The Association of an SNP in the EXOC4 Gene and Reproductive Traits Suggests Its Use as a Breeding Marker in Pigs

In mammals, the exocyst complex component 4 (EXOC4) gene has often been reported to be involved in vesicle transport. The SNP rs81471943 (C/T) is located in the intron of porcine EXOC4, while six quantitative trait loci (QTL) within 5–10 Mb around EXOC4 are associated with ovary weight, teat number, total offspring born alive, and corpus luteum number. However, the molecular mechanisms between EXOC4 and the reproductive performance of pigs remains to be elucidated. In this study, rs81471943 was genotyped from a total of 994 Duroc sows, and the genotype and allele frequency of SNP rs81471943 (C/T) were statistically analyzed. Then, the associations between SNP rs81471943 and four reproductive traits, including number of piglets born alive (NBA), litter weight at birth (LWB), number of piglets weaned (NW), and litter weight at weaning (LWW), were determined. Sanger sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) were utilized to identify the rs81471943 genotype. We found that the genotype frequency of CC was significantly higher than that of CT and TT, and CC was the most frequent genotype for NBA, LWB, NW, and LWW. Moreover, 5′-deletion and luciferase assays identified a positive transcription regulatory element in the EXOC4 promoter. After exploring the EXOC4 promoter, SNP −1781G/A linked with SNP rs81471943 (C/T) were identified by analysis of the transcription activity of the haplotypes, and SNP −1781 G/A may influence the potential binding of P53, E26 transformation specific sequence -like 1 transcription factor (ELK1), and myeloid zinc finger 1 (MZF1). These findings provide useful information for identifying a molecular marker of EXOC4-assisted selection in pig breeding.

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Association of rs81471943 and reproductive traits reveals EXOC4 as novel molecular breeding marker in pigs

10.21203/rs.3.rs-33761/v1 ◽

2020 ◽

Author(s):

Yingting He ◽

Xiaofeng Zhou ◽

Bin Hu ◽

Rongrong zheng ◽

Yao Jiang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Regulatory Element ◽

Reproductive Traits ◽

Transcription Activity ◽

Cis Acting ◽

Litter Weight ◽

Pcr Rflp ◽

Teat Number ◽

Myeloid Zinc Finger ◽

P 53

Abstract Background: In mammals, the exocyst complex component 4 ( EXOC 4 ) gene has often been reported to be involved in vesicle transport. The rs81471943 (C/T) locates at the intron of porcine EXOC 4 , and six quantitative trait loci (QTLs) within 5-10 Mb around EXOC 4 are associated with ovary weight, teat number, total born alive, and corpus luteum number. However, the molecular mechanisms between EXOC 4 and reproductive performance of pigs remains incompletely elucidated.Results: In this study, rs81471943 was genotyped from a total of 994 Duroc sows, and the genotype and allele frequency of rs81471943 (C/T) were statistically analyzed. Then the associations between rs81471943 and four reproductive traits including number of piglets born alive (NBA), litter weight at birth (LWB)，number of piglets weaned (NW), and litter weight at weaning (LWW) were determined. Besides, the sanger sequencing and PCR-restriction fragment length polymorphism (PCR-RFLP) were utilized to identify genotype of rs81471943. We found that the genotype frequency of CC was significantly higher than that of CT and TT, and TT was the favorable genotype on NW ( P =0.01) and LWW ( P <0.01). Moreover, 5’-deletion and luciferase assays identified a positive transcription regulatory element in -1826/-1551 of EXOC 4 . After exploring -1826/-1551 fragment, -1781G/A linked with rs81471943 (C/T) were identified by analysis the transcription activity of the haplotypes, and -1781 G/A might influence the potential binding of P 53 , ETS transcription factor ( ELK1 ), and myeloid zinc finger 1 ( MZF 1 ).Conclusions: In 994 Duroc pigs, rs81471943 of TT was the favorable genotype on NW (P=0.01) and LWW (P<0.01), and the haplotypes of -1781G/A and rs81471943 significantly affect the transcription activity of EXOC 4 , which might influence the binding of potential cis-acting elements P 53 , ELK 1 and/or MZF 1 . These findings provide useful information for identifying the molecular marker of EXOC 4 -assisted selection in pig breeding.

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Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements

Molecular and Cellular Biology ◽

10.1128/mcb.11.4.1944-1953.1991 ◽

1991 ◽

Vol 11 (4) ◽

pp. 1944-1953

Author(s):

I M Santoro ◽

T M Yi ◽

K Walsh

Keyword(s):

Dna Binding ◽

Binding Proteins ◽

Regulatory Element ◽

Dna Binding Proteins ◽

Binding Activity ◽

Sequence Motif ◽

Mobility Shift ◽

Specific Sequence ◽

Single Stranded Dna ◽

Muscle Gene

A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence.

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OPN gene locus is associated with the risk of knee osteoarthritis: a case–control study

Bioscience Reports ◽

10.1042/bsr20182023 ◽

2019 ◽

Vol 39 (2) ◽

Cited By ~ 2

Author(s):

Houlai Shang ◽

Yuedong Hao ◽

Wenhao Hu ◽

Xiaohui Hu ◽

Qing Jin

Keyword(s):

Knee Osteoarthritis ◽

Chinese Population ◽

Gene Locus ◽

Case Control Study ◽

Fragment Length Polymorphism ◽

Case Control ◽

Chinese Han ◽

Knee Oa ◽

Pcr Rflp ◽

Control Study

AbstractBackground/aims: Studies have demonstrated that osteopontin (OPN) was associated with the severity and development of knee osteoarthritis (OA). Methods: The purpose of this case–control study was to investigate the association between OPN gene rs11730582 polymorphism and knee OA risk in a Chinese population. Genotyping was analyzed using standard PCR and restriction fragment length polymorphism (PCR-RFLP). Results: The present study found that C allele or CC genotype of OPN gene rs11730582 polymorphism was related to decreased risk for knee OA. Furthermore, positive associations were obtained amongst the females, and body mass index (BMI) < 25 kg/m2 groups. Conclusions: To sum up, the present study reveals that OPN gene rs11730582 polymorphism decreases the risk of knee OA in Chinese Han population.

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Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements.

Molecular and Cellular Biology ◽

10.1128/mcb.11.4.1944 ◽

1991 ◽

Vol 11 (4) ◽

pp. 1944-1953 ◽

Cited By ~ 42

Author(s):

I M Santoro ◽

T M Yi ◽

K Walsh

Keyword(s):

Dna Binding ◽

Binding Proteins ◽

Regulatory Element ◽

Dna Binding Proteins ◽

Binding Activity ◽

Sequence Motif ◽

Mobility Shift ◽

Specific Sequence ◽

Single Stranded Dna ◽

Muscle Gene

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CYP27B1 Gene Polymorphism rs10877012 in Patients Diagnosed with Colorectal Cancer

Nutrients ◽

10.3390/nu12040998 ◽

2020 ◽

Vol 12 (4) ◽

pp. 998

Author(s):

Maria Latacz ◽

Jadwiga Snarska ◽

Elżbieta Kostyra ◽

Konrad Wroński ◽

Ewa Fiedorowicz ◽

...

Keyword(s):

Colorectal Cancer ◽

Vitamin D ◽

Fragment Length Polymorphism ◽

Intestinal Cells ◽

Chain Reaction ◽

The Third ◽

Pcr Rflp ◽

Study Population ◽

Polymerase Chain ◽

Peripheral Leukocytes

Colorectal cancer (CRC) is the third most commonly occurring cancer worldwide. Intestinal cells are CYP27B1 gene expression sites and, as a consequence, they are capable of converting pro-vitamin D into the active paracrine and autocrine forms. It was demonstrated that rs10877012 polymorphism in the CYP27B1 gene influenced the circulating vitamin D level. This provided a rationale for determining the role that this polymorphism plays in the risk of developing colon cancer. In this study, we investigated the association of rs10877012 (T/G) polymorphism in the CYP27B1 gene with CRC susceptibility. The study population (n = 325) included CRC patients (n = 106) and healthy controls (n = 219). DNA was extracted from peripheral leukocytes and analyzed for the CYP27B1 polymorphism using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We found an association between the presence of the T allele at the polymorphic site (odds ratio (OR) = 2.94; 95% CI 1.77–4.86; p < 0.0001) and a decreased CRC incidence.

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Association of RBP4 Genotype with Phenotypic Reproductive Traits of Sows

Genetics Research International ◽

10.1155/2016/4940532 ◽

2016 ◽

Vol 2016 ◽

pp. 1-5 ◽

Cited By ~ 4

Author(s):

A. Marantidis ◽

G. P. Laliotis ◽

M. Avdi

Keyword(s):

Litter Size ◽

Negative Impact ◽

Reproductive Traits ◽

Retinol Binding Protein ◽

Rapid Improvement ◽

Retinol Binding Protein 4 ◽

Reproductive Characteristics ◽

Pcr Rflp ◽

Hardy Weinberg Equilibrium ◽

Rbp4 Gene

PCR-RFLP was applied to a commercial crossbred pig population in order to investigate the association between polymorphism (SNP) of Retinol-binding protein 4 (RBP4) gene and reproductive performance. 400 sows were genotyped and 2000 records of reproductive traits were used in order to retrieve information about the allele frequencies and the association of the RBP4 gene with main reproductive characteristics of the population. A deviation from the Hardy-Weinberg equilibrium was observed as a result of the AB genotype excess. In addition, the AA genotype saw statistically significant higher values of (i) the total number of born piglets (p<0.05), (ii) the number of piglets born alive (p<0.01), and (iii) the number of weaned piglets (p<0.01). The number of the mummified piglets and the number of the piglets born dead did not differ between the various RBP4 genotypes. Interestingly, the AA genotype had a negative impact (p<0.05) on the number of piglets born dead, resulting indirectly in a larger litter size. In conclusion, the AA genotype and in extension the A allele of RBP4 gene are in favor of producing larger litter size, suggesting that the RBP4 gene may be used in Marker-Assisted Selection (MAS) programs for a rapid improvement of the reproductive characteristics in pigs.

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Associations of biochemical changes and maternal traits with mutation 1843 (C>T) in the RYR1 gene as a common cause for porcine stress syndrome

Balkan Journal of Medical Genetics ◽

10.1515/bjmg-2016-0039 ◽

2016 ◽

Vol 19 (2) ◽

pp. 75-80 ◽

Cited By ~ 1

Author(s):

ZT Popovski ◽

B Tanaskovska ◽

E Miskoska-Milevska ◽

S Andonov ◽

S Domazetovska

Keyword(s):

Fragment Length Polymorphism ◽

Protein Product ◽

Biochemical Changes ◽

Chain Reaction ◽

Maternal Characteristics ◽

Stress Syndrome ◽

Pcr Rflp ◽

Porcine Stress Syndrome ◽

Heterozygous Carriers ◽

Polymerase Chain

AbstractStress syndrome is usually caused by a mutation in theryanodine receptorgene(ryr1) and it is widely studied in humans and swine populations. The protein product of this gene plays a crucial role in the regulation of calcium transport in muscle cells. A G>T mutation in the humanryr1gene, which results in the replacement of a conserved arginine at position 614 where a leucine occurs at the same position as the previously identified Arg→Cys mutation reported in all cases of porcine stress syndrome (PSS). Porcine stress syndrome affects biochemical pathways in stress-susceptible individuals during a stress episode and some biochemical parameters that were used as markers for diagnostic purposes. Also, PSS has remarkable influence on the maternal characteristics of sows. This study dealt with different genotypes for PSS and its association with possible biochemical changes and maternal traits of sows. Seventy-three reproductive sows genotyped for PSS by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were included in this survey. Sixty of them were stress-free (NN), 11 were heterozygous carriers (Nn) and two animals were homozygous (nn) for the 1843 (C>T) mutation. Significant differences in non stress induced animals with different PSS genotypes were found in the values of creatine phoshokinase (CPK), lactate dehydrogenase (LDH), alkaline phosphatase (AP) and aspartate aminotransferase (AST). Regarding the maternal traits, our study showed that stress susceptible animals (nn) have an increased number of stillborn piglets and a reduced number of newborn piglets compared with heterozygous and normal animals.

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Genotyping of NAD(P)H:quinone oxidoreductase (NQO1) in a panel of human tumor xenografts: relationship between genotype status, NQO1 activity and the response of xenografts to Mitomycin C chemotherapy in vivo11Abbreviations: NQO1, NAD(P)H,Quinone oxidoreductase; MMC, Mitomycin C; PCR-RFLP, Polymerase chain reaction restriction fragment length polymorphism; and RH1, 2,5-diaziridinyl-3-(hydroxymethyl)-6-methyl-1,4-benzoquinone.

Biochemical Pharmacology ◽

10.1016/s0006-2952(01)00769-9 ◽

2001 ◽

Vol 62 (10) ◽

pp. 1371-1377 ◽

Cited By ~ 14

Author(s):

Roger M. Phillips ◽

Angelika M. Burger ◽

Heinz-Herbert Fiebig ◽

John A. Double

Keyword(s):

Mitomycin C ◽

Fragment Length Polymorphism ◽

Human Tumor ◽

Chain Reaction ◽

Quinone Oxidoreductase ◽

Human Tumor Xenografts ◽

Tumor Xenografts ◽

Pcr Rflp ◽

Polymerase Chain ◽

Restriction Fragment Length

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Identifikasi Keragaman Gen DGAT1 serta Asosiasinya terhadap Karakteristik Karkas dan Sifat Perlemakan Domba

Jurnal Ilmu dan Teknologi Peternakan Tropis ◽

10.33772/jitro.v6i2.7141 ◽

2019 ◽

Vol 6 (2) ◽

pp. 259

Author(s):

Asep Gunawan ◽

Ratna Sholatia Harahap ◽

Kasita Listyarini ◽

Cece Sumantri

Keyword(s):

Polymerase Chain Reaction ◽

Single Nucleotide Polymorphism ◽

Fragment Length Polymorphism ◽

Nucleotide Polymorphism ◽

Chain Reaction ◽

Single Nucleotide ◽

Dgat1 Gene ◽

Pcr Rflp ◽

Polymerase Chain ◽

Restriction Fragment Length

ABSTRAK Karakteristik karkas dan sifat perlemakan pada daging domba dikontrol oleh banyak gen salah satunya gen DGAT1 (Diacylglycerol Acyltransferasel 1). Penelitian ini bertujuan mengidentifikasi SNP (Single Nucleotide Polymorphism) gen DGAT1 pada titik mutasi g.8539 C>T dan asosiasinya terhadap karakteristik karkas dan sifat perlemakan pada domba Indonesia. Total sampel domba yang digunakan sebanyak 150 buah terdiri dari 35 sampel domba compass agrinak (DCA), 36 sampel domba barbados cross (DBC), 41 sampel domba komposit garut (DKG), 20 sampel domba ekor gemuk (DEG), dan 18 sampel domba ekor tipis (DET). Karakteristik karkas dan sifat perlemakan diukur dari domba jantan berumur 10-12 bulan. Identifikasi keragaman DGAT1|ALuI dianalisis dengan metode PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). Hasil keragaman gen DGAT1 bersifat polimorfik dalam DET dan DEG, sedangkan DCA, DBC, dan DKG bersifat monomorfik. Dua genotipe disebut CC dan CT ditemukan dalam DET dan DEG. Titik mutasi gen DGAT1 berasosiasi (P<0.05) dengan karakteristik karkas, yaitu bobot dan panjang karkas. Selain itu, keragaman gen DGAT1 juga berasosiasi signifikan (P<0.05) dengan asam lemak jenuh, yaitu asam stearat (C18:0) dan asam arakidat (C20:0) dan asam lemak tak jenuh tunggal, yaitu asam oleat (C18:1n9c). Gen DGAT1 memiliki kontribusi dalam karakteristik karkas dan komposisi asam lemak pada domba.Kata Kunci: domba, gen DGAT1, karakteristik karkas, PCR-RFLP, sifat perlemakan ABSTRACT Characteristic of carcass and fatness traits of sheep is regulated by many genes such as DGAT1 (Diacylglycerol Acyltransferasel 1) gene. The research was aimed to investigate SNP (Single Nucleotide Polymorphism) of DGAT1 and its association with characteristic of carcass and fatness traits in Indonesian sheep. A total sample of sheeps used 150 rams of 10–12 months consisted 35 samples of compas agrinak sheep (CAS), 36 of barbados cross (BCS), 41 of garut composite (GCS), 20 of javanese fat tailed (JFT), and 18 of javanese thin tailed (JTT). Identification variant of DGAT1|ALuI were performed by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The results of polymorphism of DGAT1 were found in JTT and JFT. However, SNP of DGAT1 in CAS, BCS and GCS were monomorfic. Two genotype namely CC and CT were found in JTT and JFT populations. A SNP of the DGAT1 was associated (P<0.05) with characteristic of carcass, including weight and length of carcass. The variant of DGAT1 was associated too with saturated fatty acids (SFA) including stearic acid (C18:0) and arachidic acid (C20:0), and mono unsaturated fatty acid (MUFA) including oleic acid (C18:1n9c). The DGAT1 gene was contribute to characteristic carcass and fatty acid composition in sheep.Keywords: DGAT1 gene, characteristic carcass, fatness traits, PCR-RFLP, sheep

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Association of non-synonymous SNPs of <i>OPN</i> gene with litter size traits in pigs

Archives Animal Breeding ◽

10.5194/aab-58-317-2015 ◽

2015 ◽

Vol 58 (2) ◽

pp. 317-323 ◽

Cited By ~ 3

Author(s):

T. Kumchoo ◽

S. Mekchay

Keyword(s):

Litter Size ◽

Reproductive Traits ◽

Snp Markers ◽

Strong Linkage Disequilibrium ◽

Nucleotide Polymorphisms ◽

Large White ◽

Single Nucleotide ◽

Pcr Rflp ◽

Polymerase Chain ◽

Acid Exchange

Abstract. Osteopontin (OPN) gene is a secreted phosphoprotein which appears to play a key function in the conceptus implantation, placentation and maintenance of pregnancy in pigs. The objectives of this study were to verify the non-synonymous single nucleotide polymorphisms (SNPs) and their association with litter size traits in commercial Thai Large White pigs. A total of 320 Thai Large White sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three SNPs at c.425G> A, c.573T> C and c.881C> T revealed amino acid exchange rates of p.110Ala> Thr, p.159Val> Ala and p.262Pro> Ser, respectively, and were then segregated. These three SNPs were significantly associated with total number born (TNB) and number born alive (NBA) traits. No polymorphisms of the two SNP markers (c.278A> G and c.452T> G) were observed in this study. Moreover, the SNPs at c.425G> A and c.573T> C were found to be in strong linkage disequilibrium. The association of OPN with litter size emphasizes the importance of porcine OPN as a candidate gene for reproductive traits in pig breeding.

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