Identification of KLF3 gene polymorphism in Indonesian Friesian Holstein cattle

The KLF3 gene was a potential genetic marker candidate due to its involvement in many biological processes such as cell proliferation, cell differentiation, and apoptosis. This study was conducted to identify the KLF3 gene polymorphism in the Indonesian FH cattle. A total of 302 individual cattle blood samples from West Java (n=138), Central Java (n=34), and East Java (n=130) provincies were used to obtainDNA samples. The DNA sequencing was performed using 9 samples (each location of sampling represented by 3 samples) for initial identification of the KLF3 gene polymorphismand followed by PCR-RFLP analysis using all DNA samples. There were two SNPs identified in the intron region of the KLF3 gene i.e. SNP g.59607486delC and SNP g.59607554A>G. The SNP g.59607554A>G could be detected using PCR-RFLP method with HpyCH4IV restriction enzyme and resulted three genotypes of the KLF3 gene (AA, AG, and GG) but its heterozygosity value was low in the Indonesian FH cattle. The AA genotype has the highest frequency (0.73), while the AGand GG genotypes frequency were 0.24 and 0.03, respectively. Information about the KLF3 gene polymorphism in this study can be considered for further study to analyse its association with milk and protein yield traits.

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Identifikasi Keragaman Gen FTO Pada Bangsa Sapi Potong Indonesia

Jurnal Ilmu dan Teknologi Peternakan Tropis ◽

10.33772/jitro.v6i2.5655 ◽

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.

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Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v8i3.6748 ◽

2016 ◽

Vol 8 (3) ◽

pp. 362

Author(s):

Fidia Fibriana ◽

Lutfia Nur Hadiyanti

Keyword(s):

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Morphological Characteristics ◽

Biology Education ◽

Rflp Analysis ◽

Restriction Pattern ◽

Internal Transcribed Spacers ◽

Central Java ◽

Pcr Rflp ◽

Pcr Products

In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian.How to CiteFibriana, F., & Hadiyanti, L. N. (2016). Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA. Biosaintifika: Journal of Biology & Biology Education, 8(3), 362-370.

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Polymorphism of ADIPOQ and EDG1 genes in Indonesian beef cattle

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.43.4.323-332 ◽

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.

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Association of growth hormone (GH) gene polymorphism with growth and carcass in Sumba Ongole (SO) cattle

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.42.3.153-159 ◽

2017 ◽

Vol 42 (3) ◽

pp. 153 ◽

Cited By ~ 2

Author(s):

P. P. Agung ◽

S. Anwar ◽

W. P. B. Putra ◽

M. S. A. Zein ◽

A. S. Wulandari ◽

...

Keyword(s):

Growth Hormone ◽

Gene Polymorphism ◽

Fragment Length Polymorphism ◽

Growth Parameters ◽

Rflp Analysis ◽

Cattle Breeding ◽

Pcr Rflp ◽

Gh Gene ◽

Polymerase Chain ◽

Dressing Percentage

A study was conducted to identify the polymorphism in the intron 3 of the Growth Hormone (GH) gene and also to evaluate the association of the GH gene polymorphism with growth parameters and dressing percentage in the Sumba Ongole (SO) cattle. A total of 267 individual DNA samples were used in the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The SO cattle growth parameters data (n=44) including birth weight (BW), weaning weight at 205 days of age (WW205), yearling weight at 365 days of age (YW365) and also dressing percentage (DP) (n=122) were investigated in this study. There were three genotypes (AA, AB, and BB) of the GH gene based on the PCR-RFLP analysis with allele frequency was 0.87 and 0.13 for A allele and B allele respectively. The highest genotype frequency in the SO cattle is AA (0.76) and the lowest is BB (0.02). The Heterozygosity Observed (Ho) value in the SO cattle population is 0.23 and Polymorphism Information Content (PIC) value is 0.20. Therefore, the genetic diversity in the SO cattle based on the GH gene polymorphism is quite low. There is no association (P>0.05) in BW, WW205, YW365, and DP with genotypes of the GH gene. As the result, the GH gene in this study cannot be used as a genetic marker in the SO cattle breeding program.

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CHARACTERISTIC OF MILK PRODUCTIVITY OF COWS-HEIFERS WITH DIFFERENT GENOTYPES OF SOMATOTROPIN (GH)

Vestnik of Kazan state agrarin university ◽

10.12737/article_5db9535ed384a3.87060395 ◽

2019 ◽

Vol 14 (3) ◽

pp. 58-61

Author(s):

Наталья Сафина ◽

Natal'ya Safina ◽

Ильназ Гилемханов ◽

Il'naz Gilemhanov ◽

Фарида Зиннатова ◽

...

Keyword(s):

Gene Polymorphism ◽

Agricultural Production ◽

Selection Criteria ◽

Rflp Analysis ◽

Analysis Method ◽

Milk Productivity ◽

Cattle Breeding ◽

Pcr Rflp ◽

Dairy Cattle Breeding ◽

The Republic

. Polymorphisms of genes may be useful as genetic markers for additional selection criteria in dairy cattle breeding for economically advantageous traits. The presented study is dedicated to the influence of gene polymorphism, responsible for milk quality and milk productivity was carried out among Holstein cow-heifers in Integrated Agricultural Production Centre “Stud farm named after Lenin” of Atninsky district of the Republic of Tatarstan. DNA samples were isolated from blood samples of 130 cows for genotyping according to gene of growth hormone (GH) by PCR-RFLP analysis method. The genotypes distribution of the somatotropin gene were as follows: LL – 63.8% (83 animals), LV – 30.0% (39 animals), VV – 6.2% (8 animals), the distribution in frequency of occurrence of alleles L - 0.788 and V - 0.212. When considering the gene polymorphism association with the signs of milk production and the qualitative composition of milk showed prominent results cow-heifers with a LL genotype. The identified relationships indicate the possible genetic improvement of the investigated herds using marker-assisted selection.

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Melanocortin 4 receptor (Mc4r) gene polymorphism and its association with body weights of some breeds of rabbit

Nigerian Journal of Animal Production ◽

10.51791/njap.v47i2.48 ◽

2020 ◽

Vol 47 (2) ◽

pp. 1-7

Author(s):

O. H. Osaiyuwu ◽

U. F. O. Bolaji ◽

O. A. Adeyinka ◽

M. O. Akinyemi ◽

A. E. Salako

Keyword(s):

Body Weight ◽

New Zealand ◽

Gene Polymorphism ◽

Rflp Analysis ◽

The Body ◽

Chi Square ◽

Mc4r Gene ◽

Fta Cards ◽

Melanocortin 4 Receptor ◽

Pcr Rflp

In livestock production, traditional methods of selection have always been the way to go. However, with the advent of genomics techniques, methods such as PCR-RFLP is been employed to identify single nucleotide polymorphism of likely candidate genes useful for livestock selection and improvement. Therefore, the aim of this study was to investigate the association of Melanocortin 4 Receptor (MC4R) gene polymorphism with the body weight ofrabbits. Seventy-four rabbits were used for this study consisting of six breeds; 26 Chinchilla, 3 Californian, 11 Dutch, 4 English Spot, 10 New Zealand White and 20 Fauve de Bourgogne (FDB) breeds. Blood samples were collected from the animals with needle and syringe and transferred unto FTA cards and stored away from light. Body weight measurements on the animals were recorded from 2 weeks to 20 weeks. PCR-RFLP analysis produced threegenotypes AA, AG, GG with genotype frequency of 0.14, 0.69 and 0.18 respectively. Allele frequency 0.48 and 0.52 for allele A and G respectively was obtained. Chi-square test showed that the population was not in Hardy-Weinberg equilibrium. Association analysis between the MC4R “c.101G>A” SNP and body weight of rabbit was tested using GLM procedure of SAS programme. Genotype GG had higher body weight (p<0.05) at 12, 16 and 20 weeks inthe Dutch rabbits while genotype AA recorded a higher (p<0.05) body weight value at 12 weeks in New Zealand White rabbits. More so, female Dutch rabbits had higher (p<0.05) mean weight than the males at 12, 16 and 20 weeks of age. Male New Zealand White breeds recorded higher (p<0.05) mean weight than the female animals. The result of the study showed that MC4R “c.101G>A” SNP was not associated with the body weight in the studied rabbit population, although, genotype AA had higher mean weight values at 12, 16 and 20 weeks of age than genotypes AG and GG.

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PCR-RFLP Analysis of D-Loop mtDNA in Indonesian Domestic Waterfowl

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v9i3.12177 ◽

2017 ◽

Vol 9 (3) ◽

pp. 537

Author(s):

R Susanti ◽

Fidia Fibriana ◽

Ari Yuniastuti

Keyword(s):

Restriction Fragment ◽

Rflp Analysis ◽

Muscovy Duck ◽

Genetic Characteristics ◽

Fragment Pattern ◽

Central Java ◽

Pcr Rflp ◽

Restriction Sites ◽

D Loop ◽

Restriction Fragment Pattern

Phylogenetic or population genetic studies have been focused on finding genetic variations in mitochondrial DNA (mtDNA) because mutations in this region contained five times higher than other genetic materials. The aim of this research was to generate PCR-RFLP D-loop mtDNA profiles of some Indonesian domestic waterfowl. The samples were 35 local ducks, 5 muscovy duck, and 5 geese. These local ducks included on seven types of Javanese ducks in Central Java, i.e. Magelang duck, Peking duck, Pengging duck, Tegal Branjangan duck, Tegal Jarakan duck, Tegal Blorong duck, and Tegal Lemahan duck. PCR technique was used to amplify the D-loop genes, and RFLP analysis of the D-loop was performed with AluIand RsaI. The results show that muscovy duck has no restriction sites in D-loop gene. Moreover, goose has a restriction site of AluI in D-loop gene at 550 bp and 187 bp; and it has no restriction site of RsaI. The analysis of RsaI-RFLP in mtDNA D-loop region of ducks resulted in 1 restriction fragment pattern which can be applied in the identification of duck to differentiate it from goose and muscovy duck. PCR-RFLP analysis duck D-loop mtDNA using AluI and RsaI restriction enzyme resulted in 3 combinations of restriction fragment pattern shown in 3 haplotypes (A, B, and C). Genetic diversity of Indonesian domestic waterfowl population could be identified by using PCR-RFLP analysis on mtDNA D-loop region. So far, there are few results of research on Indonesian domestic waterfowl genetic characteristics based on PCR-RFLP mtDNA D-loop marker. Also, this research has a good contribution on genetic characterization of local duck. The characterization is an important aspect to maintain breed quality and manage the genetic resources of Indonesian germplasm and in facilitating the breeding program.

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Calpastatin (CAST) Gene Polymorphism in Tsigai and Merinoland Sheep Breeds Under Conditions of the Republic of Crimea

BIO Web of Conferences ◽

10.1051/bioconf/20213606002 ◽

2021 ◽

Vol 36 ◽

pp. 06002

Author(s):

Veronika Uppe ◽

Tatiana Kuevda ◽

Denis Zubochenko ◽

Elena Usmanova ◽

Pavel Ostapchuk

Keyword(s):

Gene Polymorphism ◽

Research Methods ◽

Rflp Analysis ◽

Primary Objective ◽

Ongoing Study ◽

Allelic Variants ◽

Study Research ◽

Pcr Rflp ◽

The Republic ◽

Cast Gene

The article presents the results of studying the Calpastatin (CAST) gene polymorphism in Tsigai (n = 23) and Merinoland sheep breed (n = 13). The purpose of the research. The possibility of using PCR-RFLP analysis to detect the Calpastatin (CAST) gene polymorphism in Tsigai and Merinoland sheep was the primary objective of this ongoing study. Research methods. Calpastatin (CAST) gene polymorphism was analyzed by PCR-RFLP analysis using the MspI endonuclease restriction. Results. We revealed the diversity of genotypes and allelic variants of the Calpastatin (CAST) gene in Tsigai and Merinoland Breeds. It was found that M allele of the Calpastatin locus is the most common. Frequencies of MM, MN and NN genotypes were found to be 74, 4 and 22 % in Tsigai breed. Among the representatives of Merinoland sheep, the frequencies of MM and MN genotypes were 92 % and 8%, respectively. No animals with NN genotypes were found.

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