Association between IGF-I, IGF-IR and GHRH gene polymorphisms and growth and carcass traits in beef cattle

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.

Influence of single nucleotide polymorphism in the IGF-1 gene on performance and conformation traits in Munjal sheep

Genetic polymorphism research in livestock species aims to assess genetic differences within and among breeds, primarily for conservation and development objectives. The aim of the present study was to determine the point mutation in the IGF-1 gene (g.855G>C and g.857G>A) and its association with performance traits in Munjal sheep. In total, 50 Munjal sheep were selected and the genomic DNA was isolated using the Automated Maxell RSC DNA/RNA purification system and the Maxwell RSC whole blood DNA kit. A reported set of primers was used to amplify the 294-bp fragment encompassing the targeted region, i.e. the 5' flanking region of the IGF-1 gene. The polymerase chain reaction product of 294-bp size harbouring the g.857G>A mutation in the 5' flanking region of the IGF-1 gene was digested with HaeII enzyme. Three possible genotypes were defined by distinct banding patterns, i.e. GG (194, 100 bp), GA (294, 194, 100 bp) and AA (294 bp) in the studied population of Munjal sheep. The genotypic and allelic frequencies of g.857G>A single nucleotide polymorphism of the IGF-1 gene indicated that the frequency of the A allele was higher in the studied population, i.e. 0.59 and the GA genotype was found to be the predominant genotype (0.66). Allele A of the IGF-1 gene was found to be associated with higher body weights and can be used in selection criteria for improving the performance of Munjal sheep. The positive effect of the IGF-1 gene on several conformational traits as observed in this study suggests that this area of the ovine IGF-I gene is particularly important and warrants further investigation on a larger population size.

Effects of Concentrate and Bypass Fat Supplementations on Growth Performance, Blood Profile, and Rearing Cost of Feedlot Buffaloes

Simple Summary

Studies have shown that providing concentrate and bypass fat as feed supplements resulted in better performance of large ruminants. However, there is limited information about the effects of these supplements on the performance of buffaloes. This study evaluates the effects of concentrate and bypass fat supplementations on the growth performance, blood metabolites, and feeding cost of Murrah cross and Swamp buffaloes. Following diet supplementation, the feed intake, body weight, and body condition score were significantly improved without any side effects on the blood metabolites of both buffalo breeds. Although the mixture of concentrate and bypass fat supplement (26:4) used in this study was found to increase the cost of feed, overall, it resulted in a greater return.

Abstract

This study investigates the effects of supplementation of the basal diet with concentrate and rumen bypass fat on the dry matter intake (DMI), growth performance, blood metabolites and hormonal changes, and the feeding cost of feedlot water buffaloes. Thirty-six healthy, three- to four-month-old male Murrah crossbred (n = 18) and Swamp (n = 18) buffaloes with a similar average initial body weight of 98.64 ± 1.93 kg were each randomly allocated into three dietary experimental groups. Buffaloes were fed with Diet A, which consisted of 100% Brachiaria decumbens, Diet B, consisting of 70% Brachiaria decumbens and 30% concentrate, and Diet C, consisting of 70% Brachiaria decumbens, 26% concentrate, and 4% rumen bypass fat for a period of 730 days. Feed intake was measured daily, while blood samples were collected for every eight months. Furthermore, body scores were noted prior to and at the end of the experimental period. The results showed that the average daily gain for buffaloes fed with Diet C was the highest. The DMI, BCS, FI, and FCR for the three groups showed significant (p < 0.05) differences, in the following order: Diet C > Diet B > Diet A. At the end of the two-year feeding trial, buffaloes fed with Diet B had significantly (p < 0.05) higher cholesterol levels than Diet A and Diet C. In addition, buffaloes fed with Diet C had significantly (p < 0.05) higher levels of serum total protein, growth hormone, and insulin-like growth factor-I hormone compared to Diet A and Diet B. On the other hand, buffaloes fed with Diet B and Diet C showed significant (p < 0.05) decrease in glucose levels. Supplemented diet improved the buffalos’ weight gain to achieve the market weight in a shorter period of time, thus, giving farmers a greater return. In conclusion, concentrate and bypass fat supplementations in the diet of water buffaloes improved the growth performance without adverse effect on the blood metabolites, which enabled better farmer profitability.

Nucleotide Sequence Variation in the Insulin-Like Growth Factor 1 Gene Affects Growth and Carcass Traits in New Zealand Romney Sheep

Insulin-like growth factor 1 (IGF1) is a mediator of the effects of growth hormone and polymorphism in the IGF1 gene (IGF1) is reported to affect fat deposition in some livestock species. In this study, nucleotide sequence variation in three regions of ovine IGF1 (part of the 5′ flanking region, the exon 3 region, and the exon 4 region) was investigated in 848 New Zealand Romney lambs using PCR-single strand conformation polymorphism (SSCP) analyses to ascertain if single nucleotide polymorphisms (SNPs) existed. Six SNPs were identified across these three regions. The effect of the sequence variation in the exon 3 and exon 4 regions on growth and carcass traits were investigated. One of the PCR-SSCP sequence variants in the exon 3 region was associated with variation in hot carcass weight, carcass fat depth at the 12th rib measured using video imaging and the percentage proportion of leg lean meat, whereas the other was associated with variation in growth rate to weaning. No associations were detected for the other gene regions analyzed. The results suggest that polymorphism in exon 3 of ovine IGF1 has potential for use as a gene-marker for some carcass and growth traits.

Effects of feeding frequency on juvenile Chinese sturgeon Acipenser sinensis

In this study, the effects of different feeding frequencies on the growth and the expression of genes in the GH/IGF axis were assessed in juvenile Chinese sturgeon. The newly hatched Chinese sturgeons were bred for 38 days at three different feeding frequencies groups (feeding frequency of two times a day, TWD; three times a day, THD; and four times a day, FOD), and the expression levels of the GH/IGF axis responses to feeding frequency were determined by quantitative real-time PCR. In addition, the full-length of the Coding Sequences of IGF I and IGF II genes (489-bp and 660-bp, respectively), were cloned and analyzed from Chinese sturgeon the first time. Multiple sequence alignments of IGFs revealed that Chinese sturgeon are high sequence identity to IGFs from other species. The phylogenetic relationships based on the IGF I and IGF II amino acid sequences were consistent with the traditional classification. After 38 days of growth, the three different feeding frequencies groups of Chinese sturgeon had no significant difference of body length, body weight, specific growth rate, the survival rate, the rate of weight gain and the condition factor. However, the relative expression of Chinese sturgeon GH in the pituitary decreased with increasing feeding frequency. The relative expression of Chinese sturgeon GHR in liver and skeletal muscle was deceased with increasing feeding frequency, while the relative expression of GHR in stomach and intestines at THD group was significantly higher than that of at TWD group and FOD group (p < 0.05). The relative expression of Chinese sturgeon IGF I in liver increased significantly with increasing feeding frequency (p < 0.05). The relative expression of IGF I in stomach and skeletal muscle was similar at the three groups. The relative expression of IGF I in intestines was significantly higher at FOD group than at TWD group and THD group (p < 0.05). The relative expression of Chinese sturgeon IGF II in liver at TWD group was significantly higher than that at THD group and FOD group (p < 0.05). However, the relative expression of IGF II in stomach, intestines and skeletal muscle at THD group was higher than that at TWD group and FOD group. Based on these previous studies that liver IGF I is regarded as a biomarker of growth performance, this result suggested that the juvenile Chinese sturgeon is better for growth when feeding four times daily compared to twice and thrice daily.

Association of a polymorphism in exon 3 of the IGF1R gene with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep

This study aimed to genotype the polymorphism (c.654G > A) in the exon 3 of the insulin-like growth factor 1 receptor gene (IGF1R) and to analyze its association with growth, body size, slaughter and meat quality traits in Colored Polish Merino sheep. In total, 67 traits were analyzed. The IGF1R polymorphism was genotyped using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) method. The MIXED procedure of the SAS software was used to assess the genotypic effects of the polymorphism (c.654G > A) on production traits of interest. The IGF1R c.654G > A genotypes were found to have a significant effect on the average daily gain between the 56th and 78th day of life, cold carcass, leg part, leg cut, fore shank, and kidney weights, as well as eye of loin depth, intramuscular fat content, and water-holding capacity of meat. The results suggest that the studied polymorphism may provide useful information for marker-assisted selection for increased meat performance in Colored Polish Merino sheep.

Evaluation towards stud bulls with different mixed genotypes relating to somatotropin cascade genes by origin

A preliminary evaluation towards a breeding value of the Holstein breeding bulls with different genotypes of somatotropin cascade genes is presented: pituitary transcription factor or growth hormone factor (PIT1), prolactin (PRL), somatotropin (GH), somatotropin releasing hormone (GHRH), insulin-like (IGF-1) in the conditions of the Republic of Tatarstan. The research studies the signs (indices) of milk productivity (milk yield and fat in milk) of the closest female ancestors of bulls with different genotypes of somatotropin cascade genes. Studies and analysis have shown that the bulls with the mixed genotypes ABAALLBBAA (10269 kg), AAAALLBBAB (4.13 %) and BBAALLABBB (9402 kg and 4.06 %) had the highest and optimum evaluation by origin, judging by the bulls’ pedigree (geneological) index. The frequency to meet bulls with the desired mixed genotypes was low and amounted to 4.28–5.71 %.

Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds

BACKGROUND

As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic goats are largely unknown, particularly for economically important traits. In this study, we sequenced the whole genome of 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) and downloaded the genome sequence data of 30 goats from five other breeds (four non-Chinese and one Chinese breed) and 21 Bezoar ibexes to investigate the genetic composition and selection signatures of the Chinese goat breeds after domestication.

RESULTS

Based on population structure analysis and FST values (average FST = 0.22), the genetic composition of Chengdu Brown goats differs considerably from that of Bezoar ibexes as a result of geographic isolation. Strikingly, the genes under selection that we identified in Tibetan Cashmere goats were significantly enriched in the categories hair growth and bone and nervous system development, possibly because they are involved in adaptation to high-altitude. In particular, we found a large difference in allele frequency of one novel SNP (c.-253G>A) in the 5'-UTR of FGF5 between Cashmere goats and goat breeds with short hair. The mutation at this site introduces a start codon that results in the occurrence of a premature FGF5 protein and is likely a natural causal variant that is involved in the long hair phenotype of cashmere goats. The haplotype tagged with the AGG-allele in exon 12 of DSG3, which encodes a cell adhesion molecule that is expressed mainly in the skin, was almost fixed in Tibetan Cashmere goats, whereas this locus still segregates in the lowland goat breeds. The pigmentation gene KITLG showed a strong signature of selection in Tibetan Cashmere goats. The genes ASIP and LCORL were identified as being under positive selection in Jintang Black goats.

CONCLUSIONS

After domestication, geographic isolation of some goat breeds has resulted in distinct genetic structures. Furthermore, our work highlights several positively selected genes that likely contributed to breed-related traits in domestic goats.

Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle

Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N’Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N’Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.

Dietary Energy Levels Affect Growth Performance through Growth Hormone and Insulin-Like Growth Factor 1 in Yak (Bos grunniens)

The objective of this study was to investigate the effects of different dietary energy levels on serum concentrations of growth hormone (GH) and insulin-like growth factor 1 (IGF-1), as well as gene expression of their associated binding proteins and receptors in yak. Fifteen adult male yaks with BW of 276.1 ± 3.5 kg were allotted in three dietary groups and were fed with low (LE), medium (ME), and high energy (HE) level diet having different NEg of 5.5 MJ/kg, 6.2 MJ/kg, 6.9 MJ/kg, respectively. The effects of these treatments on ADG, BW, ADFI, and feed conversion ratio were significant (p < 0.05) throughout the experimental period. Serum GH concentration decreased (p < 0.05) with an increase in dietary energy level on d 30 and d 60. While IGF-1 concentration was higher (p < 0.05) in ME group, as compared to LE and HE groups on d 60. The expression level of growth hormone receptor (GHR) was decreased (p < 0.001) and IGF-1 was increased with the increase in the dietary energy level. The relative expression of insulin-like growth factor binding protein 3 (IGFBP-3) was higher (p < 0.001) in ME and HE groups, except the LE group. In conclusion, our findings provide a first insight into the combined effect of GH and IGF-1 in controlling the metabolism and productivity of yak. It also showed that medium energy level diet contributed to promote growth performance of yak during the cold season.

Comprehensive assessment of candidate genes associated with fattening performance in Holstein-Friesian bulls

The objective of this study was to determine the association of single nucleotide polymorphisms (SNPs) in selected candidate genes with fattening performance traits in a commercial cattle herd. Fifteen SNPs in 12 candidate genes (LEP, FABP4, DGAT1, TG, IGF1, IGF1R, MYF5, LGB, CAPN1, CAST, GHR, and OLR1) were evaluated in 296 purebred Holstein-Friesian bulls using PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism). Associations between each segregating SNP and genetic merit for fattening performance were quantified using linear mixed models. Traits included in the study were fattening period, final weight, dry matter intake, feed conversion rate, and average daily weight gain. Apart from the general determination of the above-mentioned traits, each trait was evaluated based on the fattening periods between five selected target body weights (W1  =  100 kg, W2  =  200 kg, W3  =  300 kg, W4  =  400 kg, W5  =  450 kg). All markers with the exception of CAPN1 530, IGF1R, TG, and DGAT1 were associated with at least one of the traits. Furthermore, novel associations were observed for LEP  ×  GHR, IGF1  ×  LEP, FABP4 3691  ×  FABP4 2834, and FAP4 3533  ×  LEP interactions. The results of this study confirm some previously reported associations. Moreover, novel associations have been identified, which may be incorporated into breeding programs to improve fattening performance.

Investigation of Growth Hormone Releasing Hormone, Growth Hormone and Prolactin Hormone Gene Polymorphism in Anatolian Water Buffalo

The purpose of this work was to identify GHRH, GH and PRL gene polymorphisms in Anatolian water buffalo by means of the PCR-RFLP method. A total of 126 buffalo were included in this study. PCR amplification gave a 451 bp band for the GHRH gene, a 221 bp band for the GH gene and a 156 bp band for the PRL gene. The PCR products were digested by HaeIII for the GHRH gene, AluI for the GH gene and RsaI for the PRL gene. The GH/AluI and PRL/RsaI polymorphisms were found to be polymorphic, while the GHRH/HaeIII polymorphism was not found in Anatolian water buffalo. The frequencies of GH-L (0.87) and PRL-A (0.55) alleles were found to be high in the examined Anatolian water buffalo. The chi-square test showed that the Anatolian water buffalo were in Hardy-Weinberg (HW) equilibrium for the GH gene while significant deviation was observed from HW equilibrium for the PRL gene. The present study is the first to examine GHRH/HaeIII, GH/AluI and PRL/RsaI polymorphisms in Anatolian water buffalo.

Polymorphism of Insulin-like Growth Factor 1 Gene (IGF1/TasI, IGF1/SnaBI, IGF1/RsaI) and the Association with Daily Gain of Pesisir Cattle Local Breed from West Sumatera, Indonesia

BACKGROUND AND OBJECTIVE

The insulin-like growth factor 1 gene (IGF1) is a candidate gene for marker-assisted selection strategies. Two single nucleotide polymorphism of IGF1 gene namely IGF1/SnaBI and IGF1/TasI has been reported to be associated with production traits in several cattle breeds. One single nucleotide polymorphism in exon 4 namely IGF1/Rsa1 has a significant influence (p<0.01) on birth weight, weaning weight and average daily gain of Bali cattle. The objective of this study was to determine the IGF1/SnaBI, IGF1/TasI and IGF1/RsaI polymorphisms and their associations with average daily gain in Pesisir cattle local breed from west Sumatera Indonesia.

METHODOLOGY

The isolation of DNA from 183 blood sample was performed using DNA extraction kit (Promega DNA purification kit) following the manufacture procedure. The amplification of IGF1 fragment was done by master mix from Thermo Scientific.

RESULTS

In the case of the IGF1/SnaBI polymorphism, three genotypes were observed, frequencies were 0.011, 0.011 and 0.978 for AA, AB and BB, respectively. This gives frequencies of 0.064 and 0.9836 for A and B alleles. For IGF1-TasI locus showed that AA genotype occurred with a frequency of 0.978, AC with 0.011 and CC with 0.011 with frequency for allele A and C were 0.9836 and 0.0164, respectively. In the case IGF1/RsaI polymorphism produces only TT and CT genotype with frequency 0.027 and 0.973 respectively and frequency of T and C allele were 0.5137 and 0.4863, respectively.

CONCLUSION

Among these 3 polymorphism only IGF1/RsaI was associated with average daily gain, Thus this polymorphism could be a potential for improving body weight in Pesisir cattle. Association study for IGF1/SnaBI and IGF1/TasI were strongly limited by low frequency of one allele.

Effect of the <i>IGF-I</i> gene polymorphism on growth, body size, carcass and meat quality traits in Coloured Polish Merino sheep

Abstract. Insulin-like growth factor I, encoded by the IGF-I gene, plays a role in cell growth and differentiation, embryogenesis, metabolism regulation, skeletal growth, and protein synthesis. The aims of this study were to investigate the polymorphism in the 5′ flanking region of the IGF-I gene and evaluate associations between the single-nucleotide polymorphism (SNP) in this gene and growth, body size, carcass and meat quality traits in Coloured Polish Merino sheep. In total 78 live and post mortem traits were investigated. Polymorphism in the IGF-I gene was identified with the use of the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method in 305 Coloured Polish Merino sheep. In association studies, traits of interest were analysed with the use of the MIXED and GENMOD procedures of the SAS statistical package. Two alleles named A and B, and two IGF-I genotypes – AA and AB – were detected. The A allele and the AA genotype were predominant, with the frequencies of 91.6 and 83.3 %, respectively. The IGF-I genotype was found to have a highly significant effect on fore shank weight (P  =  0.006), kidney fat class (P  =  0.002) and EUROP fat class (P  =  0.005). Furthermore, the IGF-I genotype significantly affected external fatness of carcass class (P  =  0.038), drip loss (P  =  0.049), and subjective assessment of meat colour (P  =  0.043), and it tended to be associated with longissimus dorsi (LD) muscle width (P  =  0.063) and flavour (0.067). Concluding, the IGF-I gene could be considered as a candidate gene of selected carcass and meat quality traits in sheep.

Association of a Cac8I polymorphism in the IGF1 gene with growth traits in Indian goats

The Insulin-like Growth Factor 1 (IGF1) gene is a member of somatotropic axis and plays a key role in proliferation of cells, mitosis, myogenesis, meiosis, differentiation in foetal development and post natal growth. The objectives of this study were to verify the single nucleotide polymorphisms (SNPs) in IGF1 gene and their association with growth traits in two indigenous native goat genetic groups of Kerala, viz., Malabari and Attappady Black. A total of 277 goats were genotyped using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using the restriction enzyme Cac8I. One SNP, A224G was detected in the 5′ non-coding region of the IGF1 gene, and accordingly two genotypes were revealed, GG and AG. This SNP was significantly associated with growth traits in Attappady Black goats, which is maintained as meat breed in Kerala. Results from this study demonstrated higher performance of GG animals for growth traits. The association of IGF1 gene with these traits emphasizes the importance of caprine IGF1 as a candidate gene for growth traits in goat breeding.

Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E

Background

The objective of this study was to acquire a broader, more comprehensive picture of the transcriptional changes in the L. Thoracis muscle (LT) and subcutaneous fat (SF) of lambs supplemented with vitamin E. Furthermore, we aimed to identify novel genes involved in the metabolism of vitamin E that might also be involved in meat quality. In the first treatment, seven lambs were fed a basal concentrate from weaning to slaughter (CON). In the second treatment, seven lambs received basal concentrate from weaning to 4.71 ± 2.62 days and thereafter concentrate supplemented with 500 mg dl-α-tocopheryl acetate/kg (VE) during the last 33.28 ± 1.07 days before slaughter.

Results

The addition of vitamin E to the diet increased the α-tocopherol muscle content and drastically diminished the lipid oxidation of meat. Gene expression profiles for treatments VE and CON were clearly separated from each other in the LT and SF. Vitamin E supplementation had a dramatic effect on subcutaneous fat gene expression, showing general up-regulation of significant genes, compared to CON treatment. In LT, vitamin E supplementation caused down-regulation of genes related to intracellular signaling cascade. Functional analysis of SF showed that vitamin E supplementation caused up-regulation of the lipid biosynthesis process, cholesterol, and sterol and steroid biosynthesis, and it down-regulated genes related to the stress response.

Conclusions

Different gene expression patterns were found between the SF and LT, suggesting tissue specific responses to vitamin E supplementation. Our study enabled us to identify novel genes and metabolic pathways related to vitamin E metabolism that might be implicated in meat quality. Further exploration of these genes and vitamin E could lead to a better understanding of how vitamin E affects the oxidative process that occurs in manufactured meat products.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3405-8) contains supplementary material, which is available to authorized users.

Estimation of Growth Curves and Suitable Slaughter Weight of the Liangshan Pig

The Liangshan pig is a traditional Chinese small-sized breed; it has a relatively long feeding period and low meat production ability but superior meat quality. This study utilized three non-linear growth models (Von Bertalanffy, Gompertz, and logistic) to fit the growth curve of Liangshan pigs from an unselected, random-bred pig population and estimate the pigs most suitable slaughter weight. The growth development data at 20 time points of 275 Liangshan pigs (from birth to 250 d) were collected. To analyze the relative gene expression related to development, seven slaughter weight phases (50, 58, 66, 74, 82, 90, and 98 kg) (20 pigs per phase) were examined. We found that the Liangshan pig growth curve fit the typical S-curve well and that their growth turning point was 193.4 days at a weight of 62.5 kg, according to the best fit Von Bertalanffy model based on the goodness of fit criteria. Furthermore, we estimated that the most suitable slaughter weight was 62.5 to 74.9 kg based on the growth curve and the relative expression levels of growth-related genes.

Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach

Background

For most domestic animal species, including bovines, it is difficult to identify causative genetic variants involved in economically relevant traits. The candidate gene approach is efficient because it investigates genes that are expected to be associated with the expression of a trait and defines whether the genetic variation present in a population is associated with phenotypic diversity. A potential limitation of this approach is the identification of candidates. This study used a bioinformatics approach to identify candidate genes via a search guided by a functional interaction network.

Results

A functional interaction network tool, BosNet, was constructed for Bos taurus. Predictions for candidate genes were performed using the guilt-by-association principle in BosNet. Association analyses identified five novel markers within BosNet-prioritized genes that had significant effects on different growth traits in Charolais and Brahman cattle.

Conclusions

BosNet is an excellent tool for the identification of single nucleotide polymorphisms that are potentially associated with complex traits.

Association of ADIPOQ, OLR1 and PPARGC1A gene polymorphisms with growth and carcass traits in Nelore cattle

In beef cattle farming, growth and carcass traits are important for genetic breeding programs. Molecular markers can be used to assist selection and increase genetic gain. The ADIPOQ, OLR1 and PPARGC1A genes are involved in lipid synthesis and fat accumulation in adipose tissue. The objective of this study was to identify polymorphisms in these genes and to assess the association with growth and carcass traits in Nelore cattle. A total of 639 animals were genotyped by PCR-RFLP for rs208549452, rs109019599 and rs109163366 in ADIPOQ, OLR1 and PPARGC1A gene, respectively. We analyzed the association of SNPs identified with birth weight, weaning weight, female yearling weight, female hip height, male yearling weight, male hip height, loin eye area, rump fat thickness, and backfat thickness. The OLR1 marker was associated with rump fat thickness and weaning weight (P < 0.05) and the PPARGC1 marker was associated with female yearling weight.

Association of a novel SNP in exon 10 of the IGF2 gene with growth traits in Egyptian water buffalo (Bubalus bubalis)

Insulin-like growth factor 2 (IGF2) plays an important role in muscle growth and it might be used as a marker for the growth traits selection strategies in farm animals. The objectives of this study were to detect polymorphisms in exon 10 of IGF2 and to determine associations between these polymorphisms and growth traits in Egyptian water buffalo. PCR-single-strand conformation polymorphism (SSCP) and DNA sequencing methods were used to detect any prospective polymorphism. A novel single nucleotide polymorphism (SNP), C287A, was detected. It was a non-synonymous mutation and led to replacement of glutamine (Q) amino acid (aa) by histidine (H) aa. Three different SSCP patterns were observed: AA, AC, and CC, with frequencies of 0.540, 0.325, and 0.135, respectively. Association analyses revealed that the AA individuals had a higher average daily gain (ADG) than other individuals (CC and AC) from birth to 9 months of age. We conclude that the AA genotype in C287A SNP in the exon 10 of the IGF2 gene is associated with the ADG during the age from birth to 9 months and could be used as a potential genetic marker for selection of growth traits in Egyptian buffalo.

Effects in cattle of genetic variation within the IGF1R gene on the superovulation performance and pregnancy rates after embryo transfer

The insulin-like growth factor 1 receptor (IGF1R) is a membrane glycoprotein mediating most biological actions of IGF1 and IGF2, and has an important effect on ovulation, pre-implantation embryo development and pregnancy rate. The objectives of this study were to detect IGF1R gene polymorphisms of cattle and analyze the relationship with superovulation performance and pregnancy rates after embryo transfer (ET), as well as the hormone concentrations at the day of ET. One reported SNP of IGF1R G404T and a novel SNP of IGF1R G399A were analyzed in 170 Chinese Holstein donor cows and 118 Luxi recipients cattle. Statistical analysis revealed that the G404T mutation was associated (p=0.019) with increased ovulation rate and females with this mutation had enhanced performance in producing transferable embryos. For the polymorphic locus G399A, recipients with g.399 GG and g.399 GA genotypes had greater pregnancy rates after ET than that of g.399 AA genotype. Furthermore, the same tendency was observed that the genotype groups with greater pregnancy rates had greater progesterone and lesser estrogen concentrations, but these did not reach statistical significance. Results of the present study showed, for the first time, that the polymorphism in IGF1R is associated with superovulation traits, and indicated that the IGFIR gene can be used as a potential marker for donor selection.

Novel polymorphisms of the IGF1R gene and their association with average daily gain in Egyptian buffalo (Bubalus bubalis)

The objective of this study was to detect insulin-like growth factor 1 receptor (IGF1R) polymorphisms, their allele, and genotype frequencies and to determine associations between these polymorphisms and growth traits in Egyptian water buffalo. Three loci of the IGF1R coding region were amplified by RT-PCR and, subsequently, subjected to sequence analysis, followed by single-strand conformation polymorphism to identify different allelic patterns. A total of 11 novel polymorphisms were detected; 6 SNPs among Egyptian water buffaloes and 5 polymorphisms compared with Indian buffalo (Y12700). Three of those polymorphisms; GAG Indel polymorphism, C261G, and G263C SNPs, were nonsynonymous mutations. The GAG Indel polymorphism led to deletion of E (glutamic) amino acid (aa) in the IGF1R of Egyptian water buffaloes compared with Indian buffalo. However, C261G SNP, which replaced A (alanine) by G (glycine) aa, and G263C SNP, which changed A (alanine) to P (proline) aa, were detected among Egyptian water buffaloes. Three different single-strand conformation polymorphism patterns were observed in exon 21: CC/CC, GG/GG, and CG/GC with frequencies of 0.291, 0.253, and 0.556, respectively. The heterozygous animals (CG/GC) had a higher ADG than homozygous animals (CC/CC and GG/GG) from birth to 6 mo of age. We conclude that the heterozygous haplotype, C261G/G263C, in exon 21 of the IGF1R gene is associated with the ADG during the early stages of life (from birth to 6 mo of age) and could be used as a genetic marker for selection of growth traits in Egyptian buffalo.

Association of two SNPs in the coding region of the insulin-like growth factor 1 receptor (IGF1R) gene with growth-related traits in Angus cattle

The insulin-like growth factor 1 (IGF-1) is considered to be a factor that mainly regulates growth, differentiation, and the maintenance of various function in numerous tissues through binding to a family of transmembrane tyrosine kinase receptors, signaling primarily through the insulin-like growth factor 1 receptor (IGF-1R) encoded by the IGF1R gene. The objectives of the present study were to estimate the allele and genotype frequencies of the IGF1R/MspI (silent mutation within exon 12) and the IGF1R/TaqI (within the 3' untranslated region, 3'UTR) gene polymorphisms in beef cattle and to determine associations between these polymorphisms and growth traits. In a preliminary study on 310 Angus calves, association analyses with three production traits (birth weight, BWT; weaning weight adjusted to 210 days, WWT210; and average daily gain, ADG) were conducted. The GG genotype of the IGF1R/e12/MspI polymorphism was significantly associated (P ≤ 0.05) with a higher WWT210 (+5.06 kg) compared to the AG genotype. Polymorphism within the 3'UTR had no significant effect on growth traits. The effect of combined genotypes was also examined. At WWT(210), calves with the GG/AA and GG/AG combinations were heavier than calves with the AG/AA and AG/AG combined genotypes (P ≤ 0.05). To our knowledge, this is the first report of a polymorphism within the coding region of the Bos taurus IGF1R gene.

Association of a single nucleotide polymorphism in the akirin 2 gene with economically important traits in Korean native cattle

The akirin 2 gene, located on chromosome 9 in cattle, was previously reported to be associated with nuclear factor-kappa B (NF-κB), involved in immune reactions and marbling of meat. To determine whether a single nucleotide polymorphism (SNP) in akirin 2 is associated with economically important traits of Korean native cattle, the c.*188G>A SNP DNA marker in the 3'-UTR region of akirin 2 was analyzed for its association with carcass weight, longissimus muscle area and marbling. The c.*188G>A SNP was genotyped by polymerase chain reaction restriction fragment length polymorphism, and the frequency of the AA, AG, and GG genotypes were 6.82%, 71.29% and 21.88% respectively. This SNP was significantly associated with longissimus muscle area (Bonferroni corrected P < 0.05), and marbling score (Bonferroni corrected P < 0.01). These results suggest that the c.*188G>A SNP of akirin 2 might be useful as a DNA marker for longissimus muscle area and marbling scores in Korean native cattle.

A polymorphism in the insulin-like growth factor 1 gene is associated with postpartum resumption of ovarian cyclicity in Holstein-Friesian cows under grazing conditions

Background

Insulin-like growth factor 1 (IGF-1) gene is considered as a promising candidate for the identification of polymorphisms affecting cattle performance. The objectives of the current study were to determine the association of the single nucleotide polymorphism (SNP) IGF-1/SnaBI with fertility, milk production and body condition traits in Holstein-Friesian dairy cows under grazing conditions.

Methods

Seventy multiparous cows from a commercial herd were genotyped for the SNP IGF-1/SnaBI. Fertility measures evaluated were: interval to commencement of luteal activity (CLA), calving to first service (CFS) and calving to conception (CC) intervals. Milk production and body condition score were also evaluated. The study period extended from 3 wk before calving to the fourth month of lactation.

Results and discussion

Frequencies of the SNP IGF-1/SnaBI alleles A and B were 0.59 and 0.41, respectively. Genotype frequencies were 0.31, 0.54 and 0.14 for AA, AB and BB, respectively. Cows with the AA genotype presented an early CLA and were more likely to resume ovarian cyclicity in the early postpartum than AB and BB ones. No effect of the SNP IGF-1/SnaBI genotype was evidenced on body condition change over the experimental period, suggesting that energy balance is not responsible for the outcome of postpartum ovarian resumption in this study. Traditional fertility measures were not affected by the SNP IGF-1/SnaBI.

Conclusion

To our knowledge this is the first report describing an association of the SNP IGF-1/SnaBI with an endocrine fertility measure like CLA in cattle. Results herein remark the important role of the IGF-1gene in the fertility of dairy cows on early lactation and make the SNP IGF-1/SnaBI an interesting candidate marker for genetic improvement of fertility in dairy cattle.

Novel polymorphisms of the growth hormone gene and their effect on growth traits in Chinese goats

The polymorphisms of the growth hormone (GH) gene were analyzed in 686 individuals from four goat populations, Three haplotypes (A, B and C) and three observed genotypes (AA, AB and AC) were detected at the P2 locus, and three haplotypes (E, F and G) and three observed genotypes (EE, EF and EG) were also detected at the P4 locus. In addition, five single nucleotide polymorphisms (SNPs)-A112G, C142T (Gly>Ser), C214T (P2 locus), C266A (Pro>His) and C214T (P4 locus, Arg>Trp), were identified by GH gene sequencing and PCR-SSCP analysis. The SNPs loci were in Hardy-Weinberg disequilibrium in three goat populations (P<0.05). Association of polymorphisms with growth traits was done in BG, F1 and F1 populations, which were shown to be associated with growth traits in three goat populations. The SNPs in the goat GH gene had significant effects on growth traits (P<0.05). suggesting that the GH gene is a strong candidate gene that affects growth traits in goat.

Association of IGF-I gene polymorphisms with milk yield and body size in Chinese dairy goats

The association of IGF-I gene polymorphisms with certain traits in 708 individuals of two Chinese dairy-goat breeds (Guanzhong and Xinong Saanen) was investigated. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods were employed in screening for genetic variation. Two novel mutations were detected in the 5'-flanking region and in intron 4 of IGF-I gene, viz., g.1617 G > A and g.5752 G > C (accession D26119.2), respectively. The associations of the g.1617 G > A mutation with milk yield and the body size were not significant (p > 0.05). However, in the case of g.5752 G > C, Xinong Saanen dairy goats with the CG genotype presented longer bodies (p < 0.05). Chest circumference (p < 0.05) was larger in Guanzhong goats with the GG genotype. In Xinong Saanen dairy goats with the CC genotype, milk yields were significantly higher during the first and second lactations (p < 0.05). Hence, the g.5752 G > C mutation could facilitate association analysis and serve as a genetic marker for Chinese dairy-goat breeding and genetics.

Polymorphisms in the IGF1 gene and their effect on growth traits in Mexican beef cattle

The IGF1 gene (insulin-like growth factor 1) is a candidate gene for marker-assisted selection strategies. A single nucleotide polymorphism in the promoter region (IGF1/SnaBI) has been reported to be associated with production traits in several cattle breeds. Here, we report its allelic frequencies in Charolais and Beefmaster breeds; we confirm its association with three growth traits: weaning weight, weaning weight adjusted to 210 days and preweaning weight gain in the Charolais breed. In addition, we designed a strategy to search these breeds for new polymorphisms in four coding regions of the gene. A C/A transversion was detected in intron 4, but it was not associated with the growth traits. A single nucleotide polymorphism (IGF1/SnaBI) is proposed as a selection marker for Mexican Charolais cattle; validation of its association with weaning weight, weaning weight adjusted to 210 days and preweaning weight gain, could complement the genetic evaluations of this breed through marker-assisted management strategies.

Canine fibroblast growth factor receptor 3 sequence is conserved across dogs of divergent skeletal size

BACKGROUND

Fibroblast growth factor receptor 3 (FGFR3) is expressed in the growth plate of endochondral bones and serves as a negative regulator of linear bone elongation. Activating mutations severely limit bone growth, resulting in dwarfism, while inactivating mutations significantly enhance bone elongation and overall skeletal size. Domesticated dogs exhibit the greatest skeletal size diversity of any species and, given the regulatory role of FGFR3 on growth plate proliferation, we asked whether sequence differences in FGFR3 could account for some of the size differences.

METHODS

All exons, the promoter region, and 60 bp of the 3' flanking region of the canine FGFR3 gene were sequenced for nine different dog breeds representing a spectrum of skeletal size. The resultant sequences were compared to the reference Boxer genome sequence.

RESULTS

There was no variation in sequence for any FGFR3 exons, promoter region, or 3' flanking sequence across all breeds evaluated.

CONCLUSION

The results suggest that, regardless of domestication selection pressure to develop breeds having extreme differences in skeletal size, the FGFR3 gene is conserved. This implies a critical role for this gene in normal skeletal integrity and indicates that other genes account for size variability in dogs.