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

Caprine and Ovine Genomic Selection-Progress and Application

The advancement of sequencing technology and molecular breeding methods has provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding, and it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animal breeding, especially in cattle. However, there are still limited studies on the application and research of GS in sheep and goats. This paper outlines the principles, analysis methods, and influential factors of GS and elaborates on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects, this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding.

Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs

Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.

Computational screening of damaging nsSNPs in human SOD1 genes associated with amyotrophic lateral sclerosis identifies destabilising effects of G38R and G42D mutations through in silico evaluation

Amyotrophic lateral sclerosis (ALS), a complicated neurodegenerative disorder affected by hereditary and environmental variables, is a condition. In this study, the genetic makeup of ALS is investigated, with a focus on the SOD1 gene's single-nucleotide polymorphisms (SNPs) and their ability to affect disease risk. Eleven high-risk missense variations that may impair the functionality of the SOD1 protein were discovered after a thorough examination of SNPs in the SOD1 gene. These mutations were chosen using a variety of prediction approaches, highlighting their importance in the aetiology of ALS. Notably, it was discovered that the stability of the SOD1 wild-type protein structure was compromised by the G38R and G42D SOD1 variants. Additionally, Edaravone, a possible ALS medication, showed a greater affinity for binding mutant SOD1 structures, pointing to potential personalised treatment possibilities. The high-risk SNPs discovered in this investigation seem to have functional effects, especially on the stability of proteins and their interactions with other molecules. This study clarifies the complex genetics of ALS and offers insights into how these genetic variations may affect the effectiveness of therapeutic interventions, particularly in the context of edaravone. In this study advances our knowledge of the genetic mechanisms causing ALS vulnerability and prospective therapeutic strategies. Future studies are necessary to confirm these results and close the gap between individualised clinical applications and improved ALS care.

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 relationship between OXT gene polymorphisms and reproductive hormones in pregnant and lactating Awassi Ewes

BACKGROUND

Numerous genetic loci interact intricately to control reproduction in mammals. The oxytocin gene (OXT) is a promising candidate for reproductive traits in mammals. Previously, sheep and goats have been studied for the presence of the OXT polymorphism. As of yet, no polymorphisms have been identified in the OXT gene of Awassi sheep. Thus, this study was conducted to determine the effects of OXT polymorphism and litter size on reproductive hormones in pregnant and lactating Awassi ewes.

METHODS AND RESULTS

This study evaluated 232 ewes aged 3 and 4 years (123 single-progeny ewes and 109 twin-producing ewes). Serum was collected to measure reproductive hormones using ELISA kits manufactured by ELK Biotechnology. DNA was extracted from sheep blood for genotyping and sequencing to identify variations in OXT gene (exon 2, 266 bp). Genotyping analysis revealed three genotypes within 266 bp: CC, CA, and AA. Sequence analysis revealed a novel mutation in exon 2: 188 C > A. Statistical analysis showed significant associations between the 188 C > A SNP and phenotypic traits. Twin-pregnant ewes carrying CC genotypes had higher estrogen, progesterone, and follicle-stimulating hormone/luteinizing hormone levels (65.86 ± 3.87) (pg/mL), (6.51 ± 0.39) (ng/mL), and (20.22 ± 1.27) (ng/mL)/( 23.37 ± 2.14) (ng/mL) respectively, compared to CA and AA genotypes in the fourth month of twin-pregnant ewes compared to single-pregnant ewes.

CONCLUSIONS

This study found that the 188 C > A SNP negatively affected reproductive hormone levels in Awassi sheep. These findings provide breeders with a new insight into the sheep OXT gene, useful for future breeding.

Association of birth type and LHX4 gene polymorphism with reproductive hormones, growth hormone, and prolactin in Awassi ewes

BACKGROUND

LIM homeobox transcription factor 4 (LHX4) is a promising candidate gene for mammalian reproductive traits. LHX4 polymorphism has previously been associated with phenotypic traits in goats and cattle. However, there have been no LHX4 gene polymorphisms identified in Awassi sheep. Therefore, this study investigated the effects of the LHX4 polymorphism on reproductive hormones, growth hormones, and prolactin in Awassi ewes.

METHODS AND RESULTS

A total of 232 ewes between the ages of 3 and 4 years were selected for this study (123 single-progeny ewes and 109 twin-producing ewes). Serum was collected to measure reproductive hormones, growth hormone, and prolactin using ELISA kits made by ELK Biotechnology. Genomic DNA was extracted from sheep blood, genotyped, and sequenced to confirm variations in LHX4 (exon 1, 207 bp). Genotyping revealed three genotypes in 207 bp: AA, AG, and GG. Sequence analysis detected a novel mutation in exon 1: 160 A > G. Statistically, the 160 A > G SNP was significantly associated with the phenotypic traits. Ewes carrying AA genotypes had higher estrogen, progesterone, follicle-stimulating hormones/luteinizing hormones, and growth hormone, and lower prolactin levels (65.63 ± 3.84) (pg/mL), (6.67 ± 0.38) (ng/mL), (22.34 ± 1.27) (ng/mL)/(23.89 ± 2.13) (ng/mL), (1.30 ± 0.05) (ng/mL), and (13.16 ± 0.75) (pg/mL), respectively, compared to AG and GG genotypes in the fourth month of twin-pregnant ewes compared to single-pregnant ewes.

CONCLUSION

This study suggests that the 160 A > G SNP negatively affects the Awassi sheep's hormone levels. It provides valuable insight into the sheep LHX4 gene, which could be an effective marker in marker-assisted selection.

A Novel c.100C > G Mutation in the FST Gene and Its Relation With the Reproductive Traits of Awassi Ewes

Reproductive traits are affected by many factors, including ovarian function, hormones, and genetics. Genetic polymorphisms of candidate genes are associated with reproductive traits. Several candidate genes are associated with economic traits, including the follistatin (FST) gene. Thus, this study aimed to evaluate whether the genetic variations in the FST gene are associated with the reproductive traits in Awassi ewes. The genomic DNA was extracted from 109 twin ewes and 123 single-progeny ewes. Therefore, 4 sequence fragments from the FST gene were amplified using polymerase chain reaction (PCR) (exon 2/240, exon 3/268, exon 4/254, and exon 5/266 bp, respectively). For a 254 bp amplicon, 3 genotypes were identified: CC, CG, and GG. Sequencing revealed a novel mutation in CG genotypes c.100C > G. The statistical analysis of c.100C > G showed an association with reproductive characteristics. Ewes carrying the c.100C > G had significantly (P ⩽ .01) lower litter sizes, twinning rates, lambing rates, and more days to lambing compared with CG and CC genotypes. Logistic regression analysis confirmed that the c.100C > G single-nucleotide polymorphism (SNP) is responsible for decreasing litter size. According to these results, the variant c.100C > G negatively affects the traits of interest and is associated with lower reproductive traits in Awassi sheep. As a result of this study, ewes carrying the c.100C > G SNP have lower litter size and are less prolific.

A Missense p.Q>R234 Mutation in the Osteopontin Gene Is Associated With the Prolificacy of Iraqi Awassi Ewes

One of the most valuable traits in production and breeding is a sheep's prolificacy which is influenced by several genes, one of which is the osteopontin (OPN) gene. Thus, this study aimed to determine the effect of genetic variation within the OPN gene on Awassi ewe prolificacy. Genomic DNA was extracted from 123 single-progeny ewes and 109 twin ewes. Polymerase chain reaction (PCR) was used to amplify 4 sequence fragments (289, 275, 338, and 372 bp), representing exons 4, 5, 6, and 7 of the OPN gene. A 372 bp amplicon was identified with 3 different genotypes: TT, TC, and CC. Sequence analysis revealed a novel mutation in TC genotypes p.Q>R234. Statistical analysis revealed that the single nucleotide polymorphism (SNP) p.Q>R234 was associated with prolificacy. Ewes carrying the p.Q>R234 SNP had significantly (P ⩽ .01) lower litter sizes, twinning rates, and lambing rates, and more days to lambing than those with the TC and TT genotypes. The p.Q>R234 SNP was confirmed to be responsible for lower litter size through logistic regression analysis. From these results, we can conclude that the missense variant p.Q>R234 adversely affects the traits of interest and shows that the p.Q>R234 SNP negatively influences the prolificacy of Awassi sheep. Based on this study, it is evident that ewes in this population carrying the p.Q>R234 SNP have a lower litter size and are less prolific.

Polymorphism of the ADIPOQ gene and its association with productive traits in Awassi Ewes

BACKGROUND

Adiponectin (ADIPOQ) plays a critical role in energy and lipid metabolism, indicating that adiponectin could affect livestock productivity. There is an association between polymorphisms in the ADIPOQ gene and variations in livestock productive traits. Therefore, this study investigated the relationship between ADIPOQ polymorphism and productive traits in Awassi ewes.

METHODS AND RESULTS

This study included 200 sexually mature ewes, aged 2.5 to 5 years, non-pregnant and not lactating. A phenotypic measurement consisting of live weight and body dimensions, was taken. Samples of blood were taken for extraction of genomic DNA and PCR-SSCP based genotyping, followed by sequencing to confirm variants in amplified fragments. A novel c.198,473,337 C > A SNP was found in exon 1 of the ADIPOQ gene confirming heterogeneity with genotypes AA, CC, and CA. The AA genotype differed significantly (P < 0.05) by comparison with the CA and CC genotypes concerning live body weight and body measurements. An association between productive traits and the c.198,473,337 C > A SNP revealed a significant association of the A allele (odds ratio: 2.22 (95% CI: 0.94-5.30) in the additive genetic model.

CONCLUSION

Sheep with the AA genotype were heavier and had larger body dimensions, implying superior production and reproduction. Further studies are required in other breeds to prove the results.

Novel variants associated with adiponectin-related traits in Awassi ewes

Background

Adipose tissue secretes adiponectin (ADIPOQ), a hormone related to fat oxidation, glucose metabolism, and reproduction. The polymorphism of adiponectin is associated with productive traits in domestic animals. Thus, this study investigated the association of adiponectin gene polymorphism with lipid profile and reproductive hormones in Awassi ewe. In this study, 200 ewes between the ages of 2.5 and 5 years, neither pregnant nor lactating, were included. To determine the lipid profile and reproductive hormones, sera were separated from the blood. DNA extraction, genotyping, and sequencing reactions were used to verify the variants in the amplified fragments (exon 1).

Results

Three genotypes, CC, CA, and AA, were identified from 368 bp amplicons (exon 1). A sequencing reaction revealed a novel mutation, c.198473337C > A, in the CA genotype. The results revealed significant differences (P ≤ 0.05) in cholesterol and HDL levels in the AA genotype than CC and CA genotypes. The AA genotype had higher estradiol and progesterone levels (50.52 ± 0.64) (pg/ml) and (7.10 ± 0.04) (ng/ml), respectively, than those with the CC and CA genotypes.

Conclusions

These results conclude that the ADIPOQ gene affects lipid profiles and sex hormone levels in Awassi sheep. Choosing sheep that are polymorphic for the ADIPOQ gene should be a future study, as this gene could be linked to high prolificacy.

Dr Association of bone morphogenetic protein 15 and growth differentiation factor 9 with litter size in livestock: a review study

. Litter size is one of the crucial factors in livestock production and is of high economic value, which is affected by ovulation rate, hormones, and growth factors. Growth factors play a multifaceted role in reproductive physiology. This review aims to investigate the association of bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) with litter size in livestock. The transforming growth factor β (TGF- β) superfamily includes more than 34 members; GDF9 and BMP15 are among the most significant factors for regulating fertility and litter size in most livestock species. Ovarian follicles release BMP15 and GDF9 that are involved in the maturation of primary follicles into the basal form, proliferation of granulosa and theca cells, steroidogenesis, ovulation, and formation of the corpus luteum. Besides, these factors are highly expressed in oocytes and are necessary for female fertility and multiple ovulation in several livestock species. Animals with two inactive copies of these factors are sterile, while those with one inactive copy are fertile. Thus, the present review provides valuable information on the association of BMP15 and GDF9 with litter size in livestock that can be used as biological markers of multiple ovulation or for improving fertility in livestock.

lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach

Understanding the molecular pattern of fertility is considered as an important step in breeding of different species, and despite the high importance of the fertility, little success has been achieved in dissecting the interactome basis of sheep fertility. However, the complex mechanisms associated with prolificacy in sheep have not been fully understood. Therefore, this study aimed to use competitive endogenous RNA (ceRNA) networks to evaluate this trait to better understand the molecular mechanisms responsible for fertility. A competitive endogenous RNA (ceRNA) network of the corpus luteum was constructed between Romanov and Baluchi sheep breeds with either good or poor genetic merit for prolificacy using whole-transcriptome analysis. First, the main list of lncRNAs, miRNAs, and mRNA related to the corpus luteum that alter with the breed were extracted, then miRNA−mRNA and lncRNA−mRNA interactions were predicted, and the ceRNA network was constructed by integrating these interactions with the other gene regulatory networks and the protein−protein interaction (PPI). A total of 264 mRNAs, 14 lncRNAs, and 34 miRNAs were identified by combining the GO and KEGG enrichment analyses. In total, 44, 7, 7, and 6 mRNAs, lncRNAs, miRNAs, and crucial modules, respectively, were disclosed through clustering for the corpus luteum ceRNA network. All these RNAs involved in biological processes, namely proteolysis, actin cytoskeleton organization, immune system process, cell adhesion, cell differentiation, and lipid metabolic process, have an overexpression pattern (Padj < 0.01). This study increases our understanding of the contribution of different breed transcriptomes to phenotypic fertility differences and constructed a ceRNA network in sheep (Ovis aries) to provide insights into further research on the molecular mechanism and identify new biomarkers for genetic improvement.

Dr. Novel missense variant L46Q of fatty acid synthase gene and fatty acids content in Awassi sheep

This study was conducted to investigate the association between the polymorphism of the FASN gene with fatty acid content in Awassi sheep. A total of 100 male Awassi sheep between the ages of one and two and a half years old were used in this study. Phenotypic measurement was recorded at slaughter, and from each animal, the longissimus dorsi (LD) muscle samples were taken to analyze the fatty acid profile. Genotyping, sequencing reactions, and in silico tools were performed to confirm the variants in amplified fragments. The result of genotyping revealed two genotypes (AA and AB) of the ovine FASN gene (exon 3). Novel SNP (L46Q) was discovered only within the FASN gene (AB genotype). All utilized in silico tools revealed remarkably deleterious effects for the L46Q on the mutant protein structure, function, and stability. Association analysis revealed that the AB genotype has significantly (p < 0.05) higher levels of animal length and monounsaturated fatty acids (MUFA) with lower amounts of saturated fatty acids (SFA) content than the AA genotype. In conclusion, novel SNP (L46Q) was discovered within the FASN gene (AB genotype), made the animals that has the AB genotype associated with good meat quality traits and this polymorphism may serve as markers for meat quality.

Variants of the SCD gene and their association with fatty acid composition in Awassi sheep

BACKGROUND

Genetic factors affect the variability of fatty acid composition in ruminant products. Thus, this study aimed to investigate the association between the variations of the SCD gene and fatty acid composition in Awassi sheep.

METHODS AND RESULTS

A total of 100 Awassi rams between the ages of one and two and a half years old were used in this study. Blood samples were taken at abattoirs in Babylon, and from each animal, longissimus dorsi (LD) muscle samples were taken to measure the fatty acid composition. DNA samples were isolated from each blood sample, then PCR-single strand conformation polymorphism (PCR-SSCP) experiments were conducted for genotyping followed by sequencing reactions. The study identified two genotypes (TT and TA) of the SCD gene (exon 3). Several novel variants were discovered in the amplified fragments of the SCD gene.

CONCLUSIONS

The TA genotype resulted in increased intramuscular fat and monounsaturated fatty acids compared to the TT genotype. Breeding for the TA genotype could be used for producing meat containing less saturated fatty acids and more monounsaturated fatty acids, making meat more favorable for human consumption.

Association of OLR1 gene polymorphism with live body weight and body morphometric traits in Awassi ewes: short communication

BACKGROUND

Oxidized low-density lipoprotein receptor 1 (OLR1) is an endothelial receptor that binds and degrades oxidized low-density lipoproteins (Ox-LDL), thus having a physiological role in metabolism. Polymorphisms in the OLR1 gene are associated with animals with different production traits. Due to this, the study aimed to determine if OLR1 polymorphisms in Awassi ewes associate with live body weight and body measurement.

METHODS AND RESULTS

In this study, 200 ewes between the ages of 2.5 and 5 years, not pregnant or lactating, were selected. Phenotypic measurements including live body weight and body measurements were collected. A sheep's blood was collected to extract genomic DNA, genotyped, and sequenced to confirm the presence of the variants that arose from the amplified fragments. One novel C246A single nucleotide polymorphism (SNP) was identified in the OLR1 gene (exon 3) that assigned two genotypes CC and CA. The study indicated significant differences (P ≤ 0.05) in live body weight and body measurements of the genotype CC compared with the genotype CA. The genotype CC correlated positively with live body weight, height at shoulder, height at hip, chest girth, and chest width (r = 0.67, P = 0.02), (r = 0.54, P = 0.03), (r = 0.61, P = 0.02), (r = 0.53, P = 0.01) and (r = 0.66, P = 0.04) respectively.

CONCLUSIONS

Sheep with the CC genotype had a higher live body weight and larger body measurement, making them better for productivity. These genotypic data and associations can be used to better select sheep for future marker-assisted selection programs.