Novel SNPs in the leptin gene: implications for growth performance in cultured European sea bass (Dicentrarchus labrax)

Fatty acid binding proteins (FABPs), which belong to the multigene family, play an important role in homeostasis, lipid uptake and transport in tissues. Intestinal fatty acid binding protein (I-FABP) is a small cytosolic protein and is highly active in intracellular fatty acid metabolism in fish gut. The European Sea bass (Dicentrarchus labrax) is an important commercial marine fish species in the Mediterranean region. In the present study, the partial I-FABP gene region of European sea bass was sequenced for detecting single nucleotide polymorphism (SNP) using DNA sequencing. We identified one SNP (g.2450T>C) in the noncoding region of the I-FABP gene in European sea bass. In this study, the relationship between the g.2450T>C locus of the I-FABP (fabp2) gene and body length, post-anal length, body weight and fillet weight was found significant (PC locus in I-FABP which could affect growth and muscle fat content, can be used for marker-assisted selection (MAS) studies in European sea bass.

The myostatin (MSTN) gene, known as growth differentiation factor-8 (GDF-8), is a member of the transforming growth factor-β (TGF-β) superfamily and plays a specific inhibitory role during the critical phases of skeletal muscle mass development in vertebrates. This study was conducted to investigate MSTN polymorphisms in harvest size European sea bass reared in Turkey. Nine single nucleotide polymorphisms (SNPs) and two indels were identified in exons 1-3 of MSTN in the European sea bass population The associations between the g.16612A indel located in intron 1 and standard length were significant. The MSTN g.15252T > A locus in intron 2 was significantly related to the total weight, fillet weight and standard length (P < 0.05). The relationship between the g.14873C > T locus in exon 3 of MSTN and standard height, head length, body length, pre-anal length, abdominal length, post-anal length and head width was significant (P < 0.05). According to the results of the haplotype analysis, two haplogroup and eight haplotype combinations were detected in the population. The haplogroup 2 had significant associations with all measured growth traits (P < 0.05). Thus, SNPs and haplotypes identified in this study could be useful for European sea bass breeding and marker-assisted selection.

How to genetically increase fillet yield in fish: Relevant genetic parameters and methods to predict genetic gain

BackgroundGrowth performance, which can be evaluated using various body measurements, is crucial for providing red meat for human consumption. This study aims to improve the growth performance of sheep by identifying the different genotypes of leptin and IGFI genes associated with higher body measurements.MethodsIn this study, we collected blood samples from Barki (n = 30) and Farafra (n = 30) sheep, and measured their body height, width, length, and weight, and tail width and length to assess their growth performance. We used single strand conformation polymorphism polymerase chain reaction (SSCP-PCR) and sequencing analysis to identify single nucleotide polymorphisms (SNPs) and different genotypes of the leptin and insulin-like growth factor receptor (IGFI) genes associated with sheep body measurements.ResultsThe leptin gene (209 bp) and IGFR gene (345 bp) were found to have three (TT, TG, and GG) and (TT, TC, and CC) genotypes, respectively, by SSCP-PCR. Sequence analysis revealed a SNP in the leptin gene (200G > T) with two alleles (G allele: OR058867 and T allele: OR058868). This SNP resulted in the substitution of the amino acid valine with leucine, which increased the width, length, and weight of the body and tail width in the heterozygous form (TG). The IGFI gene had three SNPs: 305 G > T in TT genotype (OR260670), 184C > T, 265T > C, and 305G > T in TC genotype (OR260669), and 265T > C in CC genotype (OR260671). The TC genotype of the IGFR gene was correlated with higher values of body measurements. Barki sheep were found to have the highest values for body weight, width, length, and tail width compared to Farafra sheep.ConclusionWe recommend the use of entire Barki sheep in inbreeding programs to improve growth performance in Egyptian sheep.

In order to assess the extent of DNA sequence variation in cattle, introns and exons from both the leptin and Amyloid Precursor Protein (APP) genes have been sequenced in a panel of DNAs derived from 22 diverse animals. Direct DNA sequencing of PCR products was used; thus, 44 chromosomes were studied. Polymorphisms were identified by manual scanning of sequence chromatograms and computerized sequence analysis. Twenty Single Nucleotide Polymorphisms (SNPs) were detected in 1788 bp sequenced from the leptin gene, giving a frequency of 1 SNP per 89 bp. Twenty-four SNPs were detected in a 458-bp fragment of the APP gene; 23 of the polymorphisms were contained in a 302-bp intron 16 fragment. This equates to an SNP frequency of 1 per 13 bp for the intron. We can thus conclude that this portion of the bovine APP gene constitutes a hypermutable region. Nucleotide sequence diversity values of 0.019 and 0.0026 were obtained for APP and leptin respectively.

Genetic parameters for fillet traits and body measurements in Nile tilapia ( Oreochromis niloticus L.)

Characterization and refinement of growth related quantitative trait loci in European sea bass (Dicentrarchus labrax) using a comparative approach

The growth-correlated genes that are part of the neuroendocrine growth axis play crucial roles in the regulation of growth and development of pig. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, seven pairs of primers were designed to obtain unknown sequences of growth-correlated genes, and other 25 pairs of primers were designed to identify single nucleotide polymorphisms (SNP) using the denaturing high-performance liquid chromatography (DHPLC) technology in four pig breeds (Duroc, Landrace, Lantang and Wuzhishan), significantly differing in growth and development characteristics. A total of 101 polymorphisms were discovered in 10,707 base pairs (bp) from six genes of the ghrelin (GHRL), leptin (LEP), insulin-like growth factor II (IGF-II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin-like growth factor binding protein 3 (IGFBP-3), and somatostatin (SS). The observed average distances between the SNP in the 5'UTR, coding regions, introns and 3'UTR were 134, 521, 81 and 92 bp, respectively. Four SNPs were found in the coding regions of IGF-II, IGFBP-2 and LEP, respectively. Two synonymous mutations were obtained in IGF-II and LEP genes respectively, and two non-synonymous were found in IGFBP-2 and LEP genes, respectively. Seven other mutations were also observed. Thirty-two PCR-RFLP markers were found among 101 polymorphisms of the six genes. The SNP discovered in this study would provide suitable markers for association studies of candidate genes with growth related traits in pig.

Single nucleotide polymorphisms in GBBSI and SSIIa genes in relation to starch physicochemical properties in selected rice (Oryza sativa L.) varieties

The aim of this study was to examine whether there is an association among genetic variability in leptin (LEP) and leptin receptor (LEPR) genes and male infertility. We performed a case-control study and were searching for an association between polymorphisms of LEP and LEPR genes and male infertility. The study group consisted of 317 patients with idiopathic infertility and a control group of 241 fertile men from Slovenia. Four single nucleotide polymorphisms (SNPs) in LEP gene and four single nucleotide polymorphisms (SNPs) in LEPR gene were chosen and genotyped. Statistically significant SNP was further validated in additional 255 infertile patients and 168 controls from Serbia and Macedonia. In the Slovenian population, we found a statistically significant difference in genotype distribution for rs10244329 polymorphism in LEP gene (recessive genotype model, p value=0.048). The trend toward statistically significant difference in genotype distribution for rs10244329 polymorphism was confirmed in the Serbian and Macedonian populations (p value=0.07). Our data suggest that genetic variability in the LEP gene might be associated with male infertility warranting further confirmation and mechanistic investigations.

Abstract. Hilmia N, Ramdani D, Hidayat R, Widyastuti R, Hernaman I, Dudi, Edianingsih P, Arifin J. 2023. Single Nucleotide Polymorphism R25C and R25H on Leptin gene and their association with body weight and measurements of Pasundan cattle. Biodiversitas 24: 6310-6315. The Leptin gene is a potential candidate for genetic selection in livestock. Nonsynonimous Single Nucleotide Polymorphisms (SNP) Arg25Cys/R25C in Leptin gene associated with fat deposition mainly. This study aimed to identify polymorphism of Leptin Gene based on SNPs of Pasundan cattle and their association with body weight and measurements. This research used 64 DNA samples along with the corresponding body weight and measurement data from Pasundan cattle. About 9 and 7 DNA samples from Bali and Ongole cross (PO) cattle respectively, were also collected as comparisons. The DNA along 620 bp was multiplied by PCR. The SNPs in the Leptin gene on exon two were identified, followed by direct sequencing of the PCR product. The sequencing results were analyzed by BioEdit and Molecular Evolutionary Genetic Analysis (MEGA) 4.0. The General Linear Model analyzed the association between SNPs and body weight and measurements. The results showed there were two nonsynonymous SNP in the Leptin gene on exon two, i.e. g.1047C&gt;T/Arg25Cys/R25C (T allele) that changed amino acid Arginine to Cysteine and g.1048G&gt;A/Arg25His/R25H (A allele) which changed Arginine to Histidine. The frequency of the C allele in the Leptin gene on Pasundan cattle (0.54) was higher than mutation alleles, i.e. T ( 0.29) and A allele (0.17). There were six genotypes: CC (0.266), CT (0.390), CA (0.156), TT, TA, and AA 0.063 respectively. The Leptin gene mutation at the 25th position of amino acids, which changed Arginin to Cystein or Histidin (R25C and R25H), did not affect body weight and measurement in Pasundan Cattle. Therefore, nonsynonymous SNP R25C and R25H could not be used as marker genetic selection in Pasundan cattle.

A candidate gene suspected of affecting pigs' reproductive traits is known as the leptin (LEP) gene. Based on the information found in Leptin GenBank's DNA sequence database, this research aimed to determine single nucleotide polymorphisms (SNPs) and changes in nucleotides and phylogenetic trees in pigs. The data from NCBI GenBank was used to obtain three different DNA sequences of the Leptin gene in pigs. The DNA sequence data for leptin were aligned using BioEdit to establish the sites of SNPs and alterations in nucleotides. A phylogenetic tree was constructed using Mega X. DNA sequences were, and the pig LEP gene was sequenced resulted in 11 SNPs. These findings are based on the sequence regions. The phylogenetic analysis revealed that the sequence of the Leptin gene in pigs (Sus scrofa) clustered more closely with that of goats (Capra hircus) than it did with the sequence of the LEP gene among the cattle (Bos taurus and Bos indicus). The outcomes of this study can serve as a basis for more investigation into the connection between the LEP gene SNP and reproductive traits in pigs as one of potential genes for molecular selection.

Association analyses of single nucleotide polymorphisms in the LEP and SCD1 genes on the fatty acid profile of muscle fat in Simmental bulls

Obesity is associated with circulating levels of adiponectin and leptin and endometrial cancer risk. Little is known about whether single nucleotide polymorphisms (SNPs) in the genes that encode adiponectin (ADIPOQ), leptin (LEP), adiponectin receptor 1 (ADIPOR1), adiponectin receptor 2 (ADIPOR2), and leptin receptor (LEPR) are associated with endometrial cancer. The authors selected 87 tagging SNPs to capture common genetic variants in these 5 genes. These SNPs were evaluated in 1028 endometrial cancer cases and 1932 community controls recruited from Chinese women. Logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs). Three of the 10 SNPs evaluated in the ADIPOQ gene were significantly associated with reduced cancer risk. The OR for women homozygous for the minor allele (A/A) for rs3774262 was 0.68 (95% CI, 0.48-0.97) compared with women homozygous for the major allele (G/G). Similar results were found for SNPs rs1063539 and rs12629945 in ADIPOQ, which were in linkage disequilibrium with rs3774262. These associations became nonsignificant after Bonferroni correction was applied. Controls with the minor allele A at rs3774262 had lower weight, smaller waist and hip circumferences, and lower body mass index than controls with the major allele G (all P < .05). Women homozygous for the minor allele (T/T) of rs2071045 in the LEP gene also had significantly lower risk (OR, 0.70; 95% CI, 0.54-0.90) than women homozygous for the major allele (C/C). No other SNPs in the LEP, ADIPOR1, ADIPOR2, or LEPR genes were found to be associated with cancer risk. Although a chance finding cannot be ruled out, the consistency of findings for gene-endometrial cancer risk and gene-obesity measurements suggests that genetic polymorphisms in the ADIPOQ gene may play a role in endometrial cancer development.

IntroductionAdiponectin is an adipose tissue-specific protein with insulin-sensitizing properties. Many investigators have explored the association between adiponectin single nucleotide polymorphisms (SNPs) and type 2 diabetes mellitus (T2DM) in different ethnic populations from different regions. Leptin is a protein hormone constituting an important signal in the regulation of adipose tissue mass and body weight. The aim of this study was to explore potential associations between SNP +45 T>G of the adiponectin gene and SNP 2548G/A of leptin with T2DM and the effect of SNPs on serum adiponectin and leptin levels.Material and methodsFrom the Egyptian population, we enrolled 110 T2DM patients and 90 non-diabetic controls. Serum lipid profile, blood glucose, serum adiponectin, and leptin were measured. Genotyping for two common SNPs of the adiponectin and leptin genes was performed by polymerase chain reaction–restriction fragment length polymorphism.ResultsThe G allele and TG/GG genotype of SNP 45 occurred more frequently than the T allele and TT genotype in T2DM patients compares to the controls. Subjects with the GG + TG genotype of SNP 45 were at increased risk for T2DM (OR = 6.476; 95% CI: 3.401–12.33) and associated with a low serum adiponectin level compared with the TT genotype. The serum leptin concentration of GA + AA genotype carriers was not significantly different from that of the GG genotype in the diabetic group.ConclusionsThe G allele carriers who have reduced plasma concentrations of adiponectin may have an association with T2DM, while leptin SNP 2548 G/A is not associated with the risk of development of T2DM in the Egyptian population.