Identification of the association between FABP4 gene polymorphisms and milk production traits in Sfakia sheep

A Novel Missense SNP in the Fatty Acid-Binding Protein 4 (FABP4) Gene is Associated with Growth Traits in Karakul and Awassi Sheep

The fatty acid-binding protein 4 (FABP4) plays a crucial role in the transportation and metabolism of fatty acids. It binds to long-chain fatty acids and facilitates their transport within cells. FABP4 is involved in lipid metabolism, insulin sensitivity, inflammation, and energy homeostasis. This study was conducted to assess the association between the FABP4 gene and growth traits in Karakul and Awassi sheep. A PCR-single strand conformation polymorphism (SSCP) protocol was utilized to assess the polymorphism of FABP4 PCR products with growth traits measured at birth, three, six, nine, and twelve-month intervals. One non-synonymous SNP was identified in the second exon, in which threonine was converted to aspartate in the 61st position in FABP4 (p.61Thr > Asp). This novel SNP showed significant associations with all growth traits measured at all age intervals. The results showed that lambs with the TT genotype exhibited higher growth traits than those with the GT and GG genotypes, respectively. The conducted prediction showed a clearly deleterious effect of p.61Thr > Asp on FABP4 structure, which was accompanied by reduced fatty acid binding efficiency. Owing to the predicted damaging effects caused by p.61Thr > Asp on FABP, lower levels of lipid transport and its consequent increased weight gain and other growth trait indices are expected. Therefore, a putative mechanism through which lambs with these genotypes exhibit higher growth traits is proposed. The FABP4 gene is suggested as a promising marker to improve growth traits in Karakul and Awassi sheep. However, more research is required to validate this mechanism.

Single nucleotide polymorphisms in the 3′ UTR of follistatin-like 4 and scavenger receptor class B member 1 are associated with Dazu black goat litter size

The untranslated regions (UTR) of genes play crucial roles in regulating gene expression at the post-transcriptional level such as affecting mRNA stabilization. In this study, 26 single nucleotide polymorphisms (SNPs) and one deletion located in UTR were genotyped from 186 Dazu black goats via SNaPshot, and the correlation between genotype and litter size was analyzed. Results indicated that two SNP loci, SNP_chr17-20182525 and SNP_chr7-65652612, which are located at the 3′UTR of scavenger receptor class B member 1 and follistatin-like 4, are significantly (p<0.05) correlated with the litter size of first parity goats. SNP_chr7-65652612 is also significantly associated with the total litter size of first and second parity offspring (p<0.05). In conclusion, SNP_chr7-65652612 and SNP_chr17-20182525 have correlation with the litter size of Dazu black goat and they are potential genetic markers for litter size breeding.

Single nucleotide polymorphisms and metabolic biochemical profile of productive markers characterize three European breeds of dairy cattle

The objective of this study was to investigate polymorphisms of DGAT1, FABP, OLR1 and ATP1A1 genes using PCR-DNA sequencing, and to associate these genetic structures to changes in metabolic biochemical markers and milk composition indicators in a total of 90 dairy cows of the Holstein, Simmental, and Brown Swiss breeds (30 cows each). PCR was carried out for amplification of 411-bp of DGAT1, 525-bp of FABP, 582-bp of OLR1, and 300-bp of ATP1A1 genes. Three breeds’ nucleotide sequence variations in the form of single nucleotide polymorphisms (SNPs) were detailed by DNA sequencing analysis. Chisquare analysis showed that the distribution of all discovered SNPs varied significantly (P < 0.001). Biochemical indices in cow’s serum revealed no significant difference in serum total protein, albumin, and total cholesterol among the three breeds. However, triglyceride showed a significant increase in Simmental compared to either Holsteins or Brown Swiss, while the highest mean value of triiodothyronine (T3) and tetraiodothyronine (T4) was detected in Holstein dairy cows The milk composition indicators analysis revealed that milk protein, sugar, and density were significantly higher in Holsteins than both Simmental and Brown Swiss. Meanwhile, milk fat and total solids revealed a significantly higher increase in Simmental than both brown Swiss and Holstein. As a result, the metabolic biochemical markers profile along with the identified SNPs could be used as a candidate and a reference guide for effective characterization of the Holstein, Simmental, and Brown Swiss breeds, leading to the creation of a marker-assisted selection system for production traits in dairy cattle breeds.

Single-nucleotide polymorphism detecting of some candidate genes related to lipid metabolism in Booroola Merino-Afshari sheep by Bayesian model averaging

This study was designed to identify single-nucleotide polymorphisms (SNPs) of some candidate genes related to lipid metabolism and their association with carcass fat in male crossbred lambs. Hence, 96 of almost 11-month-old Booroola Merino-Afshari crossbred lambs (first-generation backcross) were used by considering their phenotypic carcass traits. Then, DNA was extracted and DNA targets were amplified using designed specific primers by PCR procedure. Identification of potential SNPs was done by a direct sequencing method for LEP, FABP4, DGAT1, GH, and TRIB3 genes using the sequencing-RFLP procedure. Then, the most probable statistical models based on additive and genotypic effects of identified SNPs in each trait were obtained by the Bayesian model averaging (BMA) approach of R software (Ver. 3.3.1) to assess the association of SNPs with traits. Detected SNPs in this study included two SNPs in exon 3 of LEP, one SNP in exon 2 of TRIB3, one SNP in intron 2 of FABP4, one SNP in 5' UTR of DGAT1, and two SNPs in 3' UTR of GH genes. For carcass weight trait, one of the identified SNP genotypes in the LEP (c.587G > A) had a higher probability in the model. Carcass weight of lambs with GA genotype was 2.46 kg heavier than GG genotype. Also, two genes of TRIB3 and GH2 had the highest probability in the models of fat tail and waste weight, respectively. Based on the results, these polymorphisms can be used in the marker-assisted selection of breeding programs and designing DNA chips for genomic selection.

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.

Single-nucleotide polymorphisms in FABP4 gene associated with growth traits in Egyptian sheep

Aim:

The present study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in the fatty acid-binding protein 4 (FABP4) gene with birth weight (BW), final weight (FW), and average daily gain (ADG) in three Egyptian sheep breeds.

Materials and Methods:

Genomic DNA was extracted from the blood samples of 50 male and female individuals representing Ossimi, Rahmani, and Barki sheep breeds. A 407 bp nucleotide (nt) segment from the first intron of FABP4 was amplified by polymerase chain reaction, sequenced, and analyzed in the different samples.

Results:

Sequence analysis of the determined segment (407 bp) revealed four SNPs (all transition types) at nt position 372 (CP011894.1:g.57605471) A>G, nt position 211 (CP011894.1:g.57605632) A>G, nt position 143 (CP011894.1:g.57605700) T>C, and nt position 111 (CP011894.1:g.57605732) T>C. The allelic and genotypic frequencies for the identified SNPs in the sheep breeds were calculated. At nt positions 372 and 211, two alleles were identified (A and G). Only two genotypes were present at nt position 372 (AA and AG), while three genotypes were present at nt position 211 (AA, AG, and GG). Two alleles (T and C) and three identified genotypes (TT, TC, and CC) were detected at nt positions 143 and 111. Analysis of the results revealed that AA genotype at nt position 372 is associated with higher estimates for BW, FW, and ADG when compared to all the other genotypes. Very high correlation coefficients were found between the genotypes 143-TT and 111-TT and also between 143-TC and 111-TC. The genotypes 372-AG, 211-GG, 211-AA, 143-TT, 143-CC, 111-TT, 111-TC, and 111-CC were associated with negative effects on BW, FW, and ADG.

Conclusion:

The detection of four SNPs in a partial sequence of the Egyptian ovine FABP4 gene intron 1 reflected that this gene harbors substantial diversity. In addition, a novel SNP at nt position 372 (CP011894.1:g.57605471) A>G was associated with higher estimates for BW, FW, and ADG.

Analysis of Candidate Genes for Growth and Milk Performance Traits in the Egyptian Barki Sheep

The most common sheep breeds of Egypt are Ossimi, Rahmani, and Barki breeds. The latter one is well adapted to the challenging desert environment, characterized by food shortage and a high temperature fluctuation. Growth performance of Barki sheep has an important economic value in terms of minimizing the shortage of mutton meat in Egypt. Further, milk production is of great importance for feeding newborn lambs. Eight candidate genes, recently associated with production traits in different breeds, were used to study the effect of genotype on lamb growth and ewe milk traits. The examined genes were LEP, IGF1, DGAT1, STAT5A, PRL, CSN1S2, GHR, and GHRHR, of which one representative single nucleotide polymorphism (SNP) located in the coding region was selected for genotyping. Data from 251 Barki sheep were used in this study. Association analysis between SNPs and lamb growth traits identified rs420693815 of the LEP gene to be significantly associated with weaning weight and average daily gain. In ewes, significant effects on milk yield and composition have been estimated for LEP (rs420693815), STAT5A (rs161082816), PRL (rs422713690), and GHRHR (rs414991449). The results indicated that these genes might be considered as interesting candidates for further investigations to improve growth and milk performance in Barki sheep.