scholarly journals Effect of porcine IL-6 polymorphism on litter size traits in commercial pig breeds

2020 ◽  
Vol 19 (2) ◽  
pp. 237-246
Keyword(s):  
Polymerase Chain Reaction ◽  
Litter Size ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Large White ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Restriction Fragment Length

This study aimed to verify the polymorphisms in the porcine IL-6 gene and to elucidate its effects on litter size traits in Large White and Landrace sows. Four single nucleotide polymorphisms (SNPs) of the porcine IL-6 gene (g.91506415A>G, g.91507983A>G, g.91508173C>T, and g.91508716C>T) were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. There was no polymorphism observed on the three SNPs (g.91506415A>G, g.91507983A>G, and g.91508716C>T) of the porcine IL-6 gene. The porcine IL-6 g.91508173C>T polymorphism was found to be segregating in Large White and Landrace sows. The porcine IL-6 g.91508173C>T polymorphism was significantly associated with the total number born (TNB) and the number of piglets weaned alive (NWA) traits in Large White sows (P<0.05). Moreover, the porcine IL-6 g.91508173C>T polymorphism was significantly associated with the TNB, number born alive (NBA), and NWA traits in Landrace sows (P<0.05). These results indicated that the porcine IL-6 g.91508173C>T polymorphism was associated with litter size traits. These findings confirmed the importance of the IL-6 gene as a candidate gene for litter size traits in pigs.

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

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

scholarly journals Application of polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) in the analysis of single nucleotide polymorphisms (SNPs)

2021 ◽  
Vol 17 ◽  
pp. 48-53
Author(s):  
Piotr Tarach
Keyword(s):  
Polymerase Chain Reaction ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Dna Analysis ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Polymerase Chain ◽  
Restriction Fragment Length

Polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) is a technique used to identify single nucleotide polymorphisms (SNPs) based on the recognition of restriction sites by restriction enzymes. RFLP-PCR is an easy-to-perform and inexpensive tool for initial analysis of SNPs potentially associated with some monogenic diseases, as well as in genotyping, genetic mapping, lineage screening, forensics and ancient DNA analysis. The RFLP-PCR method employs four steps: (1) isolation of genetic material and PCR; (2) restriction digestion of amplicons; (3) electrophoresis of digested fragments; and (4) visualisation. Despite its obsolescence and the presence of high-throughput DNA analysis techniques, it is still applied in the analysis of SNPs associated with disease entities and in the analysis of genetic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RFLP-PCR is a low-cost and low-throughput research method allowing for the analysis of SNPs in the absence of specialised equipment, and it is useful when there is a limited budget.

scholarly journals Μελέτη της επίδρασης πολυμορφισμών και της έκφρασης γονιδίων στις αναπαραγωγικές παραμέτρους των χοιρινών

2014 ◽  
Author(s):  
Απόστολος Μαραντίδης
Keyword(s):  
Polymerase Chain Reaction ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Chain Reaction ◽  
Large White ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Restriction Fragment Length

Σκοπός της παρούσας διδακτορικής διατριβής ήταν η μελέτη της αναπαραγωγής των χοίρων και η εν δυνάμει βελτίωση της παραγωγικότητας τους, όσων αφορά τη βελτίωση των αναπαραγωγικών χαρακτηριστικών των χοιρομητέρων με σκοπό την αύξηση των παραγόμενων χοιριδίων και την προστασία του αναπαραγωγικού συστήματος των αρσενικών και θηλυκών χοίρων από διάφορες ασθένειες. Η δομή της παρούσας διδακτορικής διατριβής χωρίζεται σε δύο Μέρη. To ΜΕΡΟΣ Α περιλαμβάνει τη μελέτη της έκφρασης γονιδίων σε διάφορα αναπαραγωγικά όργανα των χοίρων, σε σειρές κυττάρων και σε έμβρυα χοίρων παραγόμενα in vitro. Πραγματοποιήθηκε προσδιορισμός της έκφρασης των γονιδίων της οικογένειας TLR και της οικογένειας των β-defensins. Μελετήθηκε το πρότυπο έκφρασης τους στην ωοθήκη, τον ωαγωγό, τον όρχι και την επιδιδυμίδα των χοίρων, στα κοκκώδη κύτταρα που περιβάλλουν το ωάριο καθώς επίσης και σε έμβρυα χοίρων παραγόμενα in vitro. Επίσης έγινε προσδιορισμός της επίδρασης της επώασης με LPS στα επίπεδα έκφρασης των παραπάνω γονιδίων στα κοκκώδη κύτταρα για διαφορετικά χρονικά διαστήματα (0, 6, 12 και 24 ώρες) παρουσία ή μη του συστατικού LPS (Lipopolysaccharide). Το ΜΕΡΟΣ Β περιλαμβάνει τον προσδιορισμό των πολυμορφισμών γονιδίων που σχετίζονται με την αναπαραγωγή και την πιθανή τους σχέση με παραγωγικά χαρακτηριστικά των χοιρομητέρων που εκτρέφονται στην ελληνική επικράτεια. Η τεχνική που εφαρμόστηκε για την διερεύνηση των συγκεκριμένων πολυμορφισμών (SNPs) ονομάζεται PCR – RFLP (Polymerase Chain Reaction – Restriction Fragment Length Polymorphism). Συνολικά επιλέχθηκαν τρία γονίδια που σχετίζονται με αναπαραγωγικά χαρακτηριστικά σε χοιρομητέρες (γονίδιο BF, γονίδιο RBP4 και γονίδιο ESR2) τα οποία μελετήθηκαν σε 420 χοιρομητέρες που προέρχονταν από τρεις εμπορικές χοιροτροφικές μονάδες της Ελλάδας. Οι 400 προέρχονταν από μεγάλες εμπορικές μονάδες και ήταν διασταυρώσεις των φυλών Landrace/Large White ενώ τα αρσενικά Duroc/Pietrain/Landrace/Large White σε διάφορες αναλογίες. Στην πρώτη μονάδα έγινε εξαγωγή DNA σε 120 χοιρομητέρες και σε 8 αρσενικούς χοίρους ενώ στη δεύτερη μονάδα σε 280 χοιρομητέρες και σε 8 αρσενικούς χοίρους. 20 χοιρομητέρες προέρχονταν από μια εκτατική μονάδα χοίρων (ελληνικής αυτόχθονης φυλής, μαύρα ή διασταυρώσεις τους με αγριόχοιρους των ορεινών περιοχών της Μακεδονίας). Τα παραγωγικά χαρακτηριστικά που συσχετίστηκαν με τους πολυμορφισμούς των γονιδίων αφορούν το μέγεθος της τοκετομάδας και τον Αριθμό Απογαλακτισθέντων χοιριδίων.

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

2015 ◽  
Vol 58 (2) ◽  
pp. 317-323 ◽  
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.

scholarly journals Polymorphism of the kappa-casein gene in two Bosnian autochthonous cattle breeds

2010 ◽  
Vol 53 (3) ◽  
pp. 277-282
Author(s):  
M. Brka ◽  
A. Hodžić ◽  
N. Reinsch ◽  
E. P. Zečević ◽  
A. Dokso ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Restriction Fragment Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Small Population ◽  
Chain Reaction ◽  
Casein Gene ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Related Breed ◽  
Restriction Fragment Length

Abstract. Buša is an old endangered autochthonous breed of the western Balkan, especially Bosnia-Herzegovina, Kosovo and Albania. A related breed is Gatačko, derived from Buša × Tirolean Grey crossbreds. Fifteen purebred Buša cattle and thirteen Gatačko animals were genotyped for polymorphisms at the kappa-casein gene by a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) essay. The alleles A, B and C were found and the allelic frequencies were 0.46 (A), 0.46 (B) and 0.08 (C) in Buša cattle and 0.58 (A) and 0.42 (B) in Gatačko. Only AA, AB, BB and BC genotypes occurred. Further alleles were not detected and are therefore either absent in both populations or rare. The allele »B« found in this small population will be useful for a sire selection program in the future.

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