Two co-inherited novel SNPs in the MC4R gene related to live body weight and hormonal assays in Awassi and Arabi sheep breeds of Iraq

Sumbawa cattle: a study of growth hormone (GH) gene variants and their association with biometric traits

The growth hormone (GH) gene plays a vital role in regulating animal metabolism and body size, making it a potential candidate for influencing livestock performance. This study aimed to investigate the polymorphisms within the GH gene and their associations with 10 biometric traits in the Sumbawa cattle population of Indonesia. Biometric trait data and blood samples were collected from 112 Sumbawa cattle individuals, and their GH gene sequences were analyzed using two sets of primers for amplification. Seven single nucleotide polymorphisms (SNPs) were identified in the GH gene: g.442C>T, g.446G>C, g.558C>T, g.649C>A, g.1492C>A, g.1510C>A, and g.1578G>A. All SNPs were located in the intronic region except for SNP g.558C>T, which was found in the coding sequence (CDS) region. The SNP g.558C>T is classified as a synonymous variant. Haplotype analysis revealed a strong linkage disequilibrium between SNPs g.558C>T and g.649C>A. Distributions of genotypes and alleles of all SNPs were in agreement with the Hardy-Weinberg equilibrium (p > 0.05, χ2 < 15.56), except for SNPs g.446G>C and g.1492C>A. The association study showed that the SNP g.442C>T significantly (p < 0.05) affected HL, BL, SH, and PH traits in Sumbawa cattle. Additionally, the g.446G>C and g.558C>T were also found to be associated with PH and CC traits, respectively. The polymorphisms detected in the GH gene could have implications for selection programs to enhance desired biometric traits in Sumbawa cattle. Improving livestock productivity can be done by understanding genetic diversity and its relationship with phenotypic characteristics.

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.

A missense SNP in the proopiomelanocortin (POMC) gene is associated with growth traits in Awassi and Karakul sheep

This study was conducted to assess the association between proopiomelanocortin (POMC) gene and growth traits in Awassi and Karakul sheep. PCR-single strand conformation polymorphism (SSCP) method was utilized to assess the polymorphism of POMC PCR amplicons with body weight and length, wither and rump height, chest and abdominal circumference measured at birth, 3, 6, 9, and 12 months intervals. Only one missense SNP (rs424417456:C > A) was detected in exon-2, in which glycine was converted to cysteine in the 65th position in POMC (p.65Gly > Cys). rs424417456 SNP showed significant associations with all growth traits in the third, sixth, ninth, and twelfth months. At the age of 3 months onward, lambs with CC genotype showed higher body weight, body length, wither and rump heights, and chest and abdominal circumferences than lambs with CA and AA genotypes, respectively. Prediction analyses indicated a deleterious effect of p.65Gly > Cys on POMC structure, function, and stability. Owing to the strong correlation between rs424417456:CC and better growth characteristics, this genotype is proposed as a promising marker to enhance growth traits in Awassi and Karakul sheep. The predicted damaging effects caused by rs424417456:CA and rs424417456:AA genotypes may entail a putative mechanism through which lambs with these genotypes exhibit lower growth traits.

A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes

This study aimed to assess the possible association of oxytocin (OXT) gene with reproductive traits in two groups of Awassi ewes that differ in their reproductive potentials. Sheep were genotyped using PCR-single-stranded conformation polymorphism approach. Three genotypes were detected in exon 2, CC, CA, and AA, and a novel SNP was identified with a missense effect on oxytocin (c.188C > A → p.Arg55Leu). A significant (p < 0.01) association of p.Arg55Leu with the twinning rate was found as ewes with AA and CA genotypes exhibited, respectively a lower twinning ratio than those with the wild-type CC genotype. The deleterious impact of p.Arg55Leu was demonstrated by all in silico tools that were utilized to assess the effect of this variant on the structure, function, and stability of oxytocin. Molecular docking showed that p.Arg55Leu caused a dramatic alteration in the binding of oxytocin with its receptor and reduced the number of interacted amino acids between them. Our study suggests that ewes with AA and CA genotypes showed a lower reproductive performance due to the presence of p.Arg55Leu, which caused damaging impacts on oxytocin and is binding with the OXT receptor. The utilization of the p.Arg55Leu could be useful for improving Awassi reproductive potential.

The identification of a novel SNP in the resistin (RETN) gene associated with growth traits in Karakul and Awassi sheep

Resistin is one of the most important adipocytokines in mammalian cells due to its involvement in insulin resistance, obesity, and autoimmune diseases. Resistin is encoded by RETN gene that is primarily expressed in adipose tissues. Mutations in this gene have been associated with several productive traits in animals. This study was conducted to assess the possible biomarker capacity of RETN by evaluating its association with growth traits in two economically important sheep in the Middle East. Genotyping was conducted using PCR-single strand conformation polymorphism (SSCP), and the polymorphism of RETN was associated with several growth traits for three months intervals starting from birth until one year of age. In a total of 190 Karakul sheep and 245 Awassi sheep, only one SNP (233A > C) was detected in the RETN gene. The identified novel SNP showed significant associations with all growth traits at the ages of six, nine, and twelve months. At the age of six months onward, lambs with AC and CC genotypes showed respectively lower body weight and length, chest and abdominal circumferences, and wither and rump heights than those with AA genotype. Due to the remarkable association between RETN;233A > C and lower growth traits, this genotype is suggested as a promising marker to assess growth traits in Karakul and Awassi sheep. This is the first study that demonstrated the importance of RETN as a possible tool for evaluating growth traits in two breeds of sheep with a possibility to be applied to other breeds via large-scale association analysis.

Identification of SNPs and expression patterns of ALB, AHSG and GC genes and their association with growth traits in Hu sheep

Growth traits are economically important traits in sheep breeding. This study was conducted to evaluate the polymorphisms of ALB, AHSG and GC genes and their association with growth traits in Hu sheep. We measured and recorded the body weight (BW), body height (BH), body length (BL) and feed conversion ratio (FCR) of 1418 male Hu sheep raised in the same environment from 80 to 180 days of age. The total of four SNPs in the ALB, AHSG and GC genes were identified by direct sequencing technology. The results of association analysis showed that two loci (g.8699 A>T and g.13458 T>C) of ALB gene significantly affect average daily gain (ADG; P < 0.05). The genotypes of SNP g.2454 T>C in AHSG gene were significantly associated with ADG and FCR (P < 0.05). There were significant associations between GC g.19484 A>C and BW, BH and BL (P < 0.05). The results of qRT-PCR showed that ALB, AHSG, and GC genes were extremely significantly higher in H_BW sheep compared with those in the L_BW sheep (P < 0.01). These results revealed that ALB-1 g.8699 A>T, ALB-2 g.13458 T>C, AHSG g.2454 T>C and GC g.19484 A>C loci are potential molecular markers for Hu sheep breeding.

Improved Growth and High Inheritance of Melanocortin-4 Receptor (mc4r) Mutation in CRISPR/Cas-9 Gene-Edited Channel Catfish, Ictalurus punctatus

Effects of CRISPR/Cas9 knockout of the melanocortin-4 receptor (mc4r) gene in channel catfish, Ictalurus punctatus, were investigated. Three sgRNAs targeting the channel catfish mc4r gene in conjunction with Cas9 protein were microinjected in embryos and mutation rate, inheritance, and growth were studied. Efficient mutagenesis was achieved as demonstrated by PCR, Surveyor® assay, and DNA sequencing. An overall mutation rate of 33% and 33% homozygosity/bi-allelism was achieved in 2017. Approximately 71% of progeny inherited the mutation. Growth was generally higher in MC4R mutants than controls (CNTRL) at all life stages and in both pond and tank environments. There was a positive relationship between zygosity and growth, with F₁ homozygous/bi-allelic mutants reaching market size 30% faster than F₁ heterozygotes in earthen ponds (p = 0.022). At the stocker stage (~ 50 g), MC4R × MC4R mutants generated in 2019 were 40% larger than the mean of combined CNTRL × CNTRL families (p = 0.005) and 54% larger than F₁ MC4R × CNTRL mutants (p = 0.001) indicating mutation may be recessive. With a high mutation rate and inheritance of the mutation as well as improved growth, the use of gene-edited MC4R channel catfish appears to be beneficial for application on commercial farms.

Two co-inherited novel SNPs in the MC4R gene related to live body weight and hormonal assays in Awassi and Arabi sheep breeds of Iraq

Melanocortin‐4 receptor (MC4R) gene plays a key role in the regulation of body weight and energy homeostasis. This study aims to evaluate the association of single nucleotide polymorphisms (SNPs) of the MC4R gene with live body weight and hormonal assays in two breeds of sheep that differ in productive performance, Awassi and Arabi. All known coding sequences of the MC4R gene were covered in this study. DNA samples from 150 animals (Awassi and Arabi breed) were genotyped by PCR‐single‐strand conformation polymorphism (PCR‐SSCP) to assess their pattern of genetic variation. Concerning exon 1, clear heterogeneity was detected with three different SSCP‐banding patterns. The sequencing reactions confirmed these variations by detecting the presence of the two novel SNPs, 107G/C and 138A/C, and three genotypes, GC, AC and AA. The 107G/C SNP was detected in GC genotype, while the 138A/C was detected on both GC and AC genotypes. The other SSCP‐banding pattern (AA genotype) did not show any detectable unique variation. Both SNPs were closely and strongly linked in both breeds (D' and r² values were 1.00), which signifies that both loci were co‐inherited as one unit. Association analysis indicated that both breeds with GC/AC haplotype showed higher live body weight (37.250 ± 0.790) relative to the GG/AA (30.244 ± 0.968) and CC/CC (47.231 ± 1.230) haplotypes (p < .05). Concerning the genotyping of exon 2, only 362 bp showed heterogeneity with a missense mutation, with no significant association (p > .05) with the measured traits. In conclusion, the two novel SNPs (107G/C and 138 A/C) were highly associated with live body weight in both breeds. Haplotype analysis confirmed that these two novel SNPs were in strong linkage disequilibrium (LD) and could be used as genetic markers for sheep phenotypic trait improvement.