Single-strand Conformation Polymorphism Method Research Articles

Four microRNA gene polymorphisms are associated with Iraqi patients with colorectal cancer

BackgroundColorectal cancer (CRC) is a major cause to global cancer-related mortality. The development of colorectal cancer is linked to hereditary variables that exhibit variability.ObjectivesThe objective of this investigation was to assess the potential correlation between microRNA gene polymorphisms and colorectal cancer (CRC) throughout the Iraqi population.MethodsDNA samples were obtained from a cohort of 100 individuals diagnosed with the (CRC) disease, as well as 100 samples as control group. Four primers were designed to amplify four specific high-frequency variants found within microRNA molecules. These variants include Mir146a G\\C, Mir423 A\\C, Mir196a2, and Mir370. The genotyping of the PCR fragments was performed using the single-strand conformation polymorphism (SSCP) method, followed by direct sequencing of each genotype.ResultsGenotyping experiments confirmed the variability of four targeted variants, namely Mir146a G\\C, Mir 423 A\\C, Mir196a2, and Mir370 tend to exhibit a significant association with (CRC). Individuals with Mir146a: GC and Mir 423 A\\C genotype showed a possible association with the increased risk of (CRC), respectively (P = 0.001; OD 0.50; CI 95% 0.33–0.76; P = 0.002; OD 0.53; CI 95% 0.36–0.80). Individuals with Mir196a2: TT and Mir370 GG genotype exhibited a potential association with (CRC) (P = 0.017; OD 0.44; CI 95% 0.22–0.86; P ≤ 0.001; OD 0.24; CI 95% 0.11–0.50).ConclusionsThe study reveals that single nucleotide polymorphisms (SNPs) in microRNA have a notable and distinct correlation with the heightened susceptibility to colorectal cancer (CRC).

Detection of new single nucleotide polymorphisms in plasma cells carcinoma (myeloma) by polymerase chain reaction–single strand conformation polymorphism and sequencing technical methods

Abstract Background: MicroRNA (miRNA) is a short, single-stranded, non-coding sequence of RNA that does not translate into proteins. Because of their ability to control gene expression, recent studies have shown that these short, non-coding sequences play an important role in cancer. So that, detection the polymorphisms or variants in miRNA genes may help to identify their correlation to cancer susceptibility. Objectives: Study the polymorphisms in miRNA genes or variants miRNA genes and their correlation with myeloma disease. Materials and Methods: Twenty samples were collected from people who visited Marjan Hospital in Province of Babylon, Iraq, from February to July 2022. In addition, 20 samples from healthy people were collected as control. Genotyping of miRNA was accomplished using the polymorphism techniques of polymerase chain reaction and single strand conformation polymorphism (SSCP). DNA sequencing was also applied to categorize all the ranges of SSCP models detected using only gel imaging. Results: The genotypes obtained in this experiment verified that several single nucleotide polymorphisms were obtained between 5-band and 6-band miRNA National center for biotechnology information Primer3 plus reference. Conclusion: The results explain that the miRNA gene polymorphisms may have correlation with the susceptibility to myeloma disease.

Genetic variations of α-casein and K-casein genes associated with milk composition in goats

The quality of animal milk varies between individuals of the same breed. The present study aimed to detect the favorable SNPs for α-casein (CSN1S1) and k-casein (CSN3) genes associated with high-quality milk traits. Blood and milk samples of Zaraibi and Damascus goats were collected from Sakha farm in Kafr El-Shiekh. The solid non-fat, lactose, protein, and fat contents, were determined in milk using the biochemical method, and amino acids were determined using HPLC. To identify genotypes and nucleotide variations (SNPs), single-strand conformation polymorphism (SSCP) and sequencing methods were used. One-way ANOVA test was used to determine the effect of different genotypes on milk traits. The SSCP-PCR results in Zaraibi and Damascus goats showed that the CSN1S1 gene has 3 genotypes (AA, AB, and BB), and also the CSN3 gene has 3 genotypes (AA, AG, and GG). The results of sequencing showed three SNPs at positions 41G˂T, 69A˂G, and 80C˂T in the CSN1S1 gene, and three SNPs at positions 49C˂T, 111A˂G, and 340C˂T in the CSN3 gene. The milk results showed that the high protein, fat, and lactose content were associated with the AB genotype in the CSN1S1 gene while they were associated with the AG genotype in the CSN3 gene. Likewise, essential and branched-chain amino acids were increased in goat milk with the AB and AG genotypes of CSN1S1 and CSN3 genes, respectively. The essential amino acids for protein synthase were higher in Zaraibi than in Damascus goats. Therefore, the Zaraibi goats may more possess genotypes in the CSN1S1 and CSN3 genes, which affect the fat and protein level in milk.

Screening for causative mutations in ovine BMPR1B and BMP15 genes and their homologous fragments in human.

The BMPR1B and BMP15 genes are well known for their considerable associations with prolificacy in sheep. These genes may also affect fertility or prolificacy in other species, including human. This study was conducted to investigate possible causative mutations in BMPR1B and BMP15 genes in human and an indigenous breed of sheep. Blood samples were collected from 83 singleton- and prolific Mehraban ewes and 81 infertile, singleton- and twin-bearing women. A 190-bp fragment, containing the FecB mutation in ovine BMPR1B, a 380-bp fragment in ovine BMP15 gene and their homologous fragments in human were amplified and then investigated by single-stranded conformation polymorphism and DNA sequencing methods. The FecB mutation of BMPR1B (g.159A>G) was detected in the sheep population, but no polymorphic loci were found in the homologous fragment in studied human samples. The studied fragments of BMP15 were monomorphic in both sheep and human samples. A total of nine and 69 point-differences in the studied fragments of BMPR1B and BMP15 genes were detected between the species, respectively. In sheep, the G allele of BMPR1B had a positive effect on litter size (p<0.05), whereby all AG or GG ewes were prolific. The FecB mutation for the first time was detected in Mehraban sheep and therefore could be considered for marker-assisted selection in this breed. The studied fragments of BMPR1B and BMP15 genes are not responsible for reproduction variation in human. More studies on other genes, associated with fertility in human, are necessary in the future.

One intron variant in the oocyte expressed protein (OOEP) gene is associated with twinning rate, prolificacy, and several body measurement traits in Awassi ewes

Awassi breed is an important sheep in the Middle East, but its lower twinning potential is a limitation against improvement. Due to the dynamic role of oocyte-expressed protein (OOEP) gene in controlling folliculogenesis, this study was conducted to evaluate the possible association between OOEP and twinning rate, as well as body measurement traits, in Awassi ewes. A total of 232 Awassi ewes (123 ewes-producing singletons and 109 ewes-producing twins) were included in this study. Three PCR fragments (OOEP-1 to OOEP-3) were designed to cover the majority of OOEP sequences and genotyped by single-strand conformation polymorphism (SSCP) method. One nucleic acid variant was identified in the intron-2 of OOEP-3, or rs430263839:A>G. Ewes with rs430263839:AG genotype showed variable significant values of larger head length, chest and abdominal circumferences, and higher prolificacy and twinning rates than ewes with the rs430263839:AA genotype. The conducted computations predicted that the detected SNP had caused altered splicing mechanisms in ewes with rs430263839:AG genotype. The increased abdominal and chest diameters in ewes with the rs430263839:AG genotype were thought to help the uterus accommodate more lambs. The predicted splicing alteration caused by this SNP is the putative mechanism by which these ewes may improve reproductive and productive traits. This is the first study that demonstrated the importance of OOEP as a potential biomarker for the twinning rate, prolificacy, and some body measurement traits in Awassi ewes with an opportunity to be introgressed to other breeds using large-scale association analysis.

Genetic variants and altered expression of SERPINF1 confer disease susceptibility in patients with otosclerosis.

Otosclerosis (OTSC) is a focal and diffuse bone disorder of the human middle ear characterized by abnormal bone growth and deposition at the stapes' footplate. This hinders the transmission of acoustic waves to the inner ear leading to subsequent conductive hearing loss. The plausible convections for the disease are genetic and environmental factors with yet an unraveled root cause. Recently, exome sequencing of European individuals with OTSCrevealed rare pathogenic variants in the Serpin Peptidase Inhibitor, Clade F (SERPINF1)gene. Here, we sought to investigate the causal variants of SERPINF1 in the Indian population. The gene and protein expression was also evaluated in otosclerotic stapes to ameliorate our understanding of the potential effect of this gene in OTSC. A total of 230 OTSC patients and 230 healthy controls were genotyped by single-strand conformational polymorphism and Sanger sequencing methods. Bycomparing the case controls, we identified five rare variants (c.72 C > T, c.151 G > A, c.242 C > G, c.823 A > T, and c.826 T > A) only in patients. Four variants c.390 T > C (p = 0.048), c.440-39 C > T (p = 0.007), c.643 + 9 G > A (p = 0.035), and c.643 + 82 T > C (p = 0.005) were found to be significantly associated with the disease. Down-regulation of SERPINF1 transcript level in otosclerotic stapes was quantified by qRT-PCR, ddPCR and further validated by in situ hybridization. Similarly, reduced protein expression was observed by immunohistochemistry and immunofluorescence in otosclerotic stapes that corroborate with immunoblotting of patients' plasma samples. Our findings identified that SERPINF1 variants are associated with the disease. Furthermore, reduced expression of SERPINF1 in otosclerotic stapes might contribute to OTSC pathophysiology.

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

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

Two missense variants of the epidermal growth factor receptor gene are associated with non small cell lung carcinoma in the subjects from Iraq.

Lung carcinoma is a foremost cause of cancer-related mortality worldwide. Variable genetic factors are associated with the development of lung cancer. This study was performed to evaluate the possible association of epidermal growth factor receptor (EGFR) gene polymorphisms with non small cell lung carcinoma (NSCLC) in Iraqi population. DNA samples were extracted from 100 patients and 100 controls. Four PCR fragments were designed to amplify four high-frequency variants within EGFR, namely rs1050171, rs2072454, rs2227984, and rs2227983. The PCR fragments were genotyped by single-strand conformation polymorphism (SSCP) method, and each genotype was subjected to direct sequencing. Genotyping experiments confirmed the variability of three targeted variants, and logistic regression analysis showed that two of these variants (rs1050171 and rs2227983) tend to exhibit a significant association with NSCLC. Individuals with rs1050171:GA genotype showed a possible association with the increased risk of NSCLC (P = 0.0110; OD 5.2636; Cl95% 1.4630 to 18.9371). Individuals with rs2227983:GG genotype exhibited a potential association with NSCLC (P = 0.0037; OD 5.2683; Cl95% 1.7141to16.1919). Linkage disequilibrium analysis showed that the effects of the investigated variants seem to take independent actions, and no haplotype was found to be associated with the high prevalence of NSCLC. Our collective data indicated that EGFR-rs1050171G/A and EGFR-rs2227983G/G SNPs tend to exert significant and separate associations with the increased risk of NSCLC. However, this study recommends using a broader spectrum of the investigated samples to get further details of both SNPs in terms of their association with the susceptibility to NSCLC.

NOVEL ASSOCIATION BETWEEN GnRHR GENE AND GROWTH TRAITS IN AWASSI AND KARAKUL SHEEP

This study was conducted to investigate the association of the Gonadotropin-Releasing Hormone Receptor (GnRHR) gene with growth traits in Awassi (n= 123) and Karakul (n= 78) sheep. Starting from the birth-day to 12 months of age, several growth traits were investigated, namely body weight and length, wither and rump height, chest, and abdominal circumferences. Four fragments were designed to amplify three exons of GnRHR gene, P1 and P2 for exon 1, P3 for exon 2, and P4 for exon 3. The polymorphisms in these amplicons were analyzed by single-strand conformation polymorphism (SSCP) method. Genotypic and allele frequency of GnRHR gene were computed after sequence alignment. The results detected two different SSCP banding patterns GG and GA for both P2 and P3 amplicons, and two novel mutations were observed in GA genotype of P2 and P3 amplicons respectively, p.N87= and p.L242F. The identified p.N87= exhibited no relationship with all measured growth traits, while p.L242F showed significant association with the body weight, length, and abdominal circumference in month-6 and month-9. This association was increasingly observed in month-12 with all growth traits, in which individuals with GA genotype exhibited higher growth traits measurements than individuals with GG genotype (P &lt; 0.01). In conclusion, the detected polymorphism of GnRHR gene exon-2 may be useful in marker-assisted selection for growth traits in Awassi and Karakul breeds. This study is the first one to describe the effect of GnRHR polymorphisms on growth traits, which confirm the potential usefulness of this gene in marker-assisted selection in sheep.

Effects of Genetic Polymorphisms of Cathepsin A on Metabolism of Tenofovir Alafenamide

Cathepsin A (CatA) is important as a drug-metabolizing enzyme responsible for the activation of prodrugs, such as the anti-human immunodeficiency virus drug Tenofovir Alafenamide (TAF). The present study was undertaken to clarify the presence of polymorphisms of the CatA gene in healthy Japanese subjects and the influence of gene polymorphism on the expression level of CatA protein and the drug-metabolizing activity. Single-strand conformation polymorphism method was used to analyze genetic polymorphisms in healthy Japanese subjects. Nine genetic polymorphisms were identified in the CatA gene. The polymorphism (85_87CTG>-) in exon 2 was a mutation causing a deletion of leucine, resulting in the change of the leucine 9-repeat (Leu9) to 8-repeat (Leu8) in the signal peptide region of CatA protein. The effect of Leu8 on the expression level of CatA protein was evaluated in Flp-In-293 cells with a stably expressed CatA, resulting in the expression of CatA protein being significantly elevated in variant 2 with Leu8 compared with Leu9. Higher concentrations of tenofovir alanine (TFV-Ala), a metabolite of TAF, were observed in the Leu8-expressing cells than in the Leu9-expressing cells using LC/MS/MS. Our findings suggest that the drug metabolic activity of CatA is altered by the genetic polymorphism.

The ND1 and CYTB genes polymorphisms associated with in vitro early embryo development of Sanjabi sheep

This study aimed to investigate the association between polymorphisms of ND1 and CYTB genes and in vitro early embryo development of Sanjabi sheep. Blood and ovarian samples were collected from a local slaughterhouse. The cumulus-oocyte complexes with a diameter greater than 3 mm were aspirated from follicles, and in vitro maturation (IVM) and in vitro culture (IVC) rates of them were recorded. A respective 1200 bp and 980 bp fragments of ND1 and CYTB genes were genotyped using a modified single strand conformation polymorphism (SSCP) method. The results of this study revealed that four different patterns, named as A, B, C, and D were observed for both ND1 and CYTB genes. The ND1 gene polymorphisms had significant effects on the IVM and IVC rate (p < 0.05). The pattern C of the ND1 gene significantly increased the IVM rate compared to the patterns A, B and D. For the IVC, the highest and lowest means were related to the C and B patterns, respectively. The CYTB gene polymorphisms also had significant effects on IVC (p < 0.01), but the IVM did not affected (p = 0.07). Here, the pattern D had the highest and the pattern C had the lowest means for both IVM and IVC rates.

NOVEL ASSOCIATION BETWEEN GnRHR GENE AND GROWTH TRAITS IN AWASSI AND KARAKUL SHEEP: GnRHR genetic polymorphism in sheep

This study was conducted to investigate the association of the Gonadotropin-Releasing Hormone Receptor (GnRHR) gene with growth traits in Awassi (n= 123) and Karakul (n= 78) sheep. Starting from the birth-day to 12 months of age, several growth traits were investigated, namely body weight and length, wither and rump height, chest, and abdominal circumferences. Four fragments were designed to amplify three exons of GnRHR gene, P1 and P2 for exon 1, P3 for exon 2, and P4 for exon 3. The polymorphisms in these amplicons were analyzed by single-strand conformation polymorphism (SSCP) method. Genotypic and allele frequency of GnRHR gene were computed after sequence alignment. The results detected two different SSCP banding patterns GG and GA for both P2 and P3 amplicons, and two novel mutations were observed in GA genotype of P2 and P3 amplicons respectively, p.N87= and p.L242F. The identified p.N87= exhibited no relationship with all measured growth traits, while p.L242F showed significant association with the body weight, length, and abdominal circumference in month-6 and month-9. This association was increasingly observed in month-12 with all growth traits, in which individuals with GA genotype exhibited higher growth traits measurements than individuals with GG genotype (P < 0.01). In conclusion, the detected polymorphism of GnRHR gene exon-2 may be useful in marker-assisted selection for growth traits in Awassi and Karakul breeds. This study is the first one to describe the effect of GnRHR polymorphisms on growth traits, which confirm the potential usefulness of this gene in marker-assisted selection in sheep.

The relationship between mitochondrial ND5 gene polymorphisms and in vitro embryo production in Sanjabi sheep.

The aim of this study was to investigate mitochondrial ND5 gene polymorphisms and their relationship with in vitro maturation (IVM) and in vitro culture (IVC) of Sanjabi sheep. Blood and ovarian samples of adult ewes were obtained from a local slaughterhouse. For each ovarian sample, cumulus-oocyte complexes larger than 3 mm in diameter were aspirated from follicles, and their IVM and IVC rates were recorded. A 666-bp fragment of the ND5 gene was amplified using the polymerase chain reaction. The samples were genotyped using a modified single-stranded conformation polymorphism (SSCP) method, and an association study was conducted with IVM and IVC rates. Six different SSCP patterns, designated A, B, C, D, E and F with respective frequencies of 8, 47, 4, 4, 32 and 5%, respectively, were observed. According to the results of association analysis, there was no significant association between the ND1 gene polymorphisms and the IVM and IVC rates (P > 0.05).

Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method.

PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.

Investigation of Polymorphisms in the Upstream Sequence of LIF and LIFR Genes in the Infertile Women

: During pregnancy, the embryo implantation stage is a highly dynamic and molecularly controlled phenomenon. Several genes are involved in the implantation process, among which the leukemia inhibitory factor (LIF) is a marker of implantation. LIF is a multi-functional cytokine located on chromosome 22. The expression of this gene is increased in the middle of the secretion phase from the sexual cycle, and any defect in its expression will cause the implantation failure. LIF receptor or LIFR gene, as the LIF receptor, consists of two membrane proteins called LIFR and GP130. LIFR acts as a signal receptor for LIF in a low-affinity level. In this study, we focused on the screening of polymorphisms in the promoter region of the LIF and LIFR genes in the infertile women using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) method. In this study, blood samples were collected from 100 women with primary and secondary infertility and 50 healthy women as a control group. Extraction of DNA was done by the phenol-chloroform method, and in the next step, using specific primers for upstream regions of the LIF and LIFR genes, target sequences were amplified and analyzed by the SSCP method. Finally, PCR products with different configurations were selected for sequencing analysis. The results showed two polymorphisms in the upstream region of LIF and LIFR genes of two women, but there were no genetic changes in the control group. The present study was the first in this field, and the results indicated the importance of examining such genes in infertility with an unknown cause.

A Novel Missense Single Nucleotide Polymorphism in the GREM1 Gene is Highly Associated with Higher Reproductive Traits in Awassi Sheep.

GREM1 (gremlin1) is a known inhibitor for BMP15 (bone morphogenetic protein 15) family, but its genetic diversity in sheep is unknown. The present study was conducted to analyze the polymorphism of GREM1 gene using PCR- single-strand conformation polymorphism (SSCP) and DNA sequencing methods and to assess the possible association of GREM1 gene polymorphism with reproductive traits in Awassi ewes. A total of 224 ewes, 124 producing singles and 100 producing twins, were included in the study. Two SSCP patterns were detected in two amplified loci within the exon 2. Two exonic novel single nucleotide polymorphism (SNP)s were identified, c.74T > G (the silent SNP p.Met123 =) and c.30T > A with (the missense SNP p.Ile237Phe). Statistical analyses indicated a non-significant (P > 0.05) association of p.Met123 = with the analyzed reproductive traits of fecundity, prolificacy, litter size, and twinning rate. Meanwhile, p.Ile237Phe SNP exhibited a highly significant (P < 0.01) association with the measured reproductive traits, in which ewes with TA genotype (with p.Ile237Phe SNP) exhibited higher litter size, twinning ratio, fecundity, and prolificacy than those with TT genotype (without p.Ile237Phe SNP). The deleterious impact of p.Ile237Phe SNP was observed by the means of ten different state-of-the-art in silico tools that predicted a highly damaging effect of p.Ile237Phe SNP on the structure, function, and stability of gremlin1. In conclusion, the results of our study suggest that p.Ile237Phe SNP has a remarkable negative impact on the gremlin1 structure, function, and stability. Since gremlin1 is a known inhibitor of reproductive performance, a consequent higher reproductive performance was observed in ewes with damaged gremlin1 (with p.Ile237Phe SNP) than those with non-damaged gremlin1 (without p.Ile237Phe SNP). Therefore, it can be stated that the implementation of the novel p.Ile237Phe SNP in the GREM1 gene could be a useful marker in marker-assisted selection. This manuscript is the first one to describe GREM1 gene variations in sheep.

Association of a polymorphism in exon 3 of the IGF1R gene with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep

This study aimed to genotype the polymorphism (c.654G > A) in the exon 3 of the insulin-like growth factor 1 receptor gene (IGF1R) and to analyze its association with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep. In total, 67 traits were analyzed. The IGF1R polymorphism was genotyped using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) method. The MIXED procedure of the SAS software was used to assess the genotypic effects of the polymorphism (c.654G > A) on production traits of interest. The IGF1R c.654G > A genotypes were found to have a significant effect on the average daily gain between the 56th and 78th day of life, cold carcass, leg part, leg cut, fore shank, and kidney weights, as well as eye of loin depth, intramuscular fat content, and water-holding capacity of meat. The results suggest that the studied polymorphism may provide useful information for marker-assisted selection for increased meat performance in Colored Polish Merino sheep.

A Study on Keratin-Associated Protein (KAP) 3.2 Gene and Its Polymorphism in Sandyno Breed of Sheep

The current study investigates the polymorphic patterns of keratin-associated protein (KAP) 3.2 gene in Sandyno breed of sheep. Genomic DNA was isolated from blood samples of 51 numbers of Sandyno breed. Ovine specific primer associated PCR amplification of KAP 3.2 gene revealed product at 393 bp and genotyped by PCR-SSCP (Single Strand Conformation Polymorphism) method and visualized under silver staining technique. KAP 3.2 gene locus revealed 3 genotypes, viz. AA, AB and BB with a frequency of 0.84, 0.16 and 0 in Sandyno breed with allele frequencies of A(0.92) and B(0.08). Regarding population genetic indices, the effective number of alleles (Ne) for KAP 3.2 in Sandyno breed of sheep was found to be 1.1716. The PIC values was 0.1356 and FIS values was negative (– 0.0864) in this breed. The result revealed that the selected population of Sandyno breed of sheep was in Hardy-Weinberg equilibrium without any significant deviation from the population mean and was monomorphic for KAP 3.2 gene.

Effects of follicle-stimulating hormone beta subunit and nuclear receptor coactivator 1 gene polymorphisms and expressions on pink-eyed white mink reproductive traits

The present study was designed to investigate comparative expressions of follicle-stimulating hormone beta subunit (FSHβ) and nuclear receptor coactivator 1 (NCOA1) genes by real-time polymerase chain reaction, using polymerase chain reaction single-strand conformation polymorphism methods to investigate the effects of gene polymorphisms on reproductive traits, including total number of kits born (TNB) and number of born alive (NBA) in pink-eyed white mink. Four single-nucleotide polymorphisms were identified in the FSHβ and NCOA1 genes. The g.1228G&gt;A polymorphism of FSHβ was associated with NBA and TNB (P &lt; 0.01). The g.151536T&gt;C polymorphism of NCOA1 was associated with NBA and TNB (P &lt; 0.01). The NCOA1 mRNA levels in hypothalamus, ovary, and uterus during the first half of gestation were higher than during the middle term and last half of gestation (P &lt; 0.01). The FSHβ mRNA levels in the hypothalamus and uterus were higher during the first half of gestation than during the middle term and last half of gestation (P &lt; 0.05). In conclusion, the g.1866T&gt;C polymorphism of FSHβ and the g.151536T&gt;C polymorphism of NCOA1 could be molecular markers for reproductive traits, and expressions of FSHβ and NCOA1 might be involved in the regulation of embryo attachment mechanisms in pink-eyed white mink breeding.

A Novel SNPs in Alpha-Lactalbumin Gene Effects on Lactation Traits in Chinese Holstein Dairy Cows.

Simple SummaryAlpha-lactalbumin (α-LA) is a major whey protein component in mammalian milk, such as human (approximately 36%), bovine (approximately 17%), and other species, etc., It is involved in the regulation of lactose synthesis and has high nutritional value, especially in infant formula. Previous studies have confirmed that bovine α-LA gene 5′-flanking region has single nucleotide polymorphisms (SNPs), but little is known about polymorphisms in other regions, especially sequence coding for amino acids in protein (CDS) and their adjacent non-coding regions, including Chinese Holstein dairy cows. This study focused on investigated SNPs in the CDS and their adjacent non-coding regions of the α-LA gene in Chinese Holstein dairy cows, and assessed the association between SNPs and lactation traits. Sequence alignment showed that a potential SNPs (562th, G/A) in CDS2 region affect protein spatial structure, suggesting that this SNPs might affect the lactation traits of cows (milk type (Holstein and Jersey), and non-milk type (Bos Taurus)) need more in-depth study. More importantly, a novel SNPs at 1847th (T/C) bp in non-coding region near CDS4 was significantly associated with milk lactose composition, and lactose contents were significantly correlated with milk protein content, indicating that the SNPs could be used as a novel potential molecular marker for lactation traits in Chinese Holstein dairy cows.Alpha-lactalbumin (α-LA) is a major whey protein in bovine and other mammalian milk, which regulates synthesis of lactose. Little is known about its genetic polymorphism and whether can be used as a potential marker for dairy ingredients, milk yield traits, and milk properties. To investigate its polymorphisms and their relationship with milk lactation traits in Chinese Holstein dairy cows, single-strand conformation polymorphism method (PCR-SSCP) and direct sequencing method were used to mark the α-LA gene SNPs. AA (0.7402) and AB (0.2598) genotypes were screened out by PCR-SSCP bands analysis in two independent populations. Direct sequencing revealed that there is one SNP at 1847th (T/C) bp in noncoding region of α-LA gene with highly polymorphic (0.5 < PIC = 0.5623 or 0.5822), of which T is in AA genotype while C in AB. Association analysis also showed that lactose content (p < 0.05) was negatively correlated with fat and protein contents within subgroup, indicating that the SNPs (1847th, T/C) in α-LA gene could be used as a novel potential molecular marker for lactation traits in Chinese Holstein dairy cows.