Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle

Identification of hub genes associated with somatic cell score in dairy cow

CONTEXT

Somatic cell count (SCC) is used as an indicator of udder health. The log transformation of SCC is called somatic cell score (SCS).

AIM

Several QTL and genes have been identified that are associated with SCS. This study aimed to identify the most important genes associated with SCS.

METHODS

This study compiled 168 genes that were reported to be significantly linked to SCS. Pathway analysis and network analysis were used to identify hub genes.

KEY RESULTS

Pathway analysis of these genes identified 73 gene ontology (GO) terms associated with SCS. These GO terms are associated with molecular function, biological processes, and cellular components, and the identified pathways are directly or indirectly linked with the immune system. In this study, a gene network was constructed, and from this network, the 17 hub genes (CD4, CXCL8, TLR4, STAT1, TLR2, CXCL9, CCR2, IGF1, LEP, SPP1, GH1, GHR, VWF, TNFSF11, IL10RA, NOD2, and PDGFRB) associated to SCS were identified. The subnetwork analysis yielded 10 clusters, with cluster 1 containing all identified hub genes (except for the VWF gene).

CONCLUSION

Most hub genes and pathways identified in our study were mainly involved in inflammatory and cytokine responses.

IMPLICATIONS

Result obtained in current study provides knowledge of the genetic basis and biological mechanisms controlling SCS. Therefore, the identified hub genes may be regarded as the main gene for the genomic selection of mastitis resistance.

Comparative analysis of allele frequencies for DNA polymorphisms associated with disease and economically important traits in the genomes of Russian and foreign cattle breeds

The genetic makeup of a breed including its genetic differences from other breeds determines its appearance and characteristics, including economically important traits and resistance to pathologies. To date, many loci controlling significant phenotypes have been identified, which is successfully used in the world practice of marker-assisted selection to improve breed properties. The aim of this study was a comparative analysis of frequencies for known causative nucleotide substitutions, insertions and deletions associated with disease and economically important traits in Russian and foreign cattle breeds. As a result, we identified frequencies of these DNA polymorphisms in the populations of Russian cattle breeds, compared them with those of foreign populations of the same breed, as well as other foreign breeds. Our results indicate similarities in frequencies for most of such alleles within breeds (populations of Russian and foreign breeding), as well as the relationship between the causative allele prevalence and the presence of phenotypic traits under the effect. We also found an excess of some undesirable alleles in the Russian cattle populations, which should be paid attention to when designing breeding programs. We found that the alleles increasing fertility in the Hereford breed have a higher frequency in the Russian Hereford population compared to the foreign counterpart. Interestingly, unlike for the European breeds, for Asian Turano-Mongolian Wagyu and Yakut cattle, there was a less clear link between phenotypic traits and frequencies of known causative alleles. Our work points to specific genetic variants that could be used to improve and/or maintain the performance of certain cattle breeds bred in the Russian Federation.

Association of milk production traits with genetic variants in exon 5 and intron 3 of bovine growth hormone (bGH) gene in Sahiwal cattle

The main objective of this study was to determine the association of production traits with genetic variants in exon 5 and intron 3 of bovine growth hormone (bGH) gene in Sahiwal cattle. The analyses were based on the detection of single nucleotide polymorphisms (SNPs) in GH-AluI (exon 5) and GH-MspI (intron 3) using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The frequency of AluI (L/V) and MspI (T/C) alleles were 86.20/13.70 and 89.80/9.50, respectively. The distribution of the frequency of GH genotypes for LL, LV, and VV were 73.4, 25.5, and 1.0 and for TT, TC, and CC genotypes were 80.9, 17.7, and 13.0, respectively. Season of calving had none but period of calving had significant effect on the studied production traits. The phenotypic data was adjusted for non-genetic factors and regression analysis was done. There was detectable significant effect of the GH-AluI and GH-MspI on the analyzed production traits. The cows with LL genotype had significantly higher milk yield traits than the LV genotype. Similarly, the productive performance of the studied cows with TT genotype was also significantly higher than TC and CC genotypes. Results revealed that the Sahiwal cows with LL and TT genotypes of the bGH locus can be considered to be a favourable genotype for production traits, although these findings need to be confirmed by further research before SNPs can be used in a marker assisted selection program by the animal breeder.

Association of GH polymorphisms with growth traits in buffaloes

Members of the somatotrophic axis, especially GH and IGF1, are essential for growth. The association between GH polymorphisms and growth traits was numerously studied in cattle; however, no data are available for such association studies in buffalo. Therefore, this study was conducted to screen for polymorphisms in the GH gene and to study their putative association with growth traits in 200 Egyptian buffaloes. Polymerase chain reaction single-strand conformation polymorphism and sequencing were applied to look for polymorphisms in 3 loci spanning all exons and introns of buffalo GH. The C (MspI+) >T (MspI-) SNP in intron3, which is well known in cattle, was not detected in the examined buffaloes. However, 2 missense mutations were detected in exon5: one previously detected p.Leu153Val SNP, with very low frequencies for the mutant (Val) allele and one novel p.Asn174His SNP. At weaning age, the p.Leu153Val SNP was significantly associated with weaning body weight and gain with the positive effect of the wild allele (Leu) and higher GH serum, mRNA, and protein levels in animals with Leu/Asn and Leu/His haplotypes. At yearling age, the 2 SNPs associated with yearling weight and gain with positive effect for the mutant (Val and His) alleles with increased GH, and IGF1 serum, mRNA, and protein and GHR mRNA and protein levels in animals with Val/Asn haplotype. Therefore, the selection of Egyptian buffaloes with the Val/Asn haplotype could improve the growth traits of Egyptian buffaloes at yearling age which is the target age for perfect growing.

Association of GH, STAT5A, MYF5 gene polymorphisms with milk somatic cell count, EC and pH levels of Holstein dairy cattle

This study was conducted to ivnestigate the associations of GH-AluI, STAT5A-AvaI and MYF5-TaqI gene polymorphisms with milk somatic cell count (SCC), electrical conductivity (EC) and pH levels in Holstein dairy cows. For this purpose, 167 blood and 1670 milk samples of 167 Holstein cows in their 2nd lactation were used. There were significant relationships between GH-AluI genotypes and milk EC (p < 0.001) and between STAT5A-AvaI genotypes and milk EC (p = 0.007), but there were not any significant relationships between MYF5 gene polymorphism and the investigated traits (p > 0.05). The greatest EC values were observed in GH-AluI-LV and STAT5A-AvaI-TT-genotyped individuals. Just because of association of EC with mastitis, it was concluded that present GH-AluI and STAT5A-AvaI polymorphisms could be used in further studies to be conducted to improve mastitis resistance and milk quality traits of Holstein dairy cows.

Genetic mapping of distal femoral, stifle, and tibial radiographic morphology in dogs with cranial cruciate ligament disease

Cranial cruciate ligament disease (CCLD) is a complex trait. Ten measurements were made on orthogonal distal pelvic limb radiographs of 161 pure and mixed breed dogs with, and 55 without, cranial cruciate partial or complete ligament rupture. Dogs with CCLD had significantly smaller infrapatellar fat pad width, higher average tibial plateau angle, and were heavier than control dogs. The first PC weightings captured the overall size of the dog’s stifle and PC2 weightings reflected an increasing tibial plateau angle coupled with a smaller fat pad width. Of these dogs, 175 were genotyped, and 144,509 polymorphisms were used in a genome-wide association study with both a mixed linear and a multi-locus model. For both models, significant (p_genome <3.46×10⁻⁷ for the mixed and< 6.9x10^-8 for the multilocus model) associations were found for PC1, tibial diaphyseal length and width, fat pad base length, and femoral and tibial condyle width at LCORL, a known body size-regulating locus. Other body size loci with significant associations were growth hormone 1 (GH1), which was associated with the length of the fat pad base and the width of the tibial diaphysis, and a region on CFAX near IRS4 and ACSL4 in the multilocus model. The tibial plateau angle was associated significantly with a locus on CFA10 in the linear mixed model with nearest candidate genes BET1 and MYH9 and on CFA08 near candidate genes WDHD1 and GCH1. MYH9 has a major role in osteoclastogenesis. Our study indicated that tibial plateau slope is associated with CCLD and a compressed infrapatellar fat pad, a surrogate for stifle osteoarthritis. Because of the association between tibial plateau slope and CCLD, and pending independent validation, these candidate genes for tibial plateau slope may be tested in breeds susceptible to CCLD before they develop disease or are bred.

Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes.

Complex traits are controlled by more than one gene and as such are difficult to map. For complex trait mapping in the domestic dog, researchers use the current array of 173,000 variants, with only minimal success. Here, we use a method called imputation to increase the number of variants–from 173,000 to 24 million–that can be queried in canine association studies. We use sequence data from the whole genomes of 365 dogs and wolves to accurately predict variants, in a separate cohort of dogs, that are not present on the array. Using dog body size, blood phenotypes, and a common orthopedic disease that involves rupture of the cranial cruciate ligament, we show that the increase in variants results in an increase in mapping power, through the identification of new associations and the narrowing of regions of interest. This imputation panel is particularly important because of its usefulness in improving complex trait mapping in the dog, which has significant implications for discovery of variants in humans with similar diseases.

Assessment of growth hormone gene polymorphism effects on reproductive traits in Holstein dairy cattle in Tunisia

Research to assess the effect of single genes on reproductive traits in bovine species is imperative to elucidate genes' functions and acquire a better perspective of quantitative traits. The present study was undertaken to characterize genetic diversity in the bovine growth hormone (GH) gene in a population of 410 Holstein dairy cows in Tunisia. The analyses were based on single nucleotide polymorphisms, and GH-AluI and GH-MspI detections and genotyping were carried out using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Data were analyzed using a mixed linear model with the MIXED procedure to reveal the possible effect of GH genotypes on reproductive traits. The frequency data of AluI(L//V) and MspI( + // - ) alleles were 87.04//12.96 and 70.06//29.94, respectively. The distribution of the frequency of GH genotypes for LL/LV/VV and ( - / - )//( + / - )//( + / + ) were 77.75//18.59//3.66 and 15.37//29.13//55.50, respectively. The results of the statistical analyses proved that GH-AluI showed a substantial favorable effect on exanimate traits except for the age at first calving; however, only a suggestive effect of GH-MspI on the calving interval (CI) and the days open (DI) was found. The homozygous LL genotype seemed to be advantageous with respect to the CI and the DI compared with LV and VV genotypes. Heterozygous MspI( + / - ) cows tended to have a longer CI and DI than MspI( + / + ) and MspI( - / - ) cows, but the difference was not statistically significant. A significant effect of different GH-AluI-MspI combined genotypes was found on the number of inseminations per conception, the CI and the DI, and the LL/- combined genotype seemed to be associated with better reproductive performance. Based on these results, the LL genotype of the GH locus can be considered to be a favorable genotype for reproductive traits in Holstein dairy cattle, although these findings need to be confirmed by further research before polymorphisms can be used in a marker-assisted selection program.

Single nucleotide polymorphisms in candidate genes associated with milk yield in Argentinean Holstein and Holstein x Jersey cows

BACKGROUND

Research on loci influencing milk production traits of dairy cattle is one of the main topics of investigation in livestock. Many genomic regions and polymorphisms associated with dairy production have been reported worldwide. In this context, the purpose of this study was to identify candidate loci associated with milk yield in Argentinean dairy cattle. A database of candidate genes and single nucleotide polymorphisms (SNPs) for milk production and composition was developed. Thirty-nine SNPs belonging to 22 candidate genes were genotyped on 1643 animals (Holstein and Holstein x Jersey). The genotypes obtained were subjected to association studies considering the whole population and discriminating the population by Holstein breed percentage. Phenotypic data consisted of milk production values recorded during the first lactation of 1156 Holstein and 462 Holstein x Jersey cows from 18 dairy farms located in the central dairy area of Argentina. From these records, 305-day cumulative milk production values were predicted.

RESULTS

Eight SNPs (rs43375517, rs29004488, rs132812135, rs137651874, rs109191047, rs135164815, rs43706485, and rs41255693), located on six Bos taurus autosomes (BTA4, BTA6, BTA19, BTA20, BTA22, and BTA26), showed suggestive associations with 305-day cumulative milk production (under Benjamini-Hochberg procedure with a false discovery rate of 0.1). Two of those SNPs (rs43375517 and rs135164815) were significantly associated with milk production (Bonferroni adjusted p-values < 0.05) when considering the Holstein population.

CONCLUSIONS

The results obtained are consistent with previously reported associations in other Holstein populations. Furthermore, the SNPs found to influence bovine milk production in this study may be used as possible candidate SNPs for marker-assisted selection programs in Argentinean dairy cattle.

Pregnancy losses in cattle: potential for improvement

For heifers, beef and moderate-yielding dairy cows, it appears that the fertilisation rate generally lies between 90% and 100%. For high-producing dairy cows, there is a less substantive body of literature, but it would appear that the fertilisation rate is somewhat lower and possibly more variable. In cattle, the major component of embryo loss occurs in the first 16 days following breeding (Day 0), with emerging evidence of greater losses before Day 8 in high-producing dairy cows. In cattle, late embryo mortality causes serious economic losses because it is often recognised too late to rebreed females. Systemic concentrations of progesterone during both the cycle preceding and following insemination affect embryo survival, with evidence of either excessive or insufficient concentrations being negatively associated with survival rate. The application of direct progesterone supplementation or treatments to increase endogenous output of progesterone to increase embryo survival cannot be recommended at this time. Energy balance and dry matter intake during the first 4 weeks after calving are critically important in determining pregnancies per AI when cows are inseminated at 70-100 days after calving. Level of concentrate supplementation of cows at pasture during the breeding period has minimal effects on conception rates, although sudden reductions in dietary intake should be avoided. For all systems of milk production, more balanced breeding strategies with greater emphasis on fertility and feed intake and/or energy must be developed. There is genetic variability within the Holstein breed for fertility traits, which can be exploited. Genomic technology will not only provide scientists with an improved understanding of the underlying biological processes involved in fertilisation and the establishment of pregnancy, but also, in the future, could identify genes responsible for improved embryo survival. Such information could be incorporated into breeding objectives in order to increase the rate of genetic progress for embryo survival. In addition, there is a range of easily adoptable management factors, under producer control, that can either directly increase embryo survival or ameliorate the consequences of low embryo survival rates. The correction of minor deficits in several areas can have a substantial cumulative positive effect on herd reproductive performance.

Targeted high-throughput growth hormone 1 gene sequencing reveals high within-breed genetic diversity in South African goats

This study assessed the genetic diversity in the growth hormone 1 gene (GH1) within and between South African goat breeds. Polymerase chain reaction-targeted gene amplification together with Illumina MiSeq next-generation sequencing (NGS) was used to generate the full length (2.54 kb) of the growth hormone 1 gene and screen for SNPs in the South African Boer (SAB) (n = 17), Tankwa (n = 15) and South African village (n = 35) goat populations. A range of 27-58 SNPs per population were observed. Mutations resulting in amino acid changes were observed at exons 2 and 5. Higher within-breed diversity of 97.37% was observed within the population category consisting of SA village ecotypes and the Tankwa goats. Highest pairwise FST values ranging from 0.148 to 0.356 were observed between the SAB and both the South African village and Tankwa feral goat populations. Phylogenetic analysis indicated nine genetic clusters, which reflected close relationships between the South African populations and the other international breeds with the exception of the Italian Sarda breeds. Results imply greater potential for within-population selection programs, particularly with SA village goats.

Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus

Understanding the evolution and molecular architecture of complex traits is important in domestic animals. Due to phenotypic selection, genomic regions develop unique patterns of genetic diversity called signatures of selection, which are challenging to detect, especially for complex polygenic traits. In this study, we applied the composite selection signals (CSS) method to investigate evidence of positive selection in a complex polygenic trait by examining stature in phenotypically diverse cattle comprising 47 European and 8 African Bos taurus breeds, utilizing a panel of 38,033 SNPs genotyped on 1106 animals. CSS were computed for phenotypic contrasts between multibreed cohorts of cattle by classifying the breeds according to their documented wither height to detect the candidate regions under selection. Using the CSS method, clusters of signatures of selection were detected at 26 regions (9 in European and 17 in African cohorts) on 13 bovine autosomes. Using comparative mapping information on human height, 30 candidate genes mapped at 12 selection regions (on 8 autosomes) could be linked to bovine stature diversity. Of these 12 candidate gene regions, three contained known genes (i.e., NCAPG-LCORL, FBP2-PTCH1, and PLAG1-CHCHD7) related to bovine stature, and nine were not previously described in cattle (five in European and four in African cohorts). Overall, this study demonstrates the utility of CSS coupled with strategies of combining multibreed datasets in the identification and discovery of genomic regions underlying complex traits. Characterization of multiple signatures of selection and their underlying candidate genes will elucidate the polygenic nature of stature across cattle breeds.

The effect of polymorphism in gene of insulin-like growth factor-I on the serum periparturient concentration in Holstein dairy cows

OBJECTIVE

To investigate the relationship between polymorphism within the 5'-untranslated region (5'-UTR) of IGF-I gene and its periparturient concentration in Iranian Holstein dairy cows.

METHODS

Blood samples (5 mL, n = 37) were collected by caudal venipuncture from each animal into sample tubes containing the EDTA and DNA was extracted from blood. In order to measure IGF-I concentration the collection of blood samples (n = 111) was also done at 14 d before calving (prepartum), 25 and 45 d postpartum.

RESULTS

We found evidence for a significant effect of C to T mutation in position 512 of IGF-I gene on its serum concentration in dairy cows in Iran. Cows with CC genotype had significantly higher concentration (Mean±SD) of IGF-I at 14 d prepartum (91.8±18.1) µg/L compared to those with TT genotype (73.3±14.4) µg/L (P=0.04). A significant trend (quadratic) was found for IGF-I concentration, as higher in CC cows compared to ones with TT genotype, during the 14 d before calving to 45 d postpartum (P=0.01).

CONCLUSIONS

We concluded that C/T transition in the promoter region of IGF-I gene can influence the serum concentration of IGF-I in periparturient dairy cows.

MicroRNAs in domestic livestock

microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.

Genome-wide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries

Genome-wide association studies for difficult-to-measure traits are generally limited by the sample size with accurate phenotypic data. The objective of this study was to utilise data on primiparous Holstein–Friesian cows from experimental farms in Ireland, the United Kingdom, the Netherlands and Sweden to identify genomic regions associated with the feed utilisation complex: fat and protein corrected milk yield (FPCM), dry matter intake (DMI), body condition score (BCS) and live-weight (LW). Phenotypic data and 37 590 single nucleotide polymorphisms (SNPs) were available on up to 1629 animals. Genetic parameters of the traits were estimated using a linear animal model with pedigree information, and univariate genome-wide association analyses were undertaken using Bayesian stochastic search variable selection performed using Gibbs sampling. The variation in the phenotypes explained by the SNPs on each chromosome was related to the size of the chromosome and was relatively consistent for each trait with the possible exceptions of BTA4 for BCS, BTA7, BTA13, BTA14, BTA18 for LW and BTA27 for DMI. For LW, BCS, DMI and FPCM, 266, 178, 206 and 254 SNPs had a Bayes factor .3, respectively. Olfactory genes and genes involved in the sensory smell process were overrepresented in a 500 kbp window around the significant SNPs. Potential candidate genes were involved with functions linked to insulin, epidermal growth factor and tryptophan.

One novel SNP of growth hormone gene and its associations with growth and carcass traits in ducks

In this study, the growth hormone (GH) gene was studied as a candidate gene for growth and carcass traits of three duck populations (Cherry Valley duck, Muscovy duck and Jingjiang duck). Three pairs of primers were designed to detect single nucleotide polymorphisms of introns 2, 3 and 4 of the GH gene by polymerase chain reaction-restriction fragment length polymorphism and sequencing methods. Only the products amplified from intron 2 displayed polymorphism. The results showed one novel polymorphism: a variation in intron 2 of GH gene (C172T, JN408701 and JN408702). It was associated with some growth and carcass traits in three duck populations including birth weight, 8-week weight, carcass weight, breast muscle weight, leg muscle weight, eviscerated weight, lean meat rate, dressing percentage, etc. And the TT and CT genotypes were associated with superior growth and carcass traits in carcass weight, dressing percentage and percentage of eviscerated weight. Therefore, the variation in intron 2 of GH may be a molecular marker for superior growth and carcass traits in above duck populations.

Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

Background

The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility.

Results

In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952) of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612) were intronic and 9% (n = 464) were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS). Significant (P < 0.01) mean allele frequency differentials between the low and high fertility groups were observed for 720 SNPs (58 NSS). Allele frequencies for 43 of the SNPs were also determined by genotyping the 150 individual animals (Sequenom^® MassARRAY). No significant differences (P > 0.1) were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total).

Conclusions

The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving interval plausibly harbouring causative variants contributing to heritable variation. To our knowledge, this is the first report describing sequencing of targeted genomic regions in any livestock species using groups with divergent phenotypes for an economically important trait.

Polymorphisms in genes of the somatotrophic axis are independently associated with milk production, udder health, survival and animal size in Holstein-Friesian dairy cattle

The somatotrophic axis consisting of pituitary-derived growth hormone and circulating insulin-like growth factor 1 has been well established as key regulators of animal health, metabolism, lactation, fertility, body composition and growth rate. The aim of this study was to simultaneously quantify the associations between SNPs in candidate genes of the somatotrophic axis (i.e., IGF-1, GH1 and GHR) with performance traits in Holstein-Friesian (HF) dairy cattle. Both novel SNPs identified previously by this group alongside other published SNPs within these genes were analysed for associations with performance in dairy cattle. Multiple regression analyses regressing genetic merit of up to 848 HF sires on novel SNPs (n = 76) and published SNPs (n = 33) were undertaken using weighted animal mixed linear models. Twenty-three SNPs were significantly associated with at least one of 18 traits analysed and involved in milk production, udder health, fertility and growth. Eight traits including milk fat composition, carcass conformation, stature, chest width, body depth, rump width, carcass and cull cow weight were independently associated with SNPs in two genes. Furthermore, for several traits including milk fat yield, somatic cell count, survival and carcass fat, SNPs in all three genes were independently associated with performance. Milk fat yield and carcass fat showed the highest number of independent associations across all three genes with five SNPs associated with both traits. The cumulative effects of the favourable alleles of all five SNPs across GH1, GHR and IGF-1 result in an increase of 5.9 kg and 28.6 units of milk fat and carcass fat, respectively. Cow survival was associated with a single SNP in each of the three genes with a cumulative allele effect of 1.5%. Independent effects of polymorphisms in GH1, GHR and IGF-1 reinforce the central role of the somatotrophic axis on animal development and performance.

Single Nucleotide Polymorphisms in the Insulin-Like Growth Factor 1 (IGF-1) Gene are Associated with Performance in Holstein-Friesian Dairy Cattle

Insulin-like growth factor 1 (IGF-1) has been shown to be associated with fertility, growth, and development in cattle. The aim of this study was to (1) identify novel single nucleotide polymorphisms (SNPs) in the bovine IGF-1 gene and alongside previously identified SNPs (2) determine their association with traits of economic importance in Holstein-Friesian dairy cattle. Nine novel SNPs were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, and 3′ regulatory regions, encompassing ~5 kb of IGF-1. Genotyping and associations with daughter performance for milk production, fertility, survival, and measures of body size were undertaken on 848 Holstein-Friesian AI sires. Using multiple regression analysis nominal associations (P < 0.05) were identified between six SNPs (four novel and two previously identified) and milk composition, survival, body condition score, and body size. The C allele of AF017143 a previously published SNP (C-512T) in the promoter region of IGF-1 predicted to introduce binding sites for transcription factors HSF1 and ZNF217 was associated (P < 0.05) with increased cow carcass weight (i.e., an indicator of mature cow size). Novel SNPs were identified in the 3′ region of IGF-1 were associated (P < 0.05) with functional survival and chest width. The remaining four SNPs, all located within introns of IGF-1 were associated (P < 0.05) with milk protein yield, milk fat yield, milk fat concentration, somatic cell score, carcass conformation, and carcass fat. Results of this study further demonstrate the multifaceted influences of IGF-1 on milk production and growth related traits in cattle.