scholarly journals Association between the Polymorphisms of fads2a and fads2b and Poly-Unsaturated Fatty Acids in Common Carp (Cyprinus carpio)

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1780
Author(s):  
Yan Zhang ◽  
Xiao-Qing Sun ◽  
Yu-Qing Ye ◽  
Qi Wang ◽  
Qing-Song Li ◽  
...  
Keyword(s):  
Common Carp ◽  
Unsaturated Fatty Acids ◽  
Major Gene ◽  
Fatty Acid Desaturase ◽  
Mixed Linear Model ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Food Fish ◽  
Rate Limiting ◽  
Fatty Acid Desaturase 2

Fatty acid desaturase 2 (fads2) is one of the rate-limiting enzymes in PUFAs biosynthesis. Compared with the diploid fish encoding one fads2, the allo-tetraploid common carp, one most important food fish, encodes two fads2 genes (fads2a and fads2b). The associations between the contents of different PUFAs and the polymorphisms of fads2a and fads2b have not been studied. The contents of 12 PUFAs in common carp individuals were measured, and the polymorphisms in the coding sequences of fads2a and fads2b were screened. We identified five coding single nucleotide polymorphisms (cSNPs) in fads2a and eleven cSNPs in fads2b. Using the mixed linear model and analysis of variance, a synonymous fads2a cSNP was significantly associated with the content of C20:3n-6. One non-synonymous fads2b cSNP (fads2b.751) and one synonymous fads2b cSNP (fads2b.1197) were associated with the contents of seven PUFAs and the contents of six PUFAs, respectively. The heterozygous genotypes in both loci were associated with higher contents than the homozygous genotypes. The fads2b.751 genotype explained more phenotype variation than the fads2b.1197 genotype. These two SNPs were distributed in one haplotype block and associated with the contents of five common PUFAs. These results suggested that fads2b might be the major gene responding to common carp PUFA contents and that fads.751 might be the main effect SNP. These cSNPs would be potential markers for future selection to improve the PUFA contents in common carp.

scholarly journals Adaptive Evolution of the Eda Gene and Scales Loss in Schizothoracine Fishes in Response to Uplift of the Tibetan Plateau

2018 ◽  
Vol 19 (10) ◽  
pp. 2953 ◽  
Author(s):  
Cunfang Zhang ◽  
Chao Tong ◽  
Arne Ludwig ◽  
Yongtao Tang ◽  
Sijia Liu ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Major Gene ◽  
Phylogenetic Analyses ◽  
The Tibetan Plateau ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Structure Changes ◽  
Pharyngeal Teeth ◽  
Eda Gene ◽  
Schizothoracine Fish

Schizothoracine is the predominant wild fish subfamily of the Tibetan plateau (TP). Their scales, pharyngeal teeth and barbels have gradually regressed with increasing altitude. Schizothoracine have been divided into three groups: primitive, specialized and highly specialized. Ectodysplasin-A (Eda) has been considered as a major gene that contributes to the development of skin appendages. The present study cloned the Eda genes of 51 Schizothoracine fish species which represent the three groups and five Barbinae species. Phylogenetic analyses indicated that Eda may have acted as the genetic trigger for scale loss in the Schizothoracine. Furthermore, 14 single nucleotide polymorphisms (SNPs) and two deletions (18 bp and 6 bp in size), were also detected in the Eda coding sequence of the highly specialized group compared to the primitive group. The same SNPs and two indels result in four non-synonymous and two G-X-Y and 1 XY motif indels, which possibly contribute to significant structure changes in the Eda gene. The domain including (G-X-Y)n motif in the Eda gene is relatively conserved amongst teleosts. Based on the above results, we hypothesize that the evolution of Eda gene might be associated with the scale loss in Schizothoracine fishes in response to the phased uplift of the TP.

scholarly journals High-Risk Polymorphisms Associated with the Molecular Function of Human HMGCR Gene Infer the Impedance of Cholesterol Biosynthesis

2021 ◽  
Author(s):  
Keshob Chandra Das ◽  
Mohammad Uzzal Hossain ◽  
Md Moniruzzaman ◽  
Md Salimullah ◽  
Sharif Akhteruzzaman
Keyword(s):  
Solvent Accessibility ◽  
Cholesterol Biosynthesis ◽  
Functional Domain ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Functional Instability ◽  
Structural Evaluation ◽  
Coa Reductase ◽  
Rate Limiting ◽  
Major Target

Abstract Background: HMG-CoA reductase or HMGCR (3-Hydroxy-3-methylglutaryl-CoA reductase) is a rate-limiting enzyme involved in cholesterol biosynthesis. HMGCR plays an important role in the possible occurrence of hypercholesterolemia leading to atherosclerosis and coronary heart disease. This enzyme is a major target for cholesterol lowering drugs such as “statins” which blocks the synthesis of mevalonate, a precursor for cholesterol biosynthesis. This study aims to characterize deleterious mutations and classify functional Single Nucleotide Polymorphisms (SNPs) of the HMGCR gene through analysis of functional and structural evaluation, domain association, solvent accessibility, and energy minimization studies. Results: Among 6,815 SNP entries from different databases, approximately 388 SNPs were found to be missense. Analysis showed that seven missense SNPs are more likely to have deleterious effects. A tertiary model of the mutant protein was constructed to determine the functional and structural effects of the HMGCR mutation. In addition, the location of the mutations suggests that they may have deleterious effects because most of the mutations are resides in the functional domain of the protein. The findings from the bunch of bioinformatics tools predicted that rs147043821 and rs193026499 missense SNPs could cause significant structural and functional instability in the mutated proteins of the HMGCR gene. Conclusion: Therefore, the results of the current study would undoubtedly be accommodating in future endeavors concerning drug discovery and therapeutics against hypercholesterolemia.

scholarly journals Identification and Development of KASP Markers for Novel Mutant BnFAD2 Alleles Associated With Elevated Oleic Acid in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Fu ◽  
Annaliese S. Mason ◽  
Yaofeng Zhang ◽  
Huasheng Yu
Keyword(s):  
Oleic Acid ◽  
Acid Content ◽  
Allelic Variation ◽  
Fatty Acid Desaturase ◽  
Snp Markers ◽  
Oleic Acid Content ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Kasp Markers

The fatty acid desaturase FAD2 genes are the main contributors to oleic acid content, and different FAD2 alleles can result in different oleic acid contents in rapeseed oil. Hence, identification of allelic variation in FAD2 is an extremely desirable breeding goal. By performing QTL mapping using 190 F2:3 lines genotyped by genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array, four quantitative trait loci (QTL) for C18:1 content were mapped on chromosomes A01, A05, A09 and C05 over 3 years in a population segregating for oleic acid content. Two BnFAD2 genes on A05 and C05 were anchored within the QTL intervals, explaining 45–52 and 15–44% of the observed variation for C18:1 content. Sequence polymorphisms between the corresponding coding regions of the parental lines found two single-nucleotide polymorphisms (SNPs) in BnFAD2.A05 and BnFAD2.C05, respectively, which led to the amino acid changes (C421T and G1073E) in the corresponding proteins. The mutation sites of Bnfad2.A05 and Bnfad2.C05 alleles were located within the second H-box and near the third H-box motif of the protein, respectively, and were found to be novel mutant alleles. Lines resulting from the combination of these two alleles contained up to 88% oleic acid in their seed oil, compared with 63% in wild-type controls. Two competitive allele-specific PCR (KASP) markers based on these two mutation sites were successfully developed and validated in segregating F2 populations. These markers will facilitate breeding for ultra-high seed oleic acid content in oilseed rape.

scholarly journals TPH1 gene polymorphism rs211105 influences serotonin and tryptophan hydroxylase 1 concentrations in acute pancreatitis patients

2021 ◽  
Author(s):  
Jadwiga Snarska ◽  
Ewa Fiedorowicz ◽  
Dominika Rozmus ◽  
Konrad Wroński ◽  
Maria Latacz ◽  
...  
Keyword(s):  
Acute Pancreatitis ◽  
Metabolic Pathway ◽  
Tryptophan Hydroxylase ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Serotonin Synthesis ◽  
Single Nucleotide ◽  
Factors Affecting ◽  
Rate Limiting

Abstract Background The role of serotonin and its metabolic pathway in proper functioning of the pancreas has not been thoroughly investigated yet in acute pancreatitis (AP) patients. Tryptophan hydroxylase (TPH) as the rate-limiting enzyme of serotonin synthesis has been considered for possible associations in various diseases. Single-nucleotide polymorphisms (SNPs) in TPH genes have been already described in associations with psychiatric and digestive system disorders. This study aimed to explore the association of a rs211105 (T/G) polymorphism in TPH1 gene with tryptophan hydroxylase 1 concentrations in blood serum in a population of acute pancreatitis patients, and to investigate this association with acute pancreatitis susceptibility. Results Our data showed an association between the presence of the T allele at the position rs211105 (OR = 2.47, 95% CI: 0.94-6.50, p = 0.06) under conditions of a decreased AP incidence. For TT and GT genotypes in the control group, the lowest concentration of TPH was associated with higher serotonin levels (TT: Rs=-0.415, p=0.0018; GT: Rs=-0,457, p=0.0066), while for the AP group the highest levels of TPH among the TT genotype were associated with lower levels of serotonin (TT: Rs=-0.749, p<0.0001, and in the GG genotype higher levels of TPH were associated with higher levels of serotonin (GG: Rs=-0.738, p=0.037). Conclusions Here, a new insight in the potential role of a selected genetic factor in pancreatitis development was shown. Not only the metabolic pathway of serotonin, but also factors affecting serotonin synthesis may be interesting and important points in acute pancreatitis.

Identification and Development of KASP Markers for Novel Mutant BnFAD2 Alleles Associated with Elevated Oleic Acid in Brassica napus

2021 ◽  
Author(s):  
Ying Fu ◽  
Annaliese S. Mason ◽  
Yaofeng Zhang ◽  
Huasheng Yu
Keyword(s):  
Oleic Acid ◽  
Acid Content ◽  
Allelic Variation ◽  
Fatty Acid Desaturase ◽  
Snp Markers ◽  
Oleic Acid Content ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Kasp Markers

Abstract The fatty acid desaturase FAD2 genes are the main contributors to oleic acid content, and different FAD2 alleles can result in different oleic acid contents in rapeseed oil. Hence, identification of allelic variation in FAD2 is an extremely desirable breeding goal. By performing QTL mapping using 190 F2:3 lines genotyped by genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array, four quantitative trait loci (QTL) for C18:1 content were mapped on chromosomes A01, A05, A09 and C05 over three years in a population segregating for oleic acid content. Two BnFAD2 genes on A05 and C05 were anchored within the QTL intervals, explaining 45–52% and 15–44% of the observed variation for C18:1 content. Sequence polymorphisms between the corresponding coding regions of the parental lines found two single-nucleotide polymorphisms (SNPs) in BnFAD2.A05 and BnFAD2.C05, respectively, which led to the amino acid changes (C421T and G1073E) in the corresponding proteins. The mutation sites of Bnfad2.A05 and Bnfad2.C05 alleles were located within the second H-box and near the third H-box motif of the protein, respectively, and were found to be novel mutant alleles. Lines resulting from the combination of these two alleles contained up to 88% oleic acid in their seed oil, compared with 63% in wild-type controls. Two competitive allele-specific PCR (KASP) markers based on these two mutation sites were successfully developed and validated in segregating F2 populations. These markers will facilitate breeding for ultra-high seed oleic acid content in oilseed rape.

scholarly journals Genetic Variants at the Resistin Locus and Risk of Type 2 Diabetes in Caucasians

2002 ◽  
Vol 87 (9) ◽  
pp. 4407-4410 ◽  
Author(s):  
Xiaowei Ma ◽  
James H. Warram ◽  
Vincenzo Trischitta ◽  
Alessandro Doria
Keyword(s):  
Type 2 Diabetes ◽  
Confidence Interval ◽  
Major Gene ◽  
Interactive Effect ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Peripheral Tissues ◽  
Relative Risks ◽  
Caucasian Origin

Resistin is a newly identified hormone secreted by adipocytes that inhibits insulin action on peripheral tissues. The aim of our study was to investigate whether genetic variability at this locus is associated with the risk of type 2 diabetes. By sequencing 32 subjects with type 2 diabetes, we identified 8 single nucleotide polymorphisms (SNPs) in the 5′-flanking region and introns of the resistin gene. Allele and genotype distributions were determined for all 8 SNPs in 312 cases with type 2 diabetes and 303 nondiabetic controls, all of Caucasian origin. No significant association with type 2 diabetes was found at any of the polymorphic loci. However, an interactive effect of genotype at SNP 6 (IVS2 + 181G→A) and obesity was a significant determinant of type 2 diabetes risk in this population. The relative risk of diabetes for the A/A genotype was 4.8 (95% confidence interval, 1.1–21.0) in individuals above the median for body weight, but only 0.7 (95% confidence interval, 0.2–2.1) in those below the median. This difference between relative risks was significant (χ2 = 4.5; P = 0.03). A similar, but much weaker, interaction with obesity was observed for SNPs in linkage disequilibrium with SNP6. In conclusion, resistin does not appear to be a major gene for type 2 diabetes. However, our data suggest a synergistic effect of sequence differences at the resistin locus and obesity on risk of type 2 diabetes. Further studies are needed to confirm this finding in other populations.

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