusion, the results of this study indicate that the polymorphic loci of the ACSL1 gene can be used as candidate molecular markers for the growth and development of Dezhou donkeys, and provide a theoretical reference for the breeding of Dezhou donkeys.

scholarly journals Differential Expression of ACTL8 Gene and Association Study of Its Variations with Growth Traits in Chinese Cattle

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1068
Author(s):  
Cuicui Cai ◽  
Jiawei Xu ◽  
Yongzhen Huang ◽  
Xianyong Lan ◽  
Chuzhao Lei ◽  
...  
Keyword(s):  
Expression Profile ◽  
Growth Traits ◽  
Muscle Growth ◽  
Tissue Expression ◽  
Expression Level ◽  
Nucleotide Polymorphisms ◽  
Qinchuan Cattle ◽  
Base Level ◽  
Muscle Tissues ◽  
Tissue Expression Profile

Mutations are heritable changes at the base level of genomic DNA. Furthermore, mutations lead to genetic polymorphisms and may alter animal growth phenotypes. Our previous study found that mutations in the bovine Actin-like protein 8 (ACTL8) gene may be involved in muscle growth and development. This study explored several mutations of the ACTL8 gene and their influence on body size in Chinese beef cattle, as well as tested the tissue expression profile of the ACTL8 gene in Qinchuan cattle at different ages. Five single nucleotide polymorphisms (SNPs) (including one synonymous mutation (c.2135552895G > A)) and two insertion/deletion polymorphisms (indels) were identified in the ACTL8 gene from 1138 cattle by DNA-seq, RFLP and other methods. Then, the expression profile of the ACTL8 gene in Qinchuan cattle showed that it was expressed in heart, spleen, lung, liver, muscle, and fat tissues. Moreover, the expression level of ACTL8 was increased with cattle growth (p < 0.01). The ACTL8 mRNA expression level in kidney and muscle tissues was the highest in the calves, while lowest in the fetal stage. Overall, we showed that the mutations could act as markers in beef molecular breeding and selection of the growth traits of cattle.

scholarly journals Characterization and Function Analysis of β, β-carotene-9′, 10′-oxygenase 2 (BCDO2) Gene in Carotenoid Metabolism of the Red Shell Hard Clam (Meretrix meretrix)

2021 ◽  
Vol 8 ◽  
Author(s):  
Lulu Fu ◽  
Heming Shi ◽  
Wenfang Dai ◽  
Hanhan Yao ◽  
Yongbo Bao ◽  
...  
Keyword(s):  
Function Analysis ◽  
Single Layer ◽  
Hard Clam ◽  
Meretrix Meretrix ◽  
Nucleotide Polymorphisms ◽  
Shell Color ◽  
Carotenoid Metabolism ◽  
Key Enzyme ◽  
And Function ◽  
Β Carotene

The relationship between carotenoid and shellfish shell color has gained increasing attention. β, β-carotene-9′,10′-oxygenase 2 (BCDO2) is a key enzyme in animal carotenoid metabolism, and its accumulation affects the change in body color, as demonstrated in mammals, birds, and fish. However, it is unclear whether BCDO2 is involved in the formation of the red shell color of clam. To explore the molecular structure and biological function of BCDO2 gene in the process of carotenoids accumulation, in this study, the BCDO2 from hard clam Meretrix meretrix (designated as Mm-BCDO2) was cloned and characterized, and the single-nucleotide polymorphisms (SNPs) associated with shell color were detected. The results of qRT-PCR indicated that Mm-BCDO2 gene was expressed in all six tested tissues, and the expression of mantle was significantly higher than other tissues (P &lt; 0.05). The association analysis identified 20 SNPs in the exons of Mm-BCDO2, among which three loci (i.e., c.984A &gt; C, c.1148C &gt; T, and c.1187A &gt; T) were remarkably related (P &lt; 0.05) to the shell color of clam. The western blot analysis revealed that the expression level of Mm-BCDO2 in the mantle of red shell clams was stronger than that of white shell clams (P &lt; 0.05). Further, the immunofluorescence analysis indicated that the single-layer columnar cells at the edge of the mantle were the major sites for the Mm-BCDO2 secretion. This study explored the potential impacts of BCDO2 gene on the shell color of M. meretrix, which provided a theoretical basis for a better understanding of the important role of BCDO2 in carotenoid metabolism.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arika Fukushima ◽  
Masahiro Sugimoto ◽  
Satoru Hiwa ◽  
Tomoyuki Hiroyasu
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Response To Therapy ◽  
Hcv Infection ◽  
Entire Treatment Period ◽  
Time Points ◽  
Time Course Data ◽  
Conventional Methods

Abstract Background Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made using time-course data on multiple biomarkers that indicate a patient’s response to therapy contribute positively to the decision-making process associated with designing effective treatment programs for various diseases. Therefore, the development of prediction methods incorporating time-course data on multiple markers is necessary. Results We proposed new methods that may be used for prediction and gene selection via time-course gene expression profiles. Our prediction method consolidated multiple probabilities calculated using gene expression profiles collected over a series of time points to predict therapy response. Using two data sets collected from patients with hepatitis C virus (HCV) infection and multiple sclerosis (MS), we performed numerical experiments that predicted response to therapy and evaluated their accuracies. Our methods were more accurate than conventional methods and successfully selected genes, the functions of which were associated with the pathology of HCV infection and MS. Conclusions The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.

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