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Single Nucleotide Polymorphism of Ovine Leptin and Insulin-Like Growth Factor 1 Gene in Kivircik Crossbred Ewes

PJZ_50_3_851-856

 

 

Single Nucleotide Polymorphism of Ovine Leptin and Insulin-Like Growth Factor 1 Gene in Kivircik Crossbred Ewes

Selçuk Kaplan1,* and Sertaç Atalay2

1Faculty of Veterinary Medicine, Department of Genetics, Namik Kemal University, Tekirdag 59100, Turkey

2Central Research Laboratory, Namik Kemal University, Tekirdag 59100, Turkey

ABSTRACT

Kivircik crossbred sheep in the Thrace region are commonly grown for meat production. The objective of the present study was to determine the polymorphism of insulin-like growth factor 1 (IGF1) and leptin (LEP) genes in Kivircik crossbred ewes. Therefore, IGF1/BfoI and Lep/BcnI polymorphisms were examined by polymerase chain reaction- restriction fragment length polymorphism method. The single nucleotide polymorphism (SNP) in the regulatory region of the IGF1 gene was detected by amplification of the 294 bp region using specific primers and cleavage with the BfoI enzyme. Allele frequencies of A and B were found with 0.915 and 0.085 respectively. The genotype frequencies of IGF1 gene were 0.85 (AA), 0.13 (AB) and 0.02 (BB). The SNP in the exon 3 of the LEP gene was detected by amplification of the 494 bp region using specific primers and cleavage with the BcnI enzyme. The estimated frequencies of three genotypes including GG, GA and AA at Lep/BcnI polymorphism were 0.90, 0.09 and 0.01 and they were 0.055 and 0.945 for A and G alleles, respectively. LEP and IGF1 gene showed polymorphic patterns in Kivircik crossbred sheep population. There was no deviation from Hardy-Weinberg equilibrium (P>0.05) relative to LEP and IGF1 genotypes.


Article Information

Received 07 November 2017

Revised 30 November 2017

Accepted 30 December 2017

Available online 06 April 2018

Authors’ Contribution

SK and SA designed the research. SA, SK conducted the experiment. SA analyzed the data. SA and SK wrote the paper. SK revised the paper.

Key words

Leptin, Insulin Like Growth Factor 1, Single nucleotide polymorphism, SNP.

DOI: http://dx.doi.org/10.17582/journal.pjz/2018.50.3.851.856

* Corresponding author: skaplan@nku.edu.tr

0030-9923/2018/0003-0851 $ 9.00/0

Copyright 2018 Zoological Society of Pakistan



Introductıon

 

Genetic variations that affecting the physiological pathways are of great interest because these are related with different production traits in farm animals. The development of molecular genetic techniques have accelerated the identification of variations associated with economically important traits. Moreover, molecular genetic studies can determine the genetic breeding potential by identifying genetic variants in different populations (Kök et al., 2017). Kivircik sheep breed constitutes almost fifty percent of the sheep population in Turkey. Compared to other native sheep breeds, Kivircik sheep have superior meat quality (Ekiz et al., 2009). Therefore, Kivircik sheep is especially known for the delicious taste of the meat (Özcan, 1970). Insulin-like growth factor 1 (IGF1) is a growth factor that plays important role in physiological and metabolic processes in vertebrates (De la Rosa Reyna et al., 2010). IGF1 has significant biological functions including increases the stimulating myogenesis, intake of glucose, prevents apoptosis, attend the activation of cell cycle genes, interrupts in the synthesis of DNA, protein, RNA, and in cell proliferation, enhance the synthesis of lipids and stimulating the production of progesterone in granular cells (Etherton, 2004). IGF1 gene consists of 5 exons located on chromosome 3 in the ovine genome. Although, the structure of the IGF1 gene differs between species, the 70 amino acid sequence of the expressed protein is the same in all vertebrates (Upton et al., 1998). SNPs in IGF1 gene have associated with daily live weight gain (Casas-Carrillo et al., 1997; De la Rosa Reyna et al., 2010), live weight (Zhang et al., 2008; Trukhachev et al., 2016), birth weight (Curi et al., 2005; Zhang et al., 2008) and carcass traits (Islam et al., 2009).

Previous studies have suggested that the IGF1 gene is significant marker gene for growth traits. He et al. (2012) were reported that the polymorphisms in the 5ˈ regulatory region of IGF1 gene have significant effect on growth traits. Scata et al. (2010) also detected two mutations in the 5ˈ regulatory region of ovine IGF1 gene (G855C and G857A) and one mutation (C271T) in exon 3. Allele T of C271T and haplotype G-T of G855C and C271CT had a positive effect on maintaining a constant yield level during lactation in dairy sheep. Trukachev et al. (2016) were reported that SNPs in 5’ regulatory region (5363.C>T), 5’UTR (5188.G>C, 5186.G>A) and the first intron (4088.G>A) associated with live weight. Chelongar et al. (2014) were shown that the SNP in intron 1 in IGF1 gene

Table I.- Primer’s sequences and product’s sizes.

Gene region

Primer sequence (5-3)

Annealing temp. (°C)

Product size (bp)

References

IGF1 5 regulatory region

F: TGAGGGGAGCCAATTACAAAGC

R: CCGGGCATGAAGACACACACAT

55

294

He et al. (2012)

Lep, Exon 3, 170.G>A

F: TGTTGTCCCCTTCCTCCTG

R: CCCACATAGGCTCTCTTCTGC

63

463

Bakhtiar et al. (2017)

 

associated with fat thickness (the tick rump). Nazari et al. (2016) were suggested that the SNP in exon 1 in the IGF1 gene could be used as a marker for birth weight.

LEP gene is involved in the control of several important physiological functions including regulation of hematopoiesis, energy expenditure, angiogenesis, wound healing, lipolysis, fetal growth and immune system function (Reicher et al., 2011). Nucleotide sequence variants in LEP gene have relation with circulating leptin concentration (Buchanan et al., 2007; Jonas et al., 2016), growth traits (Barzehkar et al., 2009; Hajihosseinlo et al., 2012) carcass and meat quality traits (Boucher et al., 2006; Barzehkar et al., 2009) and reproduction traits (Bakhtiar et al., 2017). The LEP gene is located on the chromosome 4 in the ovine genome that encodes a 167 amino acid leptin protein (Hashemi et al., 2011).

 

Table II.- Restrictions enzymes, restriction product size and genotyping.

Gene

PCR products size (bp)

Restriction enzymes

Restriction products size (bp)

Genotyping

IGF1

294

BfoI (Bsp143II Isoschizomers)

100, 194, 294

AB

100,194

BB

294

AA

LEP

463

BcnI

193, 270, 463

GA

193, 270

GG

463

AA

 

The LEP gene is commonly used for MAS studies because it is associated with many economically important traits. Polymorphisms identified in exon 3 of the sheep LEP gene were related to body weight (Hajihosseinlo et al., 2012). The SNP in the coding region of the sheep LEP gene was correlated with muscle growth (Boucher et al., 2006). Two SNPs in intron 2 of sheep LEP gene were related to fat-tail percentage and body and carcass weight (Barzehkar et al., 2009). LEP/BcnI polymorphism (170 G>A) in exon 3 of the sheep LEP gene has significant effect on feed conversion ratio and circulating leptin concentration (Jonas et al., 2016). This SNP (170 A>G) also was associated with reproduction traits in sheep (Bakhtiar et al., 2017).

The present study was designed to investigate SNPs in ovine IGF1 (C1511G, A1513G, 5’ regulatory region) and LEP (170 A>G, exon 3) genes in Kivircik crossbreed ewes.

 

Materials and Methods

Tissue samples

A total of 100 Kivircik crossbred (Kivircik x Merino) ewes tissue samples were collected after slaughtering and stored at -20 °C in a deep freezer as far as molecular genetic studies are performed.

DNA amplification and genotyping

PCR-RFLP method was used to determine for IGF1 (He et al., 2012) and LEP (Bakhtiar et al., 2017) gene polymorphism. The sequences of the primers and the size of the PCR product are given in Table I. Restriction enzymes, the size of restriction products and genotyping are shown in Table II.

All PCR applications were performed with the Phire Tissue Direct PCR Master Mix (ThermoFisher LSG-F170L) in accordance with the manufacturer’s instructions. The PCRs for both SNPs were carried out in volumes of 50 µl using; 25 µl Phire Tissue Direct PCR Master Mix, 0,3-0,5 mm tissue sample, 5 µM each primer, and the rest was ddH2O. The amplification was performed at 98°C for 5 min, followed by 40 cycles at 98°C for 5 sec, annealing for 5 sec, 72°C for 20 sec and a final extension of 72°C for 1 min on T100 Thermal Cycler (Biorad). Annealing temperatures are also shown in Table I.

A fragment of 294 bp in the 5’ regulatory region of the IGF1 gene and a fragment of 463 bp in the exon 3 of the LEP gene were amplified using the primers given in Table I. The PCR products were subjected to electrophoresis on 2 % agarose/ethidium bromide gel (Aga003R, Bioshop, Canada) in 1× TBE buffer (TBE-001, New Bioscience). Gels were visualized under UV light and documented in WGD30S Molecular Imager apparatus (Wisd).

For IGF1/BfoI genotyping, 10 μl of PCR product were digested with 2 μl (20 U) of Fast Digest BfoI (FD2148, ThermoFisher) restriction enzymes at 37°C for 5 min. For LEP.170.G>A genotyping; 10 μl of PCR product were digested with 2 μl (20 U) of BcnI (ER0061, ThermoFisher) restriction enzymes at 37°C for 3 h. The restriction fragments were subjected to electrophoresis on 2 % agarose/ethidium bromide gel in 1× TBE buffer. Gels were visualized under UV light and documented in WGD30S Molecular Imager apparatus (Fig. 1).

Statistical analysis

In this study, The Chi-square test whether genotype frequencies of LEP/BcnI and IGF1/BfoI polymorphism were in Hardy Weinberg equilibrium estimated by PopGene Version 1.32 (Yeh et al., 1997).

 

Results and dıscussıon

 

Genotypic distribution and allele frequencies of IGF1/BfoI polymorphism

Three genotypes were determined in IGF1/BfoI polymorphism in 5′ regulatory region in Kivircik crossbred ewes (Fig. 1A). The allele frequencies of the IGF1/BfoI polymorphism in 5′ regulatory region were calculated according to Hardy-Weinberg equilibrium (Table III). Allele frequencies of A and B were found with 0.915 and 0.085, respectively. The genotype frequencies of IGF1 gene were 0.85 (AA), 0.13 (AB) and 0.02 (BB). There was no deviation from Hardy-Weinberg equilibrium (P>0.05) relative to IGF1 genotypes.

5′ regulatory region is one of the polymorphic sites of IGF1 gene. He et al. (2012) determined two polymorphism named as (C1511G and A1513G) in 5′ regulatory region of IGF1 gene. They reported allele frequencies of A and B in Small Tail Han sheep (0.809-0.191), Hu sheep (0.638-0.362), Texel sheep (0.969-0.031) and Dorset sheep (1.000-0.000), respectively. Trukhachev et al. (2016) reported the allele frequencies of 5′ regulatory region of IGF1 gene as 0.87 (C) and 0.13 (T) in Russian Soviet Merino sheep breed. The allele frequencies for 5′ regulatory region of IGF1 gene for Small Tail Han sheep, Texel sheep and Russian Soviet Merino sheep breed are similar to our study. The other researchers have reported polymorphisms of IGF1 gene with different regions. Moradian et al. (2013) found the allele frequencies of IGF1 (Exon 1) as 0.73 (A) and 0.27 (G) in Makoei Sheep.

Niznikowski et al. (2014) carried out the study to identify the polymorphisms of IGF1 (Exon 3) in Polish Lowland Sheep. They reported that there was no polymorphisms of IGF1 (Exon 3) in Polish Lowland Sheep. Kazemi et al. (2011) studied the promoter region of IGF1 gene in Zel sheep population. The researchers determined the polymorphisms of IGF1 gene and showed the allele frequencies 0.71 (A) and 0.29 (B). In other study, polymorphisms of IGF1 (Exon 3) were identified in Pomeranian Coarsewool ewes. The allele frequencies of

 

 

Table III.- Allele and genotype frequences for IGF1/BfoI and LEP/BcnI polymorphism.

  n

Genotypes

Genotype frequencies

Allel frequencies

(χ²)1

AA

AB

BB

AA

AB

BB

A

B

3.000ns

IGF1

 

 

 

 

 

 

 

 

 

 

Observed 100

85

13

2

0.85

0.13

0.12

0.9150

0.0850

 

Expected 100

83.6834

15.6332

0.6834

0.83

0.15

0.0068

 

 

LEP

 

 

 

 

 

 

 

 

 

2.10ns

Observed 100

90

9

1

0,90

0,09

0.01

0.9450

0.0550

 

Expected 100

89.2764

10.4472

0.2764

0.89

0.10

0.0027

1 χ 20.05;1 ; 3,84 test of Hardy-Weingberg equlibrium; NS, not significant (P > 0.05).

 

0.205 (C) and 0.795 (T) were given in this study (Proskura and Szewczuk, 2014). Grochowska et al. (2017) investigated the polymorphism in 5′ flanking region of the IGF1 gene in in Coloured Polish Merino sheep. The allele frequencies of A and B were found 0.92 and 0.8, respectively.

Genotypic distribution and allele frequencies of LEP/BcnI polymorphism

The genotypes of GG, GA and AA were found in LEP/BcnI polymorphism of Exon 3, 170.G>A in Kivircik crossbreed sheep (Fig. IB). The allele frequencies of the LEP/BcnI polymorphism were calculated according to Hardy-Weinberg equilibrium (Table III). The estimated frequencies of three genotypes including GG, GA and AA at LEP/BcnI polymorphism were 0.90, 0.09 and 0.01 and they were 0.055 and 0.945 for A and G alleles, respectively. There was no deviation from Hardy-Weinberg equilibrium (P>0.05) relative to LEP genotypes. In this study, G allele of LEP/BcnI (exon 3) was found homozygous in Kivircik crossbreed sheep population. Similarly, LEP/BcnI polymorphism in crossbreed Awassi-Merino sheep were reported by Jonas et al. (2016) as 0.08 and 0.92 for A and G, respectively. Mahmoud et al. (2014) reported the A and G allele frequencies for Herri sheep breed as 0.086 and 0.914, respectively. In Sanjabi rams, the allele frequencies were reported as 0.76 (G) and 0.24 (A) (Bakhtiar et al., 2017). This results are in agreement with the current study.

The LEP has different polymorphic sites in sheep breeds. Cauveri et al. (2014) determined two polymorphism in the LEP Exon 3 (16973 G>A, 17476 C>T) in Nilagiri sheep. The allele frequencies were found as 0.87 (C) and 0.13 (T). The other study carried out in Malpura sheep. LEP (Exon 3) T387G locus was found polymorphic. G and T allele frequencies were given 0.82 and 0.18, respectively (Meena et al., 2017). Mahmoud et al. (2014) have also studied different polymorphic sites of LEP gene in Herri sheep breed. There were three non-synonymous polymorphic sites at positions 248 (CTG/CCG-transition), 286 (GTG/TTG-transversion) and 332 (CGG/CAG-transition) and two synonymous polymorphic sites at positions 213 (ACC/GCC transition) and 216 (CCA/CCG transition) determined in this study. The A and G allele frequencies for polymorphic sites at positions 213, 216, 248, 286 and 332 were (0.029-0.971), (0.029-0.971), (0.014-0.986), (0.286-0.714) and (0.114-0.886), respectively.

 

Conclusıons

 

The primary aim of this study to identify the polymorphisms of LEP and IGF1 genes in Kivircik crossbreed population. Therefore, the present study provided basic information to understand the genetic diversity of Kivircik crossbred sheep in terms of IGF1 and LEP genes. The genetic improvement of economically important traits can be developed through marker assisted selection. IGF1 and LEP genes are playing pivotal role in growth and metabolism. So, these genes are well known markers for economically important traits of livestock animals. In this study, the IGF1 and LEP genes have showed polymorphic pattern in Kivircik crossbred ewes and provided valuable informations about sheep breeding. Taken together, these informations not only can be used further selection programs in sheep breeding but also contributed to the literature and ongoing studies.

 

Acknowledgements

 

This study has been supported by the project numbered as NKUBAP.10.GA.17.117 accepted by Commission of Scientific Research Projects of Namık Kemal University in Turkey. We are thankfull to Lider Meat Ipsala company for providing tissue samples.

 

Statement of conflict of ınterest

The author(s) declare(s) that there is no conflict of interests regarding the publication of this article.

 

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