scholarly journals Polymorphism of Insulin-induced gene 1 (INSIG1) of three local beef cattle in Indonesia

2021 ◽  
Vol 888 (1) ◽  
pp. 012026
Author(s):  
S D Volkandari ◽  
E T Margawati ◽  
A S Wulandari ◽  
Indriawati
Keyword(s):  
Beef Cattle ◽  
Regulatory Element ◽  
Growth Trait ◽  
Weinberg Equilibrium ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Sterol Regulatory Element ◽  
Dna Fragment ◽  
Genotype And Allele Frequencies

Abstract Insulin-induced gene 1 (INSIG1) encoded protein that blocked of proteolysis activity from protein sterol regulatory element binding proteins (SREBP). The role gene plays of cholesterol, fatty acid, and glucose metabolism. Indonesia has many several beef cattle which has good quality of growth trait. The aim of this study was to identify polymorphism of INSIG1 gene (SNP 4366 (A>G) and 4534 (T>C)) of three local beef cattle in Indonesia (Bali, Pasundan and Ongole Decendent). One hundred and twenty seven samples were used in this study consisting of Bali cattle (46) from Pulukan Bali Island, Pasundan (36) from UPTD BPPT Beef cattle Ciamis West Java and Ongole Grade (OD) (45). DNA was extracted from whole blood using High Salt method then genotyping used PCR-RFLP method with RsaI and TaqI enzymes. Parameters in this study were genotype and allele frequencies, heterozigosity observed (Ho), expected (He), Hardy-Weinberg Equilibrium (HWE) and Polymorphism Information Content (PIC). Result showed that a 428 bp of DNA fragment was successfully amplified and digested. Three variant of genotypes with two alleles were identified. For SNP 4366 (A>G) were AA, AG and GG with dominant of G allele while SNP 4534 (T>C) were CC, CT and TT with dominant C allele. Both of SNPs in each of breed populations was in Hardy-Weinberg Equilibrium and polymorphic. Additionally, PIC value reached moderate. In conclusion, polymorphism was found in beef cattle and it could be early study for genetic diversity

scholarly journals Identifikasi Keragaman Gen FTO Pada Bangsa Sapi Potong Indonesia

2019 ◽  
Vol 6 (2) ◽  
pp. 232
Author(s):  
Sutikno Sutikno ◽  
Rudy Priyanto ◽  
Cece Sumantri ◽  
Jakaria Jakaria
Keyword(s):  
Beef Cattle ◽  
Genetic Markers ◽  
Direct Sequencing ◽  
Nucleotide Position ◽  
Fto Gene ◽  
Blood Samples ◽  
Pcr Rflp ◽  
Gene Functions ◽  
Hardy Weinberg Equilibrium ◽  
Cattle Blood

ABSTRAK Gen FTO berfungsi sebagai regulasi homeostasis, deposisi lemak dan pengaturan obesitas. Penelitian ini bertujuan untuk mengidentifikasi polimorfisme SNP g.125550A>T di ekson 3 gen FTO pada bangsa sapi potong Indonesia. Sampel darah diperoleh dari 209 ekor sapi, terdiri atas sapi bali (44), madura (20), Pesisir (20), katingan (20), Peranakan ongole (PO) (22), Pasundan (20), Sumba Ongole (SO) (11), brahman (20), simental (15), dan limousin (18). Polimorfisme gen FTO dianalisis menggunakan metode PCR-RFLP (HpyCH4III) dan direct sequencing. Hasil genotiping SNP g.125550A>T adalah polimorfik (genotipe AA, AT, dan TT) pada sapi madura, pesisir, katingan, PO, pasundan, SO, brahman, simental, dan limousin. Frekuensi alel A dan T masing-masing adalah 0,70, 0,68, 0,84, 0,89, 0,70, 0,86, 0,90, 0,73, 0,69 dan 0,30, 0,33, 0,16, 0,11, 0,30, 0,14, 0,10, 0,27, 0,31. Nilai Ho dan He masing-masing adalah 0,60-0,14 dan 0,44-0,18 serta dalam keseimbangan Hardy-Weinberg (P>0.05). Sementara pada sapi bali bersifat monomorfik hanya bergenotipe AA. Hasil sekuensing SNP g.125550A>T ditemukan mutasi tranvesi A menjadi T pada posisi nukleotida  g.125550. Berdasarkan hasil penelitian ini, dapat disimpulkan bahwa SNP 125550A>T gen FTO beragam dan berpotensi dijadikan marka genetik untuk kualitas daging pada bangsa sapi potong Indonesia.Kata Kunci: gen FTO, PCR-RFLP, Sapi, SNP g.125550A>TABSTRACTThe FTO gene functions as regulation of homeostasis, fat deposition and regulation of obesity. This study aimed to identify the polymorphism of SNP g.125550A>T in exon 3 of FTO gene in Indonesian beef cattle. Blood samples were collected from 209 cattle, including bali (44), madura (20), pesisir (20), katingan (20), PO (22), pasundan (20), SO (11), brahman (20), simental (15), and limousin (18). Polymorphism of the FTO gene was analyzed using PCR-RFLP (HpyCH4III) and direct sequencing methods. The results of genotyping SNP g.125550A>T was polymorphic (AA, AT and TT genotypes) in madura, pesisir, katingan, PO, pasundan, SO, brahman, simental, and limousin cattle. The frequency of A and T alleles were 0,70, 0,68, 0,84, 0,89, 0,70, 0,86, 0,90, 0,73, 0,69 and 0,30, 0,33, 0,16, 0,11, 0,30, 0,14, 0,10, 0,27, 0,31 respectively. The values of Ho and He were 0,60-0,14 and 0,44-0,18 respectively and in Hardy-Weinberg equilibrium (P>0,05). While in Bali cattle was monomorphic (AA genotype). Results of sequencing SNP g.125550A>T of the FTO gene found a transverse mutation A to T at the nucleotide position g.125550. As a result of this study, it can be concluded that SNP 125550A>T of the FTO gene was diverse and potentially used as genetic markers for meat quality in Indonesian beef cattle.Keywords: cattle, FTO gene, PCR-RFLP, SNP g.125550A>T.

scholarly journals Effects of genetic variation in the 20th intron of Sansui duck ATP2A2 gene on eggshell quality

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Junhan Mei ◽  
Yiyu Zhang ◽  
Minfang You ◽  
Chaomei Liao ◽  
Guanghui Tan ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Strong Linkage Disequilibrium ◽  
Strong Linkage ◽  
Weinberg Equilibrium ◽  
Atp2a2 Gene ◽  
Eggshell Quality ◽  
Hardy Weinberg Equilibrium ◽  
Intron Region ◽  
The Relationship

In order to explore the influence of the polymorphism in the 20 intron region of the Sansui duck ATP2A2 gene on the eggshell quality, this study used Primer Premier 5 software to design and synthesize a pair of primers in the 20 intron region, two-way direct sequencing and sequence alignment to mine SNPs Sites, SPSS 18.0 software was used to analyze the relationship between SNP sites and eggshell quality of Sansui duck. Results Three SNP sites were found in the 20 intron region of the ATP2A2 gene: g.40874 T>C, g.40920 G>A and g.40990 T=C, all of which were moderately polymorphic, at the site g.40874 T ＞C and g.40920 G＞A both deviated significantly from Hardy-Weinberg equilibrium (P>0.05), position g.40990 T=C accords with Hardy-Weinberg equilibrium (P<0.05), and position g.40874 T＞C There is a strong linkage disequilibrium between g.40990 T=C; a total of 4 haplotypes and 9 double types were detected at 3 SNP loci; the results of association analysis show that g.40874 T＞C mutation has an effect on eggshell strength The eggshell strength of CC genotype was significantly higher than that of TC and TT genotypes (P<0.05), and the eggshell weight of CC genotype was significantly higher than that of TC genotype (P<0.05), g. The 40990 T=C mutation has a significant effect on the eggshell strength, and the eggshell strength of the TC genotype is significantly higher than that of the TT genotype (P<0.05). In summary, the g.40874 T>C and g.40990 T=C found in the 20th intron region of the Sansui duck ATP2A2 gene may be the marker sites that affect the quality of the eggshell.

scholarly journals Polymorphism of ADIPOQ and EDG1 genes in Indonesian beef cattle

2018 ◽  
Vol 43 (4) ◽  
pp. 323
Author(s):  
S. Sutikno ◽  
R. Priyanto ◽  
C. Sumantri ◽  
J. Jakaria
Keyword(s):  
Beef Cattle ◽  
Promoter Region ◽  
Marbling Score ◽  
Blood Samples ◽  
Adipoq Gene ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Cattle Blood ◽  
Bali Cattle ◽  
Novel Snp

The ADIPOQ and EDG1 genes were responsible in intramuscular fat deposition and marbling scores. This study was aimed to identify polymorphism of indel g.81966364D>I in promoter region of ADIPOQ gene and SNP c.-312A>G in 5' UTR of EDG1 gene in Indonesian beef cattle. Blood samples were collected from 211 cattle, including Bali (44), Madura (20), Pesisir (18), Katingan (20), PO (22), Pasundan (20), SO (12), Brahman (20), Simmental (15) and Limousin (18). Polymorphism of ADIPOQ gene was analyzed using PCR and direct sequencingmethods, whereas EDG1 gene was analyzed using PCR-RFLP (MscI enzyme) and direct sequencingmethods. Results of genotyping indel g.81966364D>I was monomorphic (DD genotype). The SNP c.-312A>G was polymorphic (AA and AG genotype) in Madura, Pesisir, Pasundan, Brahman, and Limousine. The Frequencies of allele A and G were 0.95, 0.92, 0.98, 0.95, 0.94 and 0.05, 0.08, 0.02, 0.05, 0.06 respectively. The values of Ho and He were 0.05-0.17 and 0.05-0.15 respectively and in Hardy-Weinberg equilibrium (P>0.05). In Bali, Katingan, PO, SO and Simmental were monomorphic (GG genotype). In Bali cattle, two novel SNP candidates were found in position of c.-399C>T and c.-273C>G which were potential to be used as genetic markers of marbling score for Bali cattle. As result this study, it can be concluded that ADIPOQ gene was similar while EDG1 gene was different in Indonesian beef cattle. in addition, found two candidates potential SNP in Bali cattle.

scholarly journals Effect of β-lactoglobulin gene polymorphism, lactation stage and breed on milk traits in Chios and Karagouniko sheep breeds

2017 ◽  
Vol 17 (2) ◽  
pp. 371-384 ◽  
Author(s):  
Kostas A. Triantaphyllopoulos ◽  
Panagiota Koutsouli ◽  
Athanassios Kandris ◽  
Dimitris Papachristou ◽  
Kalliopi E. Markopoulou ◽  
...  
Keyword(s):  
Milk Yield ◽  
Milk Traits ◽  
Weinberg Equilibrium ◽  
Sheep Breeds ◽  
Lactation Stage ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Daily Milk Yield ◽  
Β Lactoglobulin ◽  
Daily Milk

Abstract The animal selection with favourable phenotypes of the past has been, currently, replaced by the genotype selection on quantitative traits, assisted by the expanding molecular techniques in the context of livestock improvement. In this study, the c.112T>C polymorphism in exon II of β-lactoglobulin (β-LG) gene was investigated in Karagouniko and Chios sheep breeds by using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP), and possible associations with milk traits were examined. In total, 125 blood DNA samples were isolated for PCR-RFLP analysis and the respective 217 milk samples′ composition profile was obtained. The goodness of fit test to Hardy-Weinberg equilibrium (HWE) for β-LG genotypes was estimated and associations found between β-LG genotypes and raw milk composition. Two alleles and three genotypes were observed (AA, AB and BB) in both breeds, and Chios breed significantly deviated (P≤0.05) from Hardy-Weinberg equilibrium (HWE). Conclusively, linear mixed model analysis on samples, from both breeds collectively, showed significant effects of β-LG genotype on lactose percentage and somatic cell count (SCC), lactation stage on daily milk yield and protein, while the breed effect was significant only on daily milk yield.

scholarly journals ABCB1 variants C3435T and T129C are not associated with colorectal cancer risk

2019 ◽  
Vol 19 (3) ◽  
pp. 2476-2483 ◽  
Author(s):  
Areej M Al Qahtani ◽  
Ayat B Al-Ghafari ◽  
Huda A Al Doghaither ◽  
Anas H Alzahrani ◽  
Ulfat M Omar ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Saudi Arabia ◽  
Goodness Of Fit ◽  
Allele Frequencies ◽  
Genotype Distribution ◽  
Exact Test ◽  
Weinberg Equilibrium ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
And Control

Background: Colorectal cancer (CRC) is one of the most prevalent cancers in Saudi Arabia that is highly characterized with poor survival rate and advanced metastasis. Many studies contribute this poor outcome to the expression of ABC transporters on the surface of cancer cells.Objectives: In this study, two ABCB1 variants, C3435T and T129C, were examined to evaluate their contribution to CRC risk.Methods: 125 subjects (62 CRC patients and 63 healthy controls) were involved. The DNA was isolated and analyzed with PCR-RFLP to determine the different genotypes. The hardy-Weinberg equilibrium was performed to determine genotype distribution and allele frequencies. Fisher’s exact test (two-tailed) was used to compare allele frequencies between patients and control subjects. Results: The study showed that for SNP C3435T, the population of both CRC patients and controls were out of Hardy-Weinberg equilibrium. Genotype distribution for CRC patients was (Goodness of fit χ2 = 20, df= 1, P≤0.05), whereas, for the controls the genotype distribution was (Goodness of fit χ2 = 21, df =1, P ≤0.05). For SNP T129C, all subjects showed normal (TT) genotype.Conclusion: There was no significant association between ABCB1 3435C>T and 129T>C polymorphisms with CRC risk.Keywords: Colorectal cancer, ABCB1 gene, SNP C3435T, SNP T129C, PCR-RFLP, Saudi Arabia.

scholarly journals Analysis of Prolactin and Kappa-Casein Genes Polymorphism in Four Cattle Breeds in Turkey

2014 ◽  
Vol 14 (4) ◽  
pp. 799-806
Author(s):  
Bilal Akyüz ◽  
Mehmet Ulaş Çınar
Keyword(s):  
Restriction Enzymes ◽  
Chi Square ◽  
Brown Swiss ◽  
Weinberg Equilibrium ◽  
Cattle Breeds ◽  
Genotype Frequencies ◽  
Pcr Rflp ◽  
Chi Square Test ◽  
Hardy Weinberg Equilibrium ◽  
Casein Genes

Abstract The objective of this study was to identify allele and genotype frequencies of CSN3 and PRL genes in four cattle breeds in Turkey. For this purpose, a total of 390 cattle of East Anatolian Red (EAR), Zavot, Brown Swiss (BS) and Simmental (SIM) breeds were genotyped by PCR-RFLP method. A 443 bp fragment of CSN3 and a 156 bp fragment of PRL were amplified and digested with HindIII and RsaI restriction enzymes, respectively. For CSN3 and PRL genes, two types of alleles (A and B) and three types of genotypes (AA, BB, and AB) were observed. The highest frequencies for CSN3-A and CSN3-B alleles were estimated for the EAR breed (0.743) and for the BS breed (0.556), respectively. The highest frequency for PRL-A and PRL-B alleles was estimated for the SIM breed (0.801) and for the BS breed (0.315), respectively. The Chi-square test among the investigated cattle breeds showed that only the Zavot breed was in Hardy-Weinberg equilibrium (HWE) for both loci.

scholarly journals Genetic Polymorphism of Calpastatin (CAST) Gene in Pasundan Cattle

2018 ◽  
Vol 42 (4) ◽  
Author(s):  
Slamet Diah Volkandari ◽  
Aina Nadila ◽  
Nani Radiastuti ◽  
Endang Tri Margawati
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Fresh Blood ◽  
Weinberg Equilibrium ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Pcr Method ◽  
Variant Alleles ◽  
Cast Gene

The aim of this study was to determine genetic diversity of Calpastatin gene (CAST) in Pasundan cattle. Forty-four fresh blood samples were collected from UPTD BPPT Beef Cattle Ciamis West Java. Genomic DNA samples were extracted using High Salt method. A 523 bp fragment of Calpastatin gene was successfully amplified using PCR method. Genotyping of CAST gene was conducted by PCR-RFLP method using RsaI restriction enzyme (GT^AC). Genotypes and alleles were analyzed using software Cervus 3.0.7. Parameters were observed i.e genotypes and alleles frequencies, heterozygosity observed (Ho) and expected (He), Hardy Weinberg Equilibrium (HWE), and Polymorphic Information Content (PIC). Result showed that three variant genotypes of GG, GC and CC were found and two variant alleles of G and C. Allele G was found higher (0.77) than allele C (0.23). Population of Pasundan cattle was found polymorphism and in the Hardy Weinberg Equilibrium. Polymorphic Information Content (PIC) value showed in a moderate (0.290) condition. Values of Heterozygosity observed and expected were 0.409 and 0.355 respectively. This research concludes that there is polymorphism of CAST gene in Pasundan cattle population and has genetic diversity. This result could be used as early genetic information in exploration of Pasundan cattle.

scholarly journals Analysis of Polymorphisms on GH-MspI and IGF1-SnaBI Loci in Five Turkish Native Cattle Breeds

2018 ◽  
Vol 6 (10) ◽  
pp. 1353
Author(s):  
Yasemin Öner ◽  
Onur Yılmaz ◽  
Candan Eriş ◽  
Nezih Ata ◽  
Cihan Ünal ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Cell Differentiation ◽  
Growth Factor ◽  
Postnatal Growth ◽  
Weinberg Equilibrium ◽  
Factor I ◽  
Cattle Breeds ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Native Cattle

Growth Hormone (GH) and Insulin like Growth Factor-I (IGF1) are members of somototrophine axis pathway. They play a role in key on several mechanisms such as postnatal growth, cell differentiation and metabolism. Due to their vital importance, polymorphisms on the genes coding are worth to be understood. In this study five native cattle breeds (Native Southern Yellow (NSY), South Anatolian Red (SAR), Anatolian Grey (AG), Native Black (NB), East Anatolian Red (EAR) were investigated by PCR-RFLP method for GH-MspI and IGF1-SnaBI loci. 198 and 194 samples were analyzed for GH-MspI and IGF1-SnaBI loci, respectively. In both two loci two alleles and three genotypes were observed. Predominant alleles were A and B for GH-MspI locus IGF1-SnaBI loci, respectively. Frequencies of A and B alleles were calculated between 0.400-0.875 and 0.846-0.903 for GH-MspI locus IGF1-SnaBI loci, respectively. While among investigated population only EAR population was at Hardy-Weinberg equilibrium for IGF1-SnaBI locus, for GH-MspI only, in SAR population no deviation from Hardy-Weinberg equilibrium.

scholarly journals Polymorphism of Growth Hormone (GH) Gene in Lakor Goat from Lakor Island of Southwest Maluku Regency

2020 ◽  
Vol 44 (4) ◽  
Author(s):  
Rony Marsyal Kunda ◽  
Slamet Diah Volkandari ◽  
Maman Rumanta ◽  
Pieter Kakisina
Keyword(s):  
Growth Hormone ◽  
Polymorphic Information Content ◽  
Growth Trait ◽  
Hair Follicles ◽  
Nonrandom Mating ◽  
Economic Trait ◽  
Goat Population ◽  
Pcr Rflp ◽  
Gh Gene ◽  
Dna Fragment

Lakor goat survive in Lakor island in Southwest Maluku with high temperature and limited water. Growth trait in goat is interest to explore cause related with economic trait that encoded by growth hormone (GH) gene. The aim of this study was identify of polymorphism GH gene of Lakor goat in Lakor island. A total of 63 samples were collected from three locations (village) i.e Ketti Letpey (18), Werwawan-Yamluli (26), and Letoda (19). DNA was extracted from hair follicles. A 422 bp specific DNA fragment was successfully amplified and genotyped by PCR-RFLP method using HaeIII enzyme. Results showed that polymorphism was found with two variant of genotypes (AA and AB) and two alleles (A and B). AB genotype was dominant in all of populations (93.7%) with A and B alleles were 0.53 and 0.47, respectively. Heterozygosity observed and expected value reached 0.502 and 0.498, respectively while Polymorphic Information Content was in moderate values (0.374). All of populations were in disequilibrium genetic. It maybe caused limited buck and nonrandom mating in population that effect of low genetic variation. Inbreeding study are needed to explore it. The introgression of bucks from other families in several locations within Lakor island can be an alternative solution to increase the genetic diversity of the lakor goat population.

Haplotype combination of the bovine INSIG1 gene sequence variants and association with growth traits in Nanyang cattle

Genome ◽  
2012 ◽  
Vol 55 (6) ◽  
pp. 429-436 ◽  
Author(s):  
Jiajie Sun ◽  
Yuan Gao ◽  
Dong Liu ◽  
Wei Ma ◽  
Jing Xue ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Growth Traits ◽  
Regulatory Element ◽  
Sequence Variants ◽  
Coding Region ◽  
Dna Pooling ◽  
Proteolytic Activation ◽  
Haplotype Combination ◽  
Pcr Rflp ◽  
Sterol Regulatory Element

The insulin-induced gene 1 (INSIG1) gene encodes a protein that blocks proteolytic activation of sterol regulatory element binding proteins, which are transcription factors that activate genes that regulate cholesterol, fatty acid, and glucose metabolism. However, similar research for the bovine INSIG1 gene is lacking. Therefore, in this study, polymorphisms of the bovine INSIG1 gene were detected in 643 individuals from four cattle breeds by DNA pooling, forced PCR–RFLP, PCR–SSCP, and DNA sequencing methods. Only 10 novel SNPs were identified, which included four mutations in the coding region and the others in the introns. In Nanyang individuals, seven common haplotypes were identified based on four coding region SNPs. The haplotype GACT, with a frequency of 75.4%, was the most prevalent haplotypes and SNPs formed two linkage disequilibrium blocks with strong multi-allelic D′ (D′ = 1). Additionally, association analysis between mutations of the bovine INSIG1 gene and growth traits in Nanyang cattle at 6, 12, 18, and 24 months old was performed, and the results indicated that the polymorphisms were not significantly associated with body mass.

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