Single-strand Conformation Polymorphism Technique Research Articles

Analysis of mutational variations in TP53 tumour suppressor gene among Pakistani head and neck cancer patients.

The aim of this study was to determine the frequency of TP53 mutation among Pakistani head and neck cancer (HNC) patients who visited Nishtar Hospital Multan and Nishtar Institute of Dentistry (NID), Multan, Pakistan. While significant research has been conducted on the role of p53 in HNC throughout the world, this study is the first of its kind in Southern Punjab, Pakistan. A total of 242 samples (121 cases and 121 controls) were collected from Nishtar Hospital Multan and NID, Multan, Pakistan. After histopathological analysis to determine the stage type and grade of malignancy, DNA extraction and sequencing were carried out to assess any mutations in the TP53 region (exons 5-8). Genetic screening was performed by the polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) technique and Chromas 2.6.6 was used to visualise the sequencing results. The mean age of cases was 50.73 ±16.41 years and controls were 37.55 ± 15.51 years. The frequency of HNC was higher in male patients (65.28%) than in female patients (34.71%). Overall, this cancer was found to be significantly more prevalent in the age group of >35-55 years (p < 0.001). Smoking (51% versus 14%), naswar usage (15.7% versus 6.6%), poor oral hygiene (52.9% versus 29.8%) and anemic status (57.0% versus 4.1%) were significantly associated with cases (p ≤ 0.05) compared to controls. Only 04 samples exon 5 (1 sample), exon 7 (2 samples) and exon 8 (1 sample) with changed mobility patterns were found on the SSCP gel. All mutations were missense and heterozygous. Out of four mutant samples, three mutations were in the hotspot regions (codon 175, 245 and 248) of p53. Based on this study, there may be a weak association between the TP53 exon 5-8 mutation and HNC patients in Southern Punjab, Pakistan.

Reproduction of Awassi and Hamdani Sheep Is Associated With a Novel Missense SNP (p.24Ile>Thr) of the GnIH Gene.

Litter size is a crucial economic factor in the sheep industry. Several factors and genes influence litter size, making the identification of genes or loci involved a genetic challenge. Gonadotropin-inhibitory hormone (GnIH) is one of several genes that influence sheep's reproductive traits. Thus, this study aimed to investigate whether variations in the GnIH gene affect the reproductive performance of Awassi and Hamdani ewes. DNA was extracted from 99 single-progeny ewes and 101 twin ewes. The polymerase chain reaction (PCR) produced amplicons of 262 bp, 275 bp, and 284 bp from exons 1, 2, and 3 of the GnIH gene. Single-strand conformational polymorphism (SSCP) technique was used for genotyping experiments. Sequencing and in silico analysis were performed on each set of SSCP-resolved bands. Two genotypes of 262 bp amplicons were found: TT and TC. Sequence analysis revealed a novel missense mutation in the TC genotype at position c.122T>C. Five in silico tools were used to assess the impact of this mutation on GnIH protein structure, function, and stability, all of them demonstrated a deleterious effect. An analysis of statistical data revealed a strong correlation between the c.122T>C single-nucleotide polymorphism (SNP) and reproductive performance. Ewes with the SNP 122T>C exhibited a significant increase in litter size, twinning rates, lambing rates, and days to lambing when compared with ewes with the TT genotype. A lower number of lambs were born to ewes with the TT genotype than those with the TC genotype. These results concluded that the c.122T>C SNP variant positively influences the reproductive performance of Awassi and Hamdani sheep. Sheep that carry the c.122T>C SNP show higher litter size and increased productivity.

Association Between of the Growth Hormone Gene GH-1 with Growth Indicators of Common Carp Cyprinus carpio L. in Three Different Ecosystems

This study was conducted in the central of health laboratory/Animal and Fish Resource Research Center, Agricultural Research Department, Ministry of Science and Technology, for the period from 15/8/2021 to 15/11/2021 in order to investigate the polymorphism of the growth hormone gene GH-1 and its relationship to the productive performance (body weight, total length, age and case factor) of common carp Cyprinus carpio, in 90 fish representing three different ecosystems (30 fish for each site) including floating cages, ponds, and the environment of the Tigris River, south of Baghdad, with an average weight of (975-1517±150) g. Some physical and chemical measurements of water were measured, including temperature, dissolved oxygen concentration, pH, and salinity. These fish were transferred to the laboratory, and the weight, total length, and age of each fish were measured, as well as DNA extraction for the purpose of amplifying the size of a segment (459pb) of the growth hormone gene that includes exon 4, intron 4, and exon 5 by polymerase chain reaction PCR using primers designed for this gene. The genotypes of the growth hormone gene were investigated using the Single-Stranded Conformation Polymorphism (SSCP) technique, and the produced bands were compared to distinguish different genotypes of the gene by the electrophoresis method. The results showed that the water temperature was close to the environmental systems under study and ranged between (25.4-27 ± 0.50), the rates of dissolved oxygen concentration were (6.5 ± 0.09) mg/l, pH (7.0 ± 0.02) and salinity 0.8 g/l higher in ponds compared to the lowest value of them in the river. The analysis of the SSCP technique revealed the presence of six different genotypes of this hormone, including A, B, C, E, F, and H with a frequency of 24.4, 5.6, 15.6, 15.6, 16.4, and 22.4, respectively, for the fish community in the studied sites. The H genotype was significantly (P< 0.05) superior in the floating cages in the average body weight (1600 ± 0 g) and the relative case coefficient (2.5 ± 0). significant differences were observed in the average total body length and age, according to the multiplicity of genotypes. We conclude from this study an improvement in the growth and health status of common carp in cages and ponds compared to the river at the probability level (P<0.05) and the possibility of focusing on the polygenic genotypes of the growth hormone gene and adopting the H genotype as a guide for selecting fish mothers in genetic improvement programs for artificial propagation and achieving the largest economic return from fish breeding projects.

Polimorfismo dos genes DGAT e LEP e sua associação com características de carcaça e perfil lipídico da carne de bovinos nelore

ABSTRACT The objective of this study was to evaluate the association of polymorphisms in the diacylglycerol acyltransferase ( DGAT ) and leptin ( LEP ) genes with the performance, carcass characteristics, meat quality, and lipid profile of Nellore cattle. A total of 100 intact male Nelore cattle were used to analyze the performance, carcass, physicochemical and centesimal composition, and fatty acid profile of beef. To identify the polymorphisms, the PCR–single-strand conformation polymorphism (SSCP) technique was applied to genomic DNA extracted from muscle tissue. The SSCP technique revealed the presence of four band patterns for the DGAT gene (AC, AD, AE and BB) with five alleles (A, B, C, D and E). For the LEP gene, five band patterns (AA, AB, AC, BB and BC) with three alleles (A, B and C) were observed. For the LEP gene, the AB genotype was associated with higher backfat thickness and ribs weight, while the BB genotype was associated with lower ribs yield; higher hindquarter yield was associated with AC and BB genotypes. Higher contents of C17:0, C18:0 and lower contents of C18:2ω6C, total polyunsaturated fatty acids, total ω6 and ratio of polyunsaturated and saturated fatty acids (PUFA/SFA) were verified for the AC genotype of the LEP gene. The AC and AA genotypes of the LEP gene were associated with higher means of C15:0 and C18:1ω9t. For the DGAT gene, the highest C24:0 content was associated with the AE genotype and the lowest with the AD and BB genotypes. Polymorphisms in the DGAT and LEP genes influence carcass parameters and the lipid profile of the meat of Nellore cattle.

CRISPR/LbCas12a-mediated targeted mutation of Gracilariopsis lemaneiformis (Rhodophyta).

CRISPR/LbCas12a-mediated targeted mutation of Gracilariopsis lemaneiformis (Rhodophyta).

Detection of Polymorphism in Exon-3 Region of Leptin Gene in Bikaneri Camel

The study was undertaken on 40 Camels (Camelus dromedarius) of Bikaneri breed to identify the single nucleotide polymorphism (SNP) in leptin gene. Nucleotide sequence of Lama glama was used to design primers to amplify selected region of leptin gene in Bikaneri camel. A 540bp fragment was amplified which covered Partial intron-2, exon-3 and partial 3’ UTR region of leptin gene in Bikaneri camel. The genetic variation in partial ntron-2, exon-3 and partial 3’ UTR (540bp) region of leptin gene was studied utilising single strand conformational polymorphism (SSCP) technique followed by nucleotide sequencing. SSCP analysis revealed monomorphic pattern as only AA genotype in studied region of leptin gene was observed. For verification and validation of observed results of SSCP, amplified PCR products of 6 animals were randomly selected for sequence analysis to ascertain the sequence pattern and existence of point mutations in the selected region. All the 6 animals had same sequence pattern. Monomorphic pattern showed the conserved nature of leptin gene in dromedary camel.

Evaluation of The Mutagenicity and Oxidative Stress of Fipronil After Subchronic Exposure in Male Albino Rats

Fipronil (FPN) is a wide-ranging effective N-phenylpyrazole insecticide that is commonly used in agriculture and public health for a long time but until now no adequate data available concerning its side effect. The present study was to evaluate the oxidative stress, cytotoxicity, and mutagenic effect of FPN subchronic exposure. Twenty male Albino rats (120g±10%) were randomly assigned into four groups each has five animals, a control group, two FPN treated groups with doses of 3.9, and 2.3 mg kg-1 b.w. per day for 90 days and the fourth group is a positive control group. Superoxide Dismutase (SOD), Catalase (CAT), and Malondialdehyde level (MDA) were used as oxidative stress biomarkers. The cytotoxicity was estimated by micronucleus assay, while the mutagenic effect was studied on the P53 tumor suppressor gene using the single-strand conformation polymorphism (SSCP) technique. The results showed that SOD significantly decreased in the high and low doses treatments and insignificant changes in CAT compared to control. MDA was significantly elevated in the high dose group and remained insignificant in the low dose. The high dose of FPN was showed an increased number of micronuclei in the Normochromatic Erythrocytes (NCE) in the bone marrow. PCR-SSCP analysis by acrylamide gel didn’t show mutations in the P53 gene. This study demonstrated that FPN induces oxidative stress and micronuclei but did not show alternation of the P53 gene. The study indicated the relative safeness of fipronil to be used in the public health field with taking all use precautions.

Genetic Diversity and Population Structure of Zeugodacus Tau Walker (Diptera: Tephritidae) in Southern Thailand

The population structure of a fruit fly, Zeugodacus tau, was studied by a Single-Strand Conformation Polymorphism (SSCP) technique. Twenty haplotypes of Cytochrome Oxidase unit I (COI) sequence were found in flies collected from Southern Thailand. The phylogenetic tree and haplotype network revealed gene flow across a large geographic range. With the aid of winds, their gene flow diminished population structure. The population size of Z. tau in Southern Thailand seemed to be large and stable, but the other populations in some locations had experienced a bottleneck effect, leading to local genetic differentiation. Fruit flies from the eastern areas had large effective population sizes, whereas the populations from other areas were smaller. This pattern matched the ecological niche centroid model, in which fruit flies disperse from high population areas to lower ones.

Growth Hormone Gene Polymorphisms in Mature Healthy Male Muscovy Ducks in Egypt

Blood samples were obtained from 28 mature healthy male Muscovy ducks for screening of a partial sequence of Growth hormone gene (GH gene) for single nucleotide polymorphisms using PCR amplification of the extracted DNA. The results of our research revealed one locus of exon 2 of growth hormone gene and its partial flanking intron. Polymorphisms in this locus were investigated by using direct sequencing and single strand conformational polymorphism (SSCP) technique. One unique pattern of SSCP was detected. Nucleotide sequencing was performed to endorse the current result which proved the absence of single nucleotides' polymorphisms (SNPs) or any other type of polymorphisms in the studied locus. The DNA sequencing and PCR-SSCP patterns confirmed that there was no polymorphism in all studied birds. In turn, it is spelled that PCR-SSCP failed to produce electrophoresis patterns capable of discriminating between the GH gene loci in Muscovy duck breed revealing no polymorphism in all studied individuals. Also, we compared our sequences with the published sequence on the gene bank of GH gene in Mallard ducks under the following accession number AB158762.1. Three SNPs were detected between Muscovy and Mallard breeds which are (94 A-G, 271 C-T and 298 G-A) these SNPs led to change of two amino acids proline and valine amino acids in GH protein in mallard ducks into serine and isoleucine in Muscovy ducks. In conclusion, these changes in the nucleotide sequence, amino acid and protein chain may be the main cause of differences of the phenotypic features, productive and reproductive traits between Muscovy and mallard duck breeds.

Association analysis of polymorphism in the NR6A1 gene with the lumbar vertebrae number traits in sheep.

The vertebral number is an economically significant trait, which is associated with body length and carcass traits. Nuclear Receptor Subfamily 6, Group A, Member 1 (NR6A1) is a member of the nuclear receptor superfamily and it plays an important role in the early development of embryos. The NR6A1 gene was considered as an important candidate for influence vertebrae number, while the potential associations between this gene and the number of lumbar vertebrae traits of sheep have not been explored. In this study, we detected the genetic variants of NR6A1 gene and analyzed the associations of the polymorphisms with lumbar number traits in 130Kazakh sheep. We use single-strand conformation polymorphism (SSCP) technique to detect single nucleotide polymorphism (SNP) of NR6A1 gene, and the association of the genotype and lumbar number variation was analyzed by independent Chi-square test. We detect SNP of NR6A1 gene by PCR-SSCP technique, and polymorphisms were only found in the coding region of exon-6 and exon-8 of NR6A1 gene. In order to investigate the connection between the SNP locus and lumbar number traits in sheep, we conducted a Chi-square test for independence for exon-6 and exon-8 of NR6A1 gene, respectively. Association analysis revealed significant associations between the SNP (rs414302710: A >C) in the exon-8 of NR6A1 gene with the number of lumbar vertebrae (P < 0.01). Our study indicated that this SNP (rs414302710: A>C) locus of exon-8 of NR6A1 gene in sheep possible influence the number of lumbar vertebrae, which has the potential to be applied in selective breeding of sheep.

Differential Colonization Dynamics of Marine Biofilm-Forming Eukaryotic Microbes on Different Protective Coating Materials.

In this study, the actual anti-biofouling (AF) efficacy of three protective coatings, including a chlorinated rubber-based coating (C0) and two polydimethylsiloxane (PDMS)-based coatings (P0 and PF), were estimated via the static field exposure assays. The surface properties of these protective coatings, including surface wettability and morphology features, were characterized using the static water contact angle (WCA) and scanning electron microscope (SEM). The colonization and succession dynamics of the early-adherent biofilm-forming eukaryotic microbial communities occupied on these protective coatings were explored using the Single-stranded Conformation Polymorphism (SSCP) technique. The field data clearly revealed that coating P0 and PF performed better in the long-term static submergence, as compared with the C0 surface, while coating PF showed excellent AF efficacy in the field. Fingerprinting analysis suggested that the diversity, abundance, the clustering patterns, and colonization dynamics of the early-colonized eukaryotic microbes were significantly perturbed by these protective coatings, particularly by the PF surfaces. These differential AF efficacy and perturbation effects would be largely ascribed to the differences in the wettability and surface nanostructures between the C0, P0 and PF surfaces, as evidenced by WCA and SEM analysis.

Detection of Staphylococcal Species Diversity within Human Skin Microbiome Using a Simple PCR-SSCP Technique

&#x0D; Objective. The aim of this study was to detect the diversity of Staphylococcus species of a healthy human skin using a simple techniquevPCR-SSCP.&#x0D; Methods: Blood samples, saliva, and skin swaps samples were collected from 50 persons from Hilla City - Iraq. The genomic DNA was extracted from these samples using the Bacteria Genomic DNA Kit. The concentrations and purity of DNA extract estimated by NanoDrop spectrophotometer. Polymerase chain reaction – single-strand conformational polymorphism (PCR–SSCP) technique was performed to detect the diversity between Staphylococcal species in the human skin microbiome using a specific primer of the 16SrRNA gene.&#x0D; Results: The PCR results, indicated that the Staphylococcal species were found within the ski community, but it's not infected blood and mouth of test healthy individuals. SSCP-heteroduplex patterns of PCR products appeared the presence Staphylococcal species diversity within skin microbiome of test healthy individuals.&#x0D; Conclusion: In spite of the PCR-SSCP, heteroduplex method was simple and cheap and appeared the diversity betweenvStaphylococcalspeciesvin the human skin microbiome, but it's not diagnosed the bacterial strains. So these results required to confirm by DNAvsequencingvtechnique.&#x0D;

Effect of CNT/PDMS Nanocomposites on the Dynamics of Pioneer Bacterial Communities in the Natural Biofilms of Seawater.

In this study, the antifouling (AF) performance of different carbon nanotubes (CNTs)-modified polydimethylsiloxane (PDMS) nanocomposites (PCs) was examined directly in the natural seawater, and further analyzed using the Multidimensional Scale Analyses (MDS) method. The early-adherent bacterial communities in the natural biofilms adhering to different PC surfaces were investigated using the single-stranded conformation polymorphism (SSCP) technique. The PCs demonstrated differences and reinforced AF properties in the field, and they were prone to clustering according to the discrepancies within different CNT fillers. Furthermore, most PC surfaces only demonstrated weak modulating effects on the biological colonization and successional process of the early bacterial communities in natural biofilms, indicating that the presence of the early colonized prokaryotic microbes would be one of the primary causes of colonization and deterioration of the PCs. C6 coating seems to be promising for marine AF applications, since it has a strong perturbation effect on pioneer prokaryotic colonization.

A comparative study on the impact of the carbon nanotubes-modified polydimethylsiloxane nanocomposites on the colonization dynamics of the pioneer biofilm communities

In the current study, the AF properties of carbon nanotubes (CNTs)-modified polydimethylsiloxane (PDMS) nanocomposites were examined via the field assays. The impact of the CNTs incorporated in PDMS on the biological colonization and successional dynamics of the pioneer natural biofilm communities was investigated using the single-stranded conformation polymorphism (SSCP) technique. Coating characterizations, including water contact angle (WCA) measurement, scanning electron microscope (SEM) and atomic force microscopy (AFM) analysis were conducted in order to characterize the surface properties changes triggered by the incorporation of the CNT fillers. The results revealed that the incorporation of low amount of the CNT nanoparticles (0.1% wt) as fillers in the PDMS would greatly improve its AF properties under static submergence. The CNTs incorporated in the PDMS could exert significant impact on the diversity level, distribution patterns and the successional dynamics of the pioneer prokaryotic and eukaryotic microbial communities, particularly on the early eukaryotic microbial communities. Coating characterizations revealed the remarkable changes in the wettability and surface nanostructures of the PDMS resin would contribute considerably to the enhanced modulating and perturbation effects on the initial colonization of the pioneer microorganisms in the natural biofilms.

Investigation of piwi-interacting RNA pathway genes role in idiopathic non-obstructive azoospermia

Genes involved in piwi-interacting RNAs (piRNAs) pathway have an essential role in spermatogenesis. HIWI and TDRD proteins are critical for piRNA biogenesis and function. Therefore, Mutations and polymorphisms in HIWI and TDRD genes may play role in male infertility. The aim of the present study was to investigate the role of HIWI2 rs508485 (T>C) and HIWI3 rs11703684 (C>T) polymorphisms and mutational analysis of TDRD5 gene in idiopathic non-obstructive azoospermia in a case-control study including 226 non-obstructive azoospermia patients and 200 fertile males. Genotyping for both polymorphisms was performed using Tetra-Primer ARMS PCR. Mutation analysis of TDRD5 gene was done using multi-temperature single strand conformation polymorphism technique (MSSCP). The frequency of rs508485TC genotype was significantly different in the studied groups (P = 0.0032; OR = 2.12; 95% CI, 1.29–3.48). In addition, the genotype frequencies showed a significant difference under dominant model (P = 0.005; OR = 2.79; 95% CI, 1.22–3.13). No mutation was detected in the Tudor domain of the TDRD5 in the studied patients. In conclusion, we provide evidence for association between genetic variation in the HIWI2 gene and idiopathic non-obstructive azoospermia in Iranian patients. Therefore, piRNA pathway genes variants can be considered as risk factors for male infertility.

Association analysis between genetic diversity of the melanocortin4 receptor (MC4R) gene and production traits in turkey

Melanocortin receptor (MC4R) plays an important role in central melanocortin system and regulating feeding behavior in humans and birds. The current study was designed to estimate the frequency of MC4R gene polymorphism and investigate if their polymorphisms have association with production traits Turkeys (Meleagris gallopavo) by PCR-SSCP method. For this purpose, a number of 100 turkeys were randomly chosen and blood samples were collected. DNA were extracted from blood samples, and amplified a fragment of 469 bp in size from MC4R gene. Single strand conformation polymorphism technique (SSCP) was used to determine genotypes. Electrophoresis of SSCP-PCR products on 6% polyacrylamide gel indicated that the polymorphism of the MC4R gene. Also, results of electrophoresis showed that three genotypes AA, and BB, with frequencies of 0.2397, 0.4998 and 0.2605, respectively. Shanon index, Nei index and observed heterozygosity with frequencies of 0.6929, 0.4998 and 0.5208, respectively. Significant associations (P&lt;0.01) were obtained for genotypes with live body weight. But no significant relationship between the genotypes with egg performance (egg mass, mean egg weight and the number of eggs) is found. These results suggest that, the turkey MC4R gene can be selected as the major candidate gene for the carcass traits such as body weight, and at future more study is required to confirm these results in Turkey.

Polymorphism of IL-4 (−590) and IL-6 (−174) is not associated with Chronic Periodontitis in Babylonian Population

Aim: Study was aimed to find the relationship between chronic periodontitis with polymorphism of IL-4 and IL-6 genes and their concentration in saliva and serum. Material and method: the study was included patients with chronic periodontitis (60 subjects) and healthy control (40 subjects), bacteria associated with both subjects have been isolated. The genetic variation in the sequence of the IL-4 and IL-6 has been detected by single strand conformation polymorphism (SSCP) technique. the level of IL-4 and IL-6 in saliva and serum was measured by enzyme linked immunosorbent assay (ELISA). Results: The total viable count of bacteria that collect from patients with chronic periodontitis and healthy control showed that There was significant differences (increase in the number of bacteria) between study groups in the aerobic bacteria , the number of bacteria in healthy groups was 3.1×103±39.15 CFU/ml, and in patient was 2.4×105 ±65.93 CFU/ml P<0.001 and the anaerobic bacteria in healthy and patient was 2.3×102±22.61 CFU/ml and 1.2×104±45.95 CFU/ml respectively (P= 0.05).The most common bacteria isolated in this study were P. Porphyromonasgingivalis, P .Prevotellaintermedia, Tannerellaforsythensis, Peptostreptococcus spp., Aggregatibacter actinomycetemcomitans, Streptococcus spp. And Staphylococcus aureus. SSCP technique showed that there weren’t any sequence variation between patients with periodontitis and healthy control subjects in the sequence of IL-4 and IL-6 genes in Babylonian population. Conclusion: Polymorphism of IL-4 and IL-6 is not associated with chronic periodontitis in Babylonian population.

Evaluation of DNA damage and mutation screening of exon 26 of SCN1A gene in patients with epilepsy

BackgroundEpilepsy is one of the most prevalent neurological disorders. Around 50 million people worldwide suffer from Epilepsy, 85% of them are from the developing countries. It is a most significant as well as common brain disorder worldwide. Sodium channel alpha 1 subunit gene (SCN1A) is most commonly mutated the gene in different forms of epilepsy. ObjectiveTo screen the genomic damage and SCN1A gene mutation in patients with epilepsy. MethodsTo screen the genetic instability of SCN1A gene using Buccal micronucleus cytome (BMCyt) assay and molecular analysis with Single Strand Conformation Polymorphism (SSCP) technique was used to observe the variations in SCN1A gene. ResultsWe found significant differences in buccal cells of patients than controls. So, we can interpret that BMCyt assay would be a minimally invasive biomarker to detect DNA damage and mutation screening in the SCN1A gene with SSCP technique showed no variation in epileptic patients. ConclusionThese data confirmed that there is certainly DNA damage and no mutations in the SCN1A gene; hence the genetic instability has occurred in epileptic patients.

New polymorphism in the 5' flanking region of IGF-1 gene and its association with wool traits in Egyptian Barki sheep.

Insulin-like growth factor-1 gene (IGF-1) is considered as a major candidate gene for the economic traits of animal production. Polymorphism of 5′ flanking region of IGF-1 gene in Barki sheep (n = 91) and its association with wool traits were studied using the polymerase chain reaction coupled with single-strand conformation polymorphism technique (PCR-SSCP), PCR-restriction fragment length polymorphism (PCR-RFLP), sequence analysis and different measurements of wool traits (clean fleece weight and fiber diameter). PCR-SSCP analysis revealed three different banding patterns corresponding with three genotypes frequencies GG (0.25), GA (0.58), AA (0.17). PCR-RFLP and corresponding sequence analysis revealed nucleotide transversion from Guanine (G) to Cytosine (C) at nucleotide position 85 and transition from (G) to Adenine (A) at position 87. This is the first study that recorded two SNPs within the 5′ flanking region of IGF-1 gene in Egyptian Barki sheep, which were submitted to DNA Data Bank OF Japan (DDBJ) with Accession No. LC151463.1. The genotype GG showed positive significant association (P < 0.001) with clean fleece weight (CFW) trait (Odd Ratio = 2.83). By contrast, genotype AA had negative significant association (P < 0.05) with such trait (Odd Ratio = 0.15). On the other hand, fiber diameter (FD) measurements showed no significant association (P > 0.05) with different IGF-1 genotypes. This study adds evidence of the association between IGF-1 gene polymorphism and CFW of wool in Egyptian Barki sheep. Therefore; it is important to consider IGF-1 gene as a candidate gene marker for wool weight traits and it should be identified before using successful breeding program.

Identification of novel single nucleotide polymorphism at thyroid hormone responsive (THRSP) gene of native goat breeds of India

Precise knowledge about the genes causing variation within a trait will provide an opportunity for more effective marker assisted selection. Thyroid hormone responsive (THRSP) gene encodes for small acidic nuclear protein, associated with growth and lactation. Therefore, the present study was planned to detect single nucleotide variations in THRSP gene of goats. Genomic DNA was isolated from 200 animals belonging to Malabari and Attapady Black goats and PCR was done to amplify intron-1 (472bp) and exon-2 (412bp) region of THRSP gene. Single strand conformation polymorphism (SSCP) technique was used to detect single nucleotide polymorphisms (SNPs).Two unique band patterns were detected in 472bp fragment of THRSP gene. The pooled population frequencies of GG and GA diplotype were 0.88 and 0.12, respectively. The haplotype frequencies were 0.94 for G and 0.06 for a haplotype. Similar pattern of three bands were noticed in exon-2 region of THRSP gene in goats and the population was found to be monomorphic. Sequencing revealed two single nucleotide variations including a novel g.56G>T and g.306A>G in intron-1 of THRSP gene. This study indicates the existence of genetic variability in THRSP gene on goats. Hence, it could be used as a marker for selection to improve growth traits in goats.