An effective method for silver-staining DNA in large numbers of polyacrylamide gels

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.

Ovine KRT81 Variants and Their Influence on Selected Wool Traits of Commercial Value

Keratins are the main structural protein components of wool fibres, and variation in them and their genes (KRTs) is thought to influence wool structure and characteristics. The PCR-single strand conformation polymorphism technique has been used previously to investigate genetic variation in selected coding and intron regions of the type II sheep keratin gene KRT81, but no variation was identified. In this study, we used the same technique to explore the 5' untranslated region of KRT81 and detected three sequence variants (A, B and C) that contain four single nucleotide polymorphisms. Among the 389 Merino × Southdown cross sheep investigated, variant B was linked to a reduction in clean fleece weight, while C was associated with an increase in both greasy fleece weight and clean fleece weight. No discernible effects on staple length or mean-fibre-diameter-related traits were observed. These findings suggest that variation in ovine KRT81 might influence wool growth by changing the density of wool follicles in the skin, the density of individual fibres, or the area of the skin producing fibre, as opposed to changing the rate of extrusion of fibres or their diameter.

Variation in the AA-NAT gene G203A is associated with Awassi and Hamdani sheep fertility

Arylalkylamine-N-acetyl-transferase (AA-NAT) is one of several genes that influence sheep reproduction. Thus, the objective of this study was to investigate whether genetic variability within the AA-NAT gene influenced the reproductive performance of Awassi and Hamdani ewes. A total of 99 twin and 101 single-progeny ewes were analyzed for genomic DNA. Polymerase chain reaction (PCR) was used to produce amplicons of 300, 313, and 287 bp from exons 1, 2, and 3 of the AA-NAT gene. A 300-bp amplicon was genotyped, resulting in two genotypes: GG and GA. Through sequence analysis, a mutation 203 G > A was identified in the GA genotype. The statistical analysis revealed a strong correlation between the single nucleotide polymorphism (SNP) 203 G > A and reproductive performance. Ewes carrying this mutation showed significantly increased litter sizes, twinning rates, lambing rates, and fewer days to lambing compared to those carrying GG. These findings demonstrate that the presence of the 203 G > A SNP variant has a significant positive impact on litter sizes and enhances the fertility of Awassi and Hamdani sheep.

The Novel PTX3 Variant g.22645332G>T Is Strongly Related to Awassi and Hamdani Sheep Litter Size

The detection of polymorphisms in genes that control livestock reproduction could be highly beneficial for identifying and enhancing economic traits. One of these genes is pentraxin 3 (PTX3), which affects the reproduction of sheep. Therefore, this study investigated whether the variability of the PTX3 gene was related to the litter size of Awassi and Hamdani ewes. A total of 200 ewes (130 Awassi and 70 Hamdani) were used for genomic DNA extraction. Polymerase chain reaction was used to amplify the sequence fragments of exons 1, 2, 3, and 4 from the PTX3 gene (Oar_v4.0; Chr 1, NC_056054.1), resulting in products of 254, 312, 302, and 253, respectively. Two genotypes, GG and GT, were identified for 302 bp amplicon. A novel mutation was discovered through sequence analysis in the GT genotype at position g.22645332G>T. The statistical analysis revealed a significant association between single nucleotide polymorphism (SNP g.22645332G>T; Oar_v4.0; Chr 1, NC_056054.1) and litter size. The presence of the SNP g.22645332G>T (Oar_v4.0; Chr 1, NC_056054.1) genotype in ewes resulted in a significant difference compared to ewes with GG genotypes. The discrepancy became apparent in several aspects, including litter sizes, twinning rates, lambing rates, litter weight at birth, and days to lambing. There were fewer lambs born to ewes with the GG genotype than to ewes with the GT genotype. The variant SNP g.22645332G>T (Oar_v4.0; Chr 1, NC_056054.1) has positive effects on the litter size of Awassi and Hamdani sheep. The SNP g.22645332G>T (Oar_v4.0; Chr 1, NC_056054.1 has been associated with an increase in litter size and higher prolificacy in ewes.

The novel C268A variant of BMP2 is linked to the reproductive performance of Awassi and Hamdani sheep

BACKGROUND

Prolificacy-associated genetic markers can be utilized to enhance litter size in the sheep breeding industry. Sheep reproduction is influenced by a multitude of genes, including bone morphogenetic protein 2 (BMP2). This study aimed to explore the potential relationship between variability in the BMP2 gene and reproductive performance in Awassi and Hamdani ewes.

METHODS AND RESULTS

The genomic DNA was extracted from 99 single-progeny ewes and 101 twin ewes. Polymerase chain reaction (PCR) was employed to produce an amplicon consisting of four sequence fragments: 277 bp, 251 bp, 331 bp, and 340 bp, from exons 1, 2, 3, and 4 of the BMP2 gene, respectively. Three genotypes were identified for amplicons in exon 4 with 340-bp lengths: CC, CA, and AA. Upon analyzing the sequence of the CA genotype 382 C > A, a novel mutation was discovered in this genotype. A robust association was identified between the single nucleotide polymorphisms (SNP) 382 C > A and reproductive performance through statistical analysis. An important distinction was discovered between ewes carrying SNP 382 C > A and those carrying CC in terms of litter sizes, twinning rates, lambing rates, and days to lambing. An analysis of logistic regression revealed a significant association between litter size and the 382 C > A SNP. There was a decrease in lamb production among ewes with the CC genotype compared to those with the CA and AA genotypes.

CONCLUSIONS

These results indicate that the SNP variant 382 C > A has a positive influence on the reproductive performance of Awassi and Hamdani sheep. Sheep carrying the 382 C > A SNP exhibit increased litter size and overall productivity compared to those without the SNP.

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.

Ovine KRTAP36-2: A New Keratin-Associated Protein Gene Related to Variation in Wool Yield

Keratin-associated proteins (KAPs) are structural components of wool fibres. High-glycine/tyrosine (HGT)-KAPs are a subset of the KAP family, and their abundance in fibres varies. In this study, we report the discovery of an ovine HGT-KAP gene to which we assigned the name KRTAP36-2. Polymerase chain reaction and single-strand conformation polymorphism (PCR-SSCP) analyses revealed four variants of this gene in a screening population of 170 sheep from a variety of breeds. The DNA sequencing of the variants revealed four single-nucleotide polymorphisms (SNPs) and a dinucleotide deletion. Three of these SNPs were in the coding region, and one of these was non-synonymous and potentially led to the amino acid substitution p.Cys27Gly near the middle of the protein. The remaining SNP was located near the putative TATA box, and the di-nucleotide deletion was near the putative transcription initiation site. The effect of this variation in KRTAP36-2 was investigated in 274 Southdown × Merino lambs that were the progeny of five sires. Variation was only found to be associated with wool yield, that is, the proportion of the greasy fleece that remained as clean fleece upon scouring (expressed as a percentage). This may have some value in increasing wool production.

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.

Identification of the Keratin-Associated Protein 22-2 Gene in the Capra hircus and Association of Its Variation with Cashmere Traits

The Cashmere goat is an excellent local goat breed in Gansu Province of China, and it is expected to improve cashmere production and cashmere quality through selection and breeding to enhance its commercial value. Keratin-associated proteins (KAPs) play an important role in maintaining wool structure. The gene encoding the keratin-associated protein 22-2 (KAP22-2) gene has been identified in selected species other than goats, such as humans, mice, and sheep. In this study, the sequence of the sheep KAP22-2 gene (KRTAP22-2) was aligned into the goat genome, and the sequence with the highest homology was assumed to be the goat KRTAP22-2 sequence and used to design primers to amplify the goat gene sequence. A total of 356 Longdong Cashmere goats (Gansu Province, China) were used for screening of genetic variants. Four specific bands were detected by polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) analysis, and they formed a total of six band types individually or in combination. Four alleles were identified by DNA sequencing of PCR amplification products. A total of four single nucleotide polymorphic sites (SNPs) were detected in the four sequenced KRTAP22-2 alleles. Two of them are in the 5'UTR region and the other two are in the coding region, and the variants in the coding region are all non-synonymous mutations. In addition, there was a 6 bp length variation in allele C. The gene was expressed in the cortical layer of primary and secondary hair follicles, the inner root sheath, as well as hair papillae and hair maternal cells in goats. The results of the correlation analysis between genotypes and cashmere traits showed that after excluding genotypes with a gene frequency of less than 5%, the mean fiber diameter (MFD) of cashmere was significantly higher in the AB genotype than in the AA and AC genotypes. That is, the KRTAP22-2 gene variants are associated with mean fiber diameter in cashmere. The above results suggest that the goat KRTAP22-2 variant can be utilized as a molecular marker candidate gene for cashmere traits.

Association of Novel C319T Variant of PITX2 Gene 3'UTR Region With Reproductive Performance in Awassi Sheep

Several genes influence sheep's reproductive performance, among them the paired-like homeodomain transcription factor 2 (PITX2) gene. Thus, this study aimed to examine whether the variability within the PITX2 gene is associated with the reproductive performance of Awassi ewes. A total of 123 single-progeny ewes and 109 twin ewes were used to extract genomic DNA. An amplicon of 4 sequence fragments from exons 2, 4, 5 (upstream portion), and 5 (downstream portion) of the PITX2 gene was generated by polymerase chain reaction (PCR), 228, 304, 381, and 382 bp, respectively. Three genotypes of 382 bp amplicons were identified: CC, CT, and TT. Sequence analysis revealed a novel mutation in the CT genotype 319C > T. Statistical analysis revealed that single-nucleotide polymorphism (SNP) 319C > T was associated with reproductive performance. Single-nucleotide polymorphism 319C > T-carrying ewes had significantly (P ⩽ .01) lower litter sizes, twinning rates, lambing rates, and more days to lambing than those carrying CT and CC genotypes. Based on a logistic regression analysis, it was confirmed that the 319C > T SNP decreased litter size. Ewes with TT genotype produced fewer lambs than ewes with CT and CC genotypes. According to these results, the variant 319C> T SNP negatively affects the reproductive performance of Awassi sheep. Ewes carrying the 319C > T SNP have a lower litter size and are less prolific than those without the SNP.

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.

Association of the IGF1 5′UTR Polymorphism in Meat-Type Sheep Breeds Considering Growth, Body Size, Slaughter, and Meat Quality Traits in Turkey

This investigation was conducted to determine how the growth and carcass traits of meat-type sheep breeds raised in Turkey are associated with IGF1 5′UTR polymorphisms. Overall, 202 lambs from five breeds were evaluated. We identified eight nucleotide changes (seven substitutions and one deletion) in three variants of IGF1 5′UTR by SSCP analysis and nucleotide sequencing. It was found that the P1 variants had a unique deletion (g.171328230 delT), while the P2 variants were identified by SNPs rs401028781, rs422604851, and g.171328404C > Y. The P3 variants possessed one heterozygous substitution (g.171328260G > R) and three homozygous substitutions (g.171328246T > A, g.171328257T > G, g.171328265T > C) not observed in P1 or P2. Based on the growth and production traits, a statistically significant difference was found only in chest width at weaning (p < 0.01) and leg circumferences at yearling (p < 0.05). The P1 variants showed a leaner profile with a higher Musculus longissimus dorsi, but the differences were not significant (p > 0.05). The P2 variants had a higher percentage of rack (p < 0.01) and loin (p > 0.05). Moreover, there was no discernible difference between variants, even though the P3 variants had a higher percentage of neck and leg and the P1 variants had a higher percentage of the shoulder. It is concluded that nucleotide changes in IGF1 5′UTR could be exploited utilizing a marker-assisted selection technique to increase growth and production attributes, as well as carcass quality traits.

The growth hormone gene polymorphism and its relationship to performance and carcass features in Egyptian Awassi lambs

The main purpose of the existing experiment was to assess the allelic and genotypic polymorphisms of the Growth hormone (GH) gene and its correlation with growth indices, efficiency of consumed feed, some body indices and carcass traits of the Egyptian Awassi sheep. Forty Egyptian Awassi male lambs were selected for their growing indices (post-weaning daily gain, marketing weight, and weaning weight), feed efficiency (consumed feed and of consumed feed), body conformational indicators (skeletal muscle index, relative body index, body mass index, and body index), and carcass features (dressing %, hot carcass weight, fore-legs %, neck %, loin %, ribs %, abdominal fat %, Tail % and hind-legs %). The polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) tool was applied to detect the genotypic and allelic GH gene polymorphisms properties. The PCR-RFLP analysis identified three main genotypes (AA, AB and BB) and two main alleles (A and B). The GH genotype (AA or AB) exhibited moderate significant influence (P < 0.05) on marketing weight, Loin% and Tail%. Also, genotype (AB or BB) of expressed GH gene significantly (P < 0.01) influence on consumed feed, post-weaning daily gain, neck% and body mass index, whereas, it had no influence on the phenotypic values of the other characteristics investigated. The presence of the A allele in the genotype was markedly associated (P < 0.01) with consumed feed, body mass index and post-weaning daily growth; conversely, the presence of the B allele in the genotype was significantly related (P < 0.05) with marketing weight, loin %, and tail %. While, GH gene expression was revealed to be highly significant (P < 0.01) in relation to post-weaning daily growth, feed intake, and neck %. According to the findings, determining the associations between GH gene variation and growth, efficiency of consumed feed, body measurements, and carcass features of Egyptian Awassi sheep and applying marker assisted selection with the GH gene to improve these traits is warranted and will be of significant economic value to sheep production.

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.

Expression and Variations in EPAS1 Associated with Oxygen Metabolism in Sheep

Endothelial PAS domain protein 1 gene (EPAS1) is a member of the HIF gene family. This gene encodes a transcription factor subunit that is involved in the induction of oxygen-regulated genes. Several studies have demonstrated that a mutation in EPAS1 could affect oxygen sensing, polycythemia, and hemoglobin level. However, whether EPAS1 mutation affects sheep oxygen metabolism is still unknown. Therefore, we explored the relationship between the variation of EPAS1 and oxygen metabolism in sheep. In this study, variations in ovine EPAS1 exon 15 were investigated in 332 Tibetan sheep and 339 Hu sheep by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. In addition, we studied the effect of these variations on blood gas in 176 Tibetan sheep and 231 Hu sheep. Finally, the mRNA expression of EPAS1 in six tissues of Hu sheep and Tibetan sheep living at different altitudes (2500 m, 3500 m, and 4500 m) was analyzed by real-time quantitative PCR (RT-qPCR). Four alleles (A, B, C, and D) were detected, and their distributions highly differed between Tibetan sheep and Hu sheep. In Tibetan sheep, B was the dominant allele, and C and D alleles were rare, whereas all four alleles were common in Hu sheep. Six single nucleotide polymorphisms (SNPs) were identified between the four alleles and one of them was non-synonymous (p.F606L). While studying the blood gas levels in Tibetan sheep and Hu sheep, one variant region was found to be associated with an elevated pO₂ and sO₂, which suggested that variations in EPAS1 are associated with oxygen metabolism in sheep. RT-qPCR results showed that EPAS1 was expressed in the six tissues of Hu sheep and Tibetan sheep at different altitudes. In addition, the expression of EPAS1 in four tissues (heart, liver, spleen, and longissimus dorsi muscle) of Hu sheep was lower than that in Tibetan sheep from three different altitudes, and the expression of EPAS1 was positively correlated with the altitude. These results indicate that the variations and expression of EPAS1 is closely related to oxygen metabolism.

Variation in Ovine DGAT1 and Its Association with Carcass Muscle Traits in Southdown Sheep

Diacylglycerol O-acyltransferase 1 (DGAT1) is a microsomal enzyme that plays a key role in the synthesis of triglycerides. Its gene (DGAT1) is regarded as a candidate gene for variation in milk and meat traits in cattle. The objective of this study was to use a PCR single-strand conformation polymorphism approach to explore sequence variation in two regions of ovine DGAT1 and to assess its effect on meat traits in New Zealand Southdown sheep. Three variant nucleotide sequences were identified in each region, with two single nucleotide polymorphisms (SNPs) and one nucleotide deletion being detected in intron 1 and two SNPs being found in exon 17. The effect of the exon 17 variation was not investigated due to one variant being predominant and the other two variants occurring at low frequencies. In intron 1, one variant (B₁) was found to be associated with increase loin meat yield, suggesting that this may have value as a gene marker for improving meat traits.

The glutamate metabotropic receptor 5 (GRM5) gene is associated with beef cattle home range and movement tortuosity

Background

The grazing behaviour of herbivores and their grazing personalities might in part be determined genetically, but there are few studies in beef cattle illustrating this. In this study, we investigated for first time the genetic variation within a candidate ‘grazing gene’, the glutamate metabotropic receptor 5 gene (GRM5), and tested associations between variation in that gene and variation in grazing personality behaviours (GP-behaviours) displayed by free-ranging cows during winter grazing in the steep and rugged rangelands of New Zealand. Mature beef cows (n = 303, from 3 to 10 years of age) were tracked with global positioning system (GPS) and, with 5-minutes (min) relocation frequency, various GP-behaviours were calculated. These included horizontal and vertical distances travelled, mean elevation, elevation range, elevation gain, slope, home range and movement tortuosity, variously calculated using daily relocation trajectories with repeated measurements (i.e., 7 to 24 days (d)) and satellite-derived digital elevation models (DEM). The different GP-behaviours were fitted into mixed models to ascertain their associations with variant sequences and genotypes of GRM5.

Results

We discovered three GRM5 variants (A, B and C) and identified the six possible genotypes in the cattle studied. The mixed models revealed that A was significantly associated with elevation range, home range and movement tortuosity. Similarly, GRM5 genotypes were associated (P < 0.05) to home range and movement tortuosity, while trends suggesting association (P <  0.1) were also revealed for elevation range and horizontal distance travelled. Most GP-behaviour models were improved by correcting for cow age-class as a fixed factor. The analysis of GP-behaviours averaged per cow age-class suggests that grazing personality is fully established as beef cows reached 4 years of age. Home range and movement tortuosity were not only associated with GRM5 variation, but also negatively correlated with each other (r = − 0.27, P < 0.001).

Conclusions

There seems to be a genetically determined trade-off between home range and movement tortuosity that may be useful in beef cattle breeding programmes aiming to improve the grazing distribution and utilisation of steep and rugged rangelands.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00755-7.

Predictive Significance of Two MMP-9 Promoter Polymorphisms and Acetylated c-Jun Transcription Factor for Papillary Thyroid Carcinoma Advancement

Papillary thyroid carcinoma represents a challenge from a prognostic standpoint. Molecular alterations responsible for PTC advancement include MMP-9 genetic promoter polymorphisms that bind transcription factors with varying degrees of affinity and, hence, constitute a predisposition for MMP-9 expression. We examined how two promoter polymorphisms (the -1562 C/T transition and -131 (CA)n tandem repeats) as well as levels of the c-Jun transcription factor and its modified form acetylated at Lys271 influence MMP-9 expression and PTC progression. A significant proportion of PTC samples were heterozygous for the (CA)n tandem repeat number, had a transcription-promoting T allele at -1562, and expressed high levels of c-Jun, acetylated c-Jun, and MMP-9 protein. The T allele at the -1562 position accompanied the elevated MMP-9 protein expression, while high acetylated c-Jun levels accompanied the high MMP-9 protein levels on mRNA. The -1562 C/T transition, MMP-9, and acetylated c-Jun were associated with the presence of extra-thyroid invasion and degree of tumor infiltration, while the T allele and acetylated c-Jun also correlated with tumor stage. We conclude that the -1562 MMP-9 polymorphism and levels of acetylated c-Jun affect PTC progression via modulation of MMP-9 levels. Genotyping the MMP-9 at -1562 and estimating the levels of MMP-9 and acetylated c-Jun in PTC may prove beneficial in identifying high-risk patients.

Sequence Variation in Caprine KRTAP6-2 Affects Cashmere Fiber Diameter

Keratin-associated proteins (KAPs) are a structural component of cashmere fibers and in part determine fiber attributes. The gene encoding the high-glycine/tyrosine KAP6-2 (called KRTAP6-2) has been described in sheep, but it has not been identified goats. In this study, a 252-bp open reading frame with similarity to ovine KRTAP6-2 was found on goat chromosome 1, with its upstream and downstream flanking sequences are closely related with ovine KRTAP6-2 but are clearly distinct from other ovine KRTAP6-n sequences. Polymerase chain reaction amplification followed by single strand conformation polymorphism analysis of this region revealed five distinct banding patterns representing five different sequences (A to E) in 230 Longdong cashmere goats. Eleven diallelic single nucleotide polymorphisms (SNPs), a three-nucleotide sequence variation, and a 12-bp insertion/deletion were found among these five sequences, with most SNPs being either outside the coding region or synonymous. The presence of variant D was found to be associated with decreased mean fiber diameter (MFD; present: 13.26 ± 0.07 µm; absent: 13.55 ± 0.04 µm; p < 0.001), suggesting that variation in KRTAP6-2 may affect fiber diameter and have value as a molecular marker for improving the cashmere fiber diameter trait.

Genetic variation in the ovine KAP22-1 gene and its effect on wool traits in Egyptian sheep

The objective of this study was to investigate the genetic polymorphisms in the keratin-associated protein (KAP22-1) gene in Barki (n=206), Rahmani (n=28) and Ossimi (n=28) as the three major sheep breeds in Egypt. Subsequently, the detected variants were correlated with important wool traits. The traits included greasy fleece weight (GFW, g), staple length (SL, cm), prickle factor (PF, %), medullated fiber (MF, %), fiber diameter (FD, µm), crimp percentage (CR, %) and the standard deviation of FD (SDfd, µm), as well as the subjectively assessed traits of kemp score (KS), handle grade (HG), greasy color grade (GCG), bulk grade (BG), luster grade (LG) and staple structure (SST). Animals were genotyped by polymerase chain reaction (PCR) – single strand conformation polymorphism (SSCP). Five SSCP banding patterns representing three different nucleotide variants (A, B and C) were detected. DNA sequencing confirmed three single nucleotide polymorphisms (SNPs). Animal age significantly affected GFW (P=0.007), SDfd (P=0.006), SL (P=0.002), CR (P=0.006), KS (P=0.001), LG (P=0.006) and SST (P=0.013). Likewise, the breed had a significant effect on all studied traits except HG and BG, which was not significant. Results showed significant associations between the KAP22-1 variants and CR (P=0.01), SL (P=0.012), KS (P<0.001) and GCG (P=0.01). Interestingly, animals with BB genotypes tended to produce more wool yield (1163.63±65.91 g) with high SL (8.38±0.20 cm), CR (8.38±0.21 %) and KS (1.98±1.88). Results of this study strongly recommend the KAP22-1 gene as a candidate gene for wool production traits in Egyptian sheep, with new useful insights into the visually assessed wool traits. The identified genetic markers may be incorporated into breeding strategies and genetic improvement programs of wool traits in Egyptian sheep.

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.

A Preliminary Investigation of Myostatin Gene (MSTN) Variation in Red Deer (Cervus elaphus) and Its Implications for Venison Production in New Zealand

Simple Summary

Myostatin is a negative regulator of skeletal muscle growth. Despite variation in the myostatin gene having been reported in livestock species, little work has been undertaken in red deer (Cervus elaphus). This study describes the presence of two nucleotide sequences of the myostatin gene in New Zealand red deer, but no association was found between this variation and selected muscle and growth traits.

Abstract

Myostatin (MSTN), also known as growth differentiation factor 8 (GDF-8), is a negative regulator of lean muscle tissue growth. Variation in the gene has been studied in many domesticated species, because of its potential to dramatically increase muscle mass. It has, however, not been investigated in red deer (Cervus elaphus). In this study, variation in MSTN intron 1 was investigated in 211 male New Zealand red deer, for which phenotypic measurements of M. Longissimus dorsi (eye muscle) (width, depth, and area, together with 12-month weight) were recorded. Two sequence variants (named A and B) differing by one nucleotide (c.373 + 224) were identified in the intron 1 region of the gene resulting in three genotypes (AA, AB, and BB; frequencies of 63.5%, 30.8%, and 5.7%, respectively), but no association between this variation and any of the quantitative measurements was detected. These results suggest that the deer MSTN is less variable than for other livestock species and that its activity may be controlled to maintain a size–growth equilibrium.

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.

Variation in caprine KRTAP1-3 and its association with cashmere fibre diameter

Keratin-associated proteins (KAPs) are components of cashmere fibres. The gene encoding the KAP1-3 protein (KRTAP1-3) has been described in goats, but little is known about sequence variation in this gene and if it affects cashmere fibre traits. In this study, we used a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique to screen for nucleotide sequence variation in caprine KRTAP1-3 in 327 Longdong cashmere goats, then analysed association between the genetic variation that was revealed and some cashmere fibre traits. Six PCR-SSCP patterns representing six different variant sequences of KRTAP1-3 (named A to F) were revealed. Among these variant sequences, seven single nucleotide polymorphisms (SNPs) were detected, with two of them being non-synonymous. Goats with genotype AC had higher mean fibre diameter (MFD) than those with genotype AB (P < 0.001), while goats with genotype AB had higher MFD than those with AA (P < 0.001). The presence of C (P < 0.001) and B (P = 0.006) in a genotype was associated with increased MFD, and together this suggests that variation in caprine KRTAP1-3 affects the key fibre trait of MFD.

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.

Dimeric G-Quadruplex: An Efficient Probe for Ultrasensitive Fluorescence Detection of Mustard Compounds

Some mustard compounds (mustards) are highly toxic chemical warfare agents. Some are explored as new anticancer drugs. Therefore, the fast, selective, and sensitive detection of mustards is extremely important for public security and cancer therapy. Mustards mostly target the N7 position on the guanine bases of DNA. The guanine-rich G-quadruplex DNA (G4) has been widely studied in the sensing area, and it was found that dimeric G4 (D-G4) could dramatically light up the fluorescence intensity of thioflavin T (ThT). Based on this, we used for the first time the D-G4 DNA as a selective probe for ultrasensitive fluorescence detection of nitrogen mustard (NM). When NM occupies the N7 on guanine, it can block the formation of the D-G4 structure due to the steric hindrance, and hence, it inhibits the combination of D-G4 with ThT, leading to a sharp decrease of fluorescence intensity. The proposed reaction mechanism is proved using ultraviolet-visible (UV-Vis) spectra, circular dichroism (CD) spectra, and polyacrylamide gel electrophoresis. Herein, the concentration of D-G4/ThT used is as low as 50 nM due to its highly fluorescent performance, enabling both high sensitivity and low cost. NM can be detected with a wide linear range from 10 to 2000 nM. The detection limit of NM reaches a surprisingly low concentration of 6 nM, which is 2 or 3 orders of magnitude lower than that of previously developed fluorescence methods for mustards and simulants.

Ovine Toll-like Receptor 9 (TLR9) Gene Variation and Its Association with Flystrike Susceptibility

Simple Summary

Flystrike is a major ectoparasitic disease of sheep and it creates both an economic impact and welfare issue for the sheep industry. Several factors control the responses of sheep to flystrike, and among these, immune response is regarded as an important factor. Toll-like receptors (TLRs) plays a crucial role in the innate immune system by recognizing pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises unmethylated cytosine-phosphate-guanine (CpG) motifs that are known to be prevalent in bacterial genomes and are also reported in Dipteran insects, including Lucilia cuprina, one of the main species associated with flystrike in sheep. In this study, we used a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique to investigate TLR9 variation in sheep with and without flystrike, and found that variation in a gene region containing the coding sequence of the putative CpG-DNA binding domain was associated with the likelihood of flystrike occurrence. This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike.

Abstract

Toll-like receptors (TLRs) are a family of proteins that play a role in innate immune responses by recognising pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises bacterial and viral DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs, and variation in TLR9 has been associated with resistance to various infectious diseases. Flystrike is a problem affecting the sheep industry globally and the immune response of the sheep has been suggested as one factor that influences the response to the disease. In this study, variation in ovine TLR9 from 178 sheep with flystrike and 134 sheep without flystrike was investigated using a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) approach. These sheep were collected from both commercial and stud farms throughout New Zealand and they were of 13 different breeds, cross-breds and composites. Four alleles of TLR9 were detected, including three previously identified alleles (*01, *02 and *03) and a new allele (*04). In total six single nucleotide polymorphisms (SNPs) were found. Of the three common alleles in the sheep studied, the presence of *03 was found to be associated with a reduced likelihood of flystrike being present (OR = 0.499, p = 0.024). This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike, and thus the gene may have value as a genetic marker for improving resistance to the disease.

Allele/haplotype variation in the MHC-DQA2 gene in Spanish sheep and its association with footrot susceptibility

Footrot is a contagious disease that affects the hoof of sheep and other ungulates. The severity of the disease varies from a slight limp to the death of the individual due to injuries that prevent them from feeding. Variants of the Major Histocompatibility Complex (MHC)-DQA2 gene (MHC-DQA2) have been associated with a greater or lesser susceptibility to footrot in Greek, New Zealand and German sheep. In this study, variation in ovine MHC-DQA2, the absence or presence of footrot and the severity of infection was analysed in 117 Spanish Merino, Black Merino and Churra Lebrijana sheep. A total of 21 alleles/haplotypes and 65 genotypes were found with different frequencies in these breeds. As found in other studies, the MHC-DQA2 allele *1101 appeared to be associated with increased susceptibility to footrot, while allele *1201 appeared to be associated with decreased susceptibility. Overall this would suggest the ovine MHC plays a role in controlling susceptibility to footrot infection and that there are breed differences in susceptibility. Sheep might therefore be able to be selected by their MHC-DQA2 alleles/haplotypes to reduce the incidence of the disease in flocks.

Sequence Variation in the Bovine Lipin-1 Gene (LPIN1) and Its Association with Milk Fat and Protein Contents in New Zealand Holstein-Friesian × Jersey (HF × J)-cross Dairy Cows

Lipin-1 is known to play a regulatory role in tissues that function in lipid metabolism. In dairy cows, the lipin-1 gene (LPIN1) is highly expressed in the mammary gland, but its function in milk production is less understood. In this study, we used PCR-single strand conformation polymorphism analysis to investigate sequence variation in three regions of bovine LPIN1 in New Zealand Holstein-Friesian × Jersey (HF × J)-cross dairy cows, including part of the 5' non-coding region, the region containing the LPIN1β-spliced exon, and the sixth coding exon that encodes the putative transcriptional activating domain of the protein. No variation was found in the LPIN1β-spliced exon, but two sequence variants containing one single nucleotide polymorphism (SNP) were identified in the 5' non-coding region and four sequence variants containing four non-synonymous SNPs were identified in the sixth coding exon. Among the three common variants of the sixth coding exon, variant C was found to be associated with an increase in milk fat percentage (presence 4.96 ± 0.034% vs. absence 4.81 ± 0.050%; p = 0.006) and milk protein percentage (presence 4.09 ± 0.017% vs. absence 3.99 ± 0.025%; p = 0.001), but no associations (p > 0.01) were detected for milk yield. These results suggest that variation in LPIN1 affect the synthesis of fat and proteins in milk and has potential as a gene-marker to improve milk production traits.

Detection of a novel single nucleotide polymorphism in IGF2 gene with a negative impact on egg production and body weight in Japanese quail (Coturnix japonica)

Background

Insulin-like growth factor 2 (IGF2) is one of three hormones that share high structural similarity to insulin. It is involved in several insulin-like growth-regulating and mitogenic activities. This study was conducted to genotype the coding regions of the IGF2 gene in Japanese quail (Coturnix japonica) using PCR-SSCP-sequencing, and to assess the possible association of the polymorphism of these regions with the main egg production traits. A total of 240 female birds with an equal number of three Japanese quail populations (Brown or BR, Black or BL, and White or WT) were included in this study.

Results

All the genotyped regions exerted no heterogeneity in their sequences with one exception detected in the exon 2. In this locus, a novel single nucleotide polymorphism (SNP) was detected in which “A” was substituted with “G” at 81 position with a silent effect (p.F79=SNP) on IGF2 protein. Association analyses indicated a significant (P < 0.05) relation of this SNP with egg number (EN) and bird weight (BW) in the analyzed populations, in which the birds with AG genotype had lower EN and BW than those with AA genotype. The p.F79=SNP was largely detected in the WT line than the other two lines.

Conclusion

The detected p.F79=SNP has a highly negative effect on EN and BW in Japanese quail. Thus, the implementation of the variations of the IGF2 gene can be a useful marker in the marker-assisted selection of Japanese quail. This is the first report to describe IGF2 gene variations in Japanese quail, which strongly suggests raising the birds from the BR line with AA genotype when breeders desire to raise Japanese quail for large-scale egg production.

Variation in the ovine FOXP3 gene and its effect on growth traits in Egyptian Barki sheep

The aim of the present study was to detect the FOXP3 gene polymorphisms in Barki sheep at a variable region covering exon 13, intron 13 and the coding sequence in exon 14 and to test the association of these polymorphisms with growth traits. 122 Barki lambs were phenotyped for various growth traits, viz., birth weight (BW), weaning weight (WW), pre-weaning daily gain in weight (ADG1), post-weaning daily gain in weight (ADG2) and marketing bodyweight (MW). The polymerase chain reaction - single-strand conformational polymorphisms (PCR-SSCP) and DNA sequencing methods were used to identify the genetic variants in the FOXP3 gene. The associations between the variation in FOXP3 gene and growth traits were tested using a general linear model. Two variants (F1 and F2 with gene frequencies of 0.64 and 0.36, respectively), and three genotypes (F1F1, F1F2 and F2F2 with frequencies of 0.37, 0.53 and 0.10, respectively) were detected. The association of FOXP3 genotype was significant (p < 0.05) with ADG2 and MW. It is concluded that FOXP3 genotype might be helpful for sheep breeders to produce fast-growing lambs. However, further studies are needed in a large population to confirm the association we found.

Variation in ovine KRTAP8-1 affects mean staple length and opacity of wool fiber

In this study, keratin-associated proteins gene (KRTAP8-1) from five different sheep breeds and breed-crosses (n = 310) was genotyped using a Polymerase Chain Reaction-Single Strand confirmation Polymorphism (PCR-SSCP). Six unique genotypes were observed: AA, AC, AD, AE, DD and EE, with AA being the most common in the different breeds and crosses. Twelve wool characteristics: yield, mean staple length (MSL), bulk, mean fiber diameter (MFD), fiber diameter standard deviation (FDSD), coefficient of variation of fiber diameter (CVFD), medullation, standard deviation of medullation (MeSD), coefficient of variation of medullation (CVMed), opacity, standard deviation of opacity (OpSD), and coefficient of variation of opacity (CVOp) were measured on wool derived from the sheep. Variation in KRTAP8-1 was found to have strong association with MSL, OpSD and CVOp (p ≤ 0.027). The MSL of sheep of genotype AE was greater (p = 0.027) than for sheep of genotype AA. The OpSD of sheep of genotype AA was less (p = 0.017) than sheep with the AE genotype, and the CVOp of sheep with genotype AA was less (p = 0.018) than sheep with genotype AE. Further studies are required to confirm the role of variation in KRTAP8-1 in improving quality wool production.

Variation in the Ovine Glycogen Synthase Kinase 3 Beta-Interaction Protein Gene (GSKIP) Affects Carcass and Growth Traits in Romney Sheep

Simple Summary

The glycogen synthase kinase 3 beta (GSK3β)-interacting protein plays a role in regulating glycogen metabolism, protein synthesis, the cell cycle, and in regulating gene expression. To date, physiological function research into the GSK3β-interacting protein has been focused on cell lines, gene ‘knockout’ models, and over-expression studies, and to our knowledge, there have been no reports on how variation in the GSK3β-interacting protein gene (GSKIP) may affect phenotypic traits. In this study, PCR-SSCP methods were used to screen for variation in exon 1 and exon 2 of GSKIP in 840 New Zealand (NZ) Romney sheep. Two variant sequences were identified in exon 1 and this variation in GSKIP was associated with variation in lamb birth weight, hot carcass weight, and fat depth at the 12th rib.

Abstract

The glycogen synthase kinase 3 beta (GSK3β)-interacting protein (encoded by the gene GSKIP) is a small A-kinase anchoring protein, which complexes with GSK3βand protein kinase A (PKA) and acts synergistically with cAMP/PKA signaling to inhibit GSK3β activity. The protein plays a role in regulating glycogen metabolism, protein synthesis, the cell cycle, and in regulating gene expression. In this study, PCR-single strand conformation polymorphism (PCR-SSCP) analyses were used to screen for variation in exon 1 and exon 2 of GSKIP in 840 New Zealand (NZ) Romney sheep. Two SSCP banding patterns representing two different nucleotide variants (A and B) were detected in an exon 1 region, whereas in an exon 2 region only one pattern was detected. Variants A and B of exon 1 had one non-synonymous nucleotide difference c.37A/G (p.Met13Val). The birthweight of sheep of genotype AA (5.9 ± 0.06 kg) was different (p = 0.023) to sheep of genotype AB (5.7 ± 0.06 kg) and BB (5.7 ± 0.06 kg). The hot carcass weight (HCW) of sheep of genotype AA (17.2 ± 0.22 kg) was different (p = 0.012) to sheep of genotype AB (17.6 ± 0.22 kg) and BB (18.0 ± 0.29 kg), and the fat depth at the 12th rib (V-GR) of sheep of genotype AA (7.7 ± 0.31 mm) was different (p = 0.016) to sheep of genotype AB (8.3 ± 0.30 mm) and BB (8.5 ± 0.39 mm). The results suggest that the c.37A/G substitution in ovine GSKIP may affect sheep growth and carcass traits.

Identification of sequence variation in the oocyte-derived bone morphogenetic protein 15 (BMP15) gene (BMP15) associated with litter size in New Zealand sheep (Ovis aries) breeds

Advances in the study of reproductive traits indicate that functional variation in fertility genes may be useful for improving sheep fertility. The aim of this study was to search for variation in the bone morphogenetic protein 15 gene (BMP15) and ascertain any association with litter size in purebred Finnish Landrace sheep (n = 148), Finnish Landrace × Texel-cross sheep (n = 45), and composite sheep (of varying breed background; n = 58) from New Zealand (NZ). A 482 bp and 312 bp fragment of exon 1 and 2, respectively, of BMP15 were analysed using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). The additive and dominance effect of BMP15 variation on litter size were estimated using animal and sire models. Two variants (A and B) were detected in exon 1; no sequence variation was detected in exon 2. Variant A had the nucleotide sequence CTT between positions c.31 and c.33, while variant B had a deletion (c.31_33del). The observed frequency for variant A in the Finnish Landrace sheep, Finnish Landrace × Texel-cross sheep and the composite sheep, was 0.77, 0.92, and 0.68, respectively while the frequency of variant B (c.31_33del) was 0.23, 0.08, and 0.32, respectively. An association between litter size and c.31_33del (P < 0.001) was observed in composite sheep. Analysis of more sheep will be required to confirm these results. Litter size did not differ significantly between sheep breeds regardless of the presence/absence of c.31_33del. Results suggested that c.31_33del might be a genetic marker for improving fecundity in some NZ sheep.

Short Communication: A highly polymorphic caprine keratin-associated protein gene identified and its effect on cashmere traits

Five keratin-associated protein 6 genes (KRTAP6) have been identified in sheep and variation in some KRTAP6 has been associated with wool fibre diameter-related traits, but none of these homologues has been identified in goats. In this study, we reported the identification of the sheep KRTAP6-5 homologue on goat chromosome 1 and PCR-single strand conformation polymorphism analysis in 300 Longdong cashmere goats revealed the existence of twelve variant sequences. Both coding region and 3'UTR of the putative caprine KRTAP6-5 displayed a biggest sequence similarity to ovine KRTAP6-5 gene. This suggested that the gene represents caprine KRTAP6-5 sequences, and these sequences composed twenty three genotypes which was the most polymorphism gene in KRTAPs that have been studied. Among these sequences, fifteen nucleotide substitutions and a 24-bp insertion/detection were identified. Variation in goat KRTAP6-5 was associated with variation in mean fibre diameter, suggesting that KRTAP6-5 is worthy of further study in the context of variation in cashmere traits.

Analysis of the eighth intron polymorphism of NR6A1 gene in sheep and its correlation with lumbar spine number

For revealing molecular markers related to the traits of multiple lumbar vertebrae in sheep, we analyze the relationship between NR6A1 gene polymorphism and lumbar vertebrae number traits in Xinjiang Kazakh sheep. Lumbar muscle tissues were collected from 6-lumbar spine (L6) Kazak sheep and 7-lumbar spine (L7) Kazak sheep and the intron-8 of NR6A1 gene was amplified by PCR. The SNP locus was detected by the PCR-SSCP method. One-Way ANOVA and an Independent Chi-square Test is adopted to analyze the genotype association with lumbar spine number variation. There were two SNP loci in the intron-8 of the NR6A1 gene: IVS8-188 and IVS8-281. One-Way ANOVA and Independent Chi-square Test indicated a significant association between IVS8-281 and lumbar spine number. The SNP locus of NR6A1 gene intron 8 (IVS8-281G > A) could play a certain role in the variation of lumbar spine number in Xinjiang Kazakh sheep and demonstrates potential to accelerate the sheep breeding of selection process.

Variation in bovine leptin gene affects milk fatty acid composition in New Zealand Holstein Friesian × Jersey dairy cows

Leptin is a protein hormone secreted from white adipose tissue. It regulates food/feed intake, body weight, immune function and reproduction. In our investigation, the polymerase chain reaction (PCR) amplification coupled with single-strand conformational polymorphism (SSCP) analysis was used to reveal variation in bovine leptin gene (LEP) in New Zealand (NZ) Holstein Friesian × Jersey (HF × J) dairy cows. Subsequent sequence analysis of a 430 bp amplicon spanning the entirety of exon 3 and part of the intron 2 region revealed three variant sequences (A3, B3 and C3) containing a total of five nucleotide substitutions, all of which have been reported previously. Using general linear mixed-effect model analyses, the presence of variant A3 (the most common variant) was associated with a decreased level of C15:1, C18:1 trans-11, C18:1 all trans, C18:2 trans-9, cis-12, C22:0 and C24:0 levels but increased levels of C12:1 and C13:0 iso (p<0.05). Variant B3 was associated with reduced levels of C6:0, C8:0, C11:0, C13:0 and C20:0 but increased C17:0 iso and C24:0 levels (p<0.05). Variant C3 was associated with decreased C17:0 iso levels but increased C20:0 (p<0.05) levels. In a genotype model, the A3B3 genotype was associated with increased levels of C22:0 and C24:0 but decreased C8:0, C10:0, C11:0, C13:0, C15:0 and grouped medium-chain fatty acid (MCFA) levels (p<0.05). Genotype A3C3 was found to be associated with decreased levels of C10:0, C11:0, C13:0 and grouped MCFA (p<0.05). This is the first report of findings of this kind in NZ HF × J cows, and they suggest that variation in exon 3 of bovine leptin gene could be explored as a means of decreasing the concentration of saturated fatty acids in milk.

Nucleotide sequence variation of the major histocompatibility complex class II DQA1 gene in different cattle breeds from Nigeria and New Zealand

The major histocompatibility complex (MHC) plays a role in immune response. Among other activities, the bovine MHC genes (BoLA) trigger immune responses, including the activation of antibody-producing B-cells. In this study, White Fulani (n = 24), Red Bororo (n = 5) and Holstein-White × Fulani-cross (n = 11) cattle from Nigeria, and New Zealand Holstein-Friesian × Jersey-cross (n = 40) cattle were used to investigate variability in exon 2 of BoLA-DQA1. Ten alleles were identified using a PCR-Single Strand Conformation Polymorphism (SSCP) approach and their nucleotide sequences confirmed by DNA sequencing. A total of 12.60 % of all nucleotide positions analysed were revealed to be variable and two novel BoLA-DQA1 alleles are reported here for the first time.

Variation in a Newly Identified Caprine KRTAP Gene Is Associated with Raw Cashmere Fiber Weight in Longdong Cashmere Goats

Keratin-associated proteins (KAPs) and keratins determine the physical and chemical properties of cashmere fibers as they are the main components of the fibers. It has been reported that ovine KRTAP1-2 affects clean fleece weight, greasy fleece weight and yield in sheep, but the gene has not been described in goats and its effects on fiber traits are unknown. In this study, we identify the keratin-associated protein 1-2 gene (KRTAP1-2) in the goat genome and describe its effect on cashmere fiber traits in 359 Longdong cashmere goats. Six sequence variants (named CAPHI-KRTAP1-2*A to CAPHI-KRTAP1-2*F) were revealed using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. These sequences have the highest homology with ovine KRTAP1-2 sequences. There were a 60-bp deletion, a 15-bp insertion and five single nucleotide polymorphisms (SNPs) including two non-synonymous SNPs in the coding sequence. The caprine KRTAP1-2 gene was expressed in the skin tissue, but a signal was not observed for the kidneys, liver, lungs, spleen, heart and longissimus dorsi muscle. Variation in caprine KRTAP1-2 was found to be associated with raw cashmere fiber weight, but not with fiber diameter and length.

Prl and B4GALT-1 gene polymorphism and their association with milk production traits in crossbred cattle of Kerala

The main objective of present study was to explore the genetic variation in exon 3 of PRL (185 bp) and exon-2 of B4GALT-1 (256 bp) locus and analyze their associations with milk production traits. The study was conducted on 200 crossbred cattle distributed in different farms under Kerala Veterinary and Animal Sciences University and field centres of ICAR-FPT scheme, Mannuthy. Polymorphism of both the genes was detected by Single Strand Confirmation Polymorphism (PCR-SSCP). Similar banding pattern were noticed in exon-3 region of PRL, population was found to be monomorphic, indicating conserved nature of this fragment in the screened crossbred cattle population of Kerala. Two unique band patterns were detected in 256 bp fragment of B4GALT-1. Sequencing revealed a nonsynonymous single nucleotide variation in c.521T>C in exon 2 of B4GALT-1, resulted in an amino acid substitution of methionine to threonine due to a codon change of ATG to ACG. Different genetic variants of B4GALT-1 was significantly associated with 305 days milk yield and protein percent. The study indicates the existence of genetic variability in B4GALT-1 gene on crossbred cattle population of Kerala and suggests a scope of considering genetic variants of B4GALT-1 gene in selection of cattle for higher milk production.

Polymorphisms in hormone-sensitive lipase and leptin receptor genes and their association with growth traits in Barki lambs

Background and Aim

Marker-assisted selection has many advantages over conventional selection in animal breeding. The candidate gene approach has been applied to identify genetic markers associated with economically important traits in livestock. This study was established to investigate variation in the hormone-sensitive lipase (HSL) and leptin receptor (LEPR) genes, and their association with growth traits in Barki lambs.

Materials and Methods

Records for birth weight (BW), pre-weaning average daily gain (ADG1), weaning weight (WW), post-weaning average daily gain (ADG2), and marketing weight (MW) were obtained from 247 Barki lambs. Polymerase chain reaction-single-stranded conformational polymorphism analyses were used to detect variation in exon 9 of HSL and exon 19 of LEPR. General linear models were used to test for associations between the variation in ovine HSL and LEPR, and growth traits.

Results

The SSCP banding patterns for HSL showed three variants (H1, H2, and H3), which contained two nucleotide-sequence differences (c.1865C>T and c.2038T>C). Two SSCP banding patterns (L1 and L2) were observed for LEPR and these contained two nucleotide-sequence differences (c.2800G>A and c.2978C>G). The HSL genotype showed no effect on the studied traits. The LEPR genotype was proven to have significant effects (p<0.05) on ADG2 and MW. The presence of the L1 variant was associated (p<0.01) with decreased ADG2 and MW.

Conclusion

The finding of an association between LEPR gene variation and growth rate after weaning in Barki lambs warrants efforts to improve this trait.