Georgios Banos

Impact of Single Nucleotide Polymorphisms in Leptin, Leptin Receptor, Growth Hormone Receptor, and Diacylglycerol Acyltransferase (DGAT1) Gene Loci on Milk Production, Feed, and Body Energy Traits of UK Dairy Cows

The impact of 9 single nucleotide polymorphisms (SNP) in the leptin (LEP), leptin receptor (LEPR), growth hormone receptor (GHR), and diacylglycerol acyltransferase (DGAT1) gene loci on daily milk production, feed intake, and feed conversion, and weekly measures of live weight, BCS, and body energy traits was evaluated using genetic and phenotypic data on 571 Holstein cows raised at the Langhill Dairy Cattle Research Center in Scotland. Six SNP were typed on the LEP gene and 1 on each of the other 3 loci. Of the 6 LEP SNP, 3 were in very high linkage disequilibrium, meaning there is little gain in typing all of them in the future. Seven LEP haplotypes were identified by parsimony-based analyses. Random-regression allele-substitution models were used to assess the impact of each SNP allele or haplotype on the traits of interest. Diacylglycerol acyltransferase had a significant effect on milk yield, whereas GHR significantly affected feed intake, feed conversion, and body energy traits. There was also evidence of dominance in allelic effects on milk yield and BCS. The LEP haplotype CCGTTT (corresponding to leptin SNP C207T, C528T, A1457G, C963T, A252T, and C305T, respectively) significantly affected milk yield and feed and dry matter intake. Animals carrying this haplotype produced 3.13 kg more milk daily and consumed 4.64 kg more feed. Furthermore, they tended to preserve more energy than average. Such results may be used to facilitate genetic selection in animal breeding programs.

Estimation of Genetic (Co)variance Components for International Evaluation of Dairy Bulls

Abstract Within- and across-country genetic parameters need to be estimated prior to an international genetic evaluation of dairy bulls. A procedure based on the Expectation Maximization algorithm to produce restricted maximum likelihood estimates of such parameters, using national evaluation results from different countries, was tested by simulation. Individual performance records were generated for two populations of dairy cattle with separate breeding programmes but considerable genetic exchange to create ties between the populations. A genotype-by-country interaction effect was generated by simulating the data according to a genetic correlation of 90 between performance in the two countries. Within-country national evaluations were computed with animal models. The estimation procedure was tested using bull national evaluation results. The impact of factors such as data connectedness, time period, and bias in national evaluations on estimated parameters was investigated. When all data were included in ...

Genetic association between body energy measured throughout lactation and fertility in dairy cattle

The objective of this study was to quantify the genetic association of body energy assessed throughout lactation with a cows fertility. Nine direct and indirect body energy traits were defined at different stages of lactation. Four were daily records of energy balance, energy content, cumulative effective energy (CEE) and body condition score (BCS) calculated between lactation days 4 and 311. The other five traits included duration of negative energy balance (DNEB), rate of recovery during DNEB (RNEB), sum of negative energy balance (SNEB), nadir of energy content (NEC) and number of days from calving to NEC. Of these traits, energy balance, DNEB, RNEB and SNEB were primarily based on individual cow feed intake and milk yield, and considered direct measures of body energy. The other traits were calculated from body lipid and protein changes, predicted from BCS and live weight profiles, and were considered indirect measures of body energy. Fertility was defined by number of days between calving and commencement of luteal activity (DLA), first observed oestrus (DH) and conception (DC), and number of services per conception. A total of 957 cows in their first four lactations were considered in the study. Genetic models fitted cubic splines to define longitudinal traits (energy balance, energy content, CEE and BCS) and calculate heritability and genetic correlation with fertility. Daily heritability estimate ranges were 0.10 to 0.34, 0.35 to 0.61, 0.32 to 0.53 and 0.24 to 0.56 for energy balance, energy content, CEE and BCS, respectively, and, in most cases, tended to increase towards the middle of lactation and remain relatively stable thereafter. Of the other body energy traits, heritability of NEC (0.44) was the most notable. Statistically significant (P < 0.05) genetic correlations of DH with daily energy balance, energy content, CEE and BCS ranged from -0.16 to -0.28, -0.35 to -0.48, -0.16 to -0.26 and -0.37 to -0.44, respectively. For DC, respective estimates were -0.28 to -0.64, -0.37 to -0.60, -0.30 to -0.48 and -0.29 to -0.53. For DLA, they ranged from -0.47 to -0.56 with energy content and from -0.50 to -0.74 with BCS. Of special interest was the genetic correlation of NEC with DH (-0.54) and DC (-0.48). Results suggest that indirect measures of body energy have the strongest genetic association with cow fertility. NEC and early lactation (circa day 50) BCS and energy content are the most useful traits for selection in terms of the correlated improvement in a cows capacity to resume her reproductive activity post partum.

Caprine PRNP polymorphisms at codons 171, 211, 222 and 240 in a Greek herd and their association with classical scrapie

The association between PRNP variation and scrapie incidence was investigated in a highly affected Greek goat herd. Four mutations were identified at codons 171Q/R, 211R/Q, 222Q/K and 240P/S. Lysine at codon 222 was found to be associated with the protection from natural scrapie (P=0.0111). Glutamine at codon 211 was observed in eight animals, all of them being scrapie-negative, indicating a possible protective role of this polymorphism although statistical analysis failed to support it (P=0.1074). A positive association (P=0.0457) between scrapie-affected goats and the wild-type Q(171)R(211)Q(222)S(240) allele is presented for the first time. In addition, a novel R(171)RQS allele, which is identical to the A(136)R(154)R(171) allele that has been associated with resistance to classical scrapie in sheep, was observed in low frequency. Resistant alleles that include K(222) and Q(211) are absent or rare in sheep and can provide the basis for the development of a feasible breeding programme for scrapie eradication in goats.

The effects of polymorphisms in the DGAT1, leptin and growth hormone receptor gene loci on body energy, blood metabolic and reproductive traits of Holstein cows.

The objective of this study was to examine the impact of polymorphisms in the acyl-CoA:diacylglycerol acyltransferase (DGAT1), leptin and growth hormone receptor genes on body energy (body condition score, total body energy content and cumulative effective energy balance) and blood metabolic traits (levels of beta-hydroxybutyrate, glucose and non-esterified fatty acids), measured once before the first calving and then repeatedly throughout first lactation in 497 Holstein cows. The influence of the same polymorphisms on cow reproductive performance and health during the first and second lactations was also assessed. Several reproductive traits were considered including interval, conception and insemination traits, as well as incidence of metritis and reproductive problems. Genotyping was performed using PCR-RFLP (DGAT1, leptin) or allele-specific PCR (growth hormone receptor). For each locus, the effect of allele substitution on body energy and blood metabolic traits was estimated using random regression models. The same effect on reproductive traits was assessed with single-trait mixed linear models. Significant (P<0.05) effects on specific reproductive traits were observed. DGAT1 and growth hormone receptor alleles responsible for significant increases in milk production were found to have an adverse effect on reproduction, while the leptin allele responsible for significant increase in milk production was linked to marginally increased metritis frequency. Furthermore, the three studied loci were also found to significantly (P<0.05) affect certain body energy and blood metabolic traits. Several associations are published for the first time, but these should be confirmed by other investigators before the polymorphisms are used in gene-assisted selection.

A comparison of six methods for genomic DNA extraction suitable for PCR-based genotyping applications using ovine milk samples

Isolation of amplifiable genomic DNA is a prerequisite for the genetic assessment of diseases and disease susceptibility in farm animals. Milk somatic cells are a practical, animal friendly and cost-effective source of genomic DNA in milking ruminants. In this study, six different DNA extraction methods were optimized, evaluated and compared for the isolation of DNA from ovine milk samples. Methods 1 and 2 were direct applications of two commercial kits, Nucleospin((R)) Blood and Nucleospin((R)) Tissue, respectively. Methods 3 and 4 were based on modified protocols of methods 1 and 2, respectively, aiming at increasing DNA recovery and integrity, and eliminating PCR inhibitors. Method 5 was a standard Phenol-Chloroform protocol application and method 6 was based on an in-house developed protocol using silica as the affinity matrix. Spectrophotometer, gel electrophoresis and real-time PCR measurements were used as criteria for evaluating quantity and quality of the extracted DNA. Processing time, intensity of labor and cost for each method were also evaluated. Results suggested that methods 1-4 were considered suitable for molecular downstream applications and performed better than methods 5 and 6. Modifications of protocols 3 and 4 increased the quantity and quality of the extracted DNA from ovine milk samples. Method 3 was proved to be highly efficient and robust for large scale use as demonstrated by its successful application to 1000 individual ovine milk and 50 bulk milk samples.

Dependent Variables in International Sire Evaluations

Abstract Stochastic simulation was used to assess the suitability of alternative dependent variables in international sire evaluation. Three such variables were considered: daughter yield deviations (DYD), national proofs (ETA), and de-regressed national proofs (DPRF). Data from two dairy cattle populations considering 10 generations were simulated. Genetic ties necessary for a joint evaluation of the two populations were established with bull exchange in each generation. De-regressed national proofs were the best and ETA were the worst in estimating genetic difference between the two populations and ranking bulls across country. Further, de-regressed national proofs can be easily computed and, contrary to DYD, are always available. De-regressed national proofs are recommended as dependent variables in across country sire evaluation.

Eating quality of lamb meat: effects of breed, sex, degree of maturity and nutritional management

The eating quality of lamb meat of three indigenous Greek dairy breeds of sheep, reared under different nutritional management conditions, was assessed by Taste Panel Tests (TPT). Lean samples from the leg joints of 69 lamb carcasses of the Boutsko (B), Serres (S) and Karagouniko (K) breed were used. For the first TPT, 24 lambs (four males and four females of each breed) were reared in individual pens on a concentrate ration fed ad libitum. For the second TPT, 27 individual penned male lambs were fed on Lucerne hay ad libitum and on three different levels of concentrate: High (H), Medium, (M) and Low (L). For the third TPT, 18 male lambs were used; initially the groups were fed indoors for 63 days on three different levels of concentrate (H, M and L) together with ad libitum Lucerne hay, and subsequently finished on irrigated, sown pasture. For TPT 1, leg joints were obtained from lambs that had been slaughtered at 30, 45, 60 or 90% of mature weight (PMW) for each breed. For TPT 2, lambs were slaughtered at 23, 28 or 33 kg target slaughter live weights (TSLW), common for all breeds. For TPT 3, lambs were slaughtered at 48 or 55% of PMW for each breed. Panellists assessed warm, roasted lean samples of leg joints and rated Flavour, Juiciness, Tenderness and Overall Acceptability. In TPT 1, degree of maturity significantly affected Flavour, Tenderness and Overall Acceptability whereas sex affected only Flavour. In TPT 2, breed and concentrate level significantly affected the quality characteristics, but concentrate level had no significant effect in TPT 3. Effects associated with slaughter weight were significant for most characteristics in all TPT, with decreasing acceptability for older/heavier lambs. Significant interactions were found between breed and the other factors in TPT 2 and TPT 3 for most quality characteristics. Results from these studies suggest changing traditional production systems may enhance the eating quality of lamb meat.

Identification of immune traits correlated with dairy cow health, reproduction and productivity.

Detailed biological analyses (e.g. epidemiological, genetic) of animal health and fitness in the field are limited by the lack of large-scale recording of individual animals. An alternative approach is to identify immune traits that are associated with these important functions and can be subsequently used in more detailed studies. We have used an experimental dairy herd with uniquely dense phenotypic data to identify a range of potentially useful immune traits correlated with enhanced (or depressed) health and fitness. Blood samples from 248 dairy cows were collected at two-monthly intervals over a 10-month period and analysed for a number of immune traits, including levels of serum proteins associated with the innate immune response and circulating leukocyte populations. Immune measures were matched to individual cow records related to productivity, fertility and disease. Correlations between traits were calculated using bivariate analyses based on animal repeatability and random regression models with a Bonferroni correction to account for multiple testing. A number of significant correlations were found between immune traits and other recorded traits including: CD4+:CD8+ T lymphocyte ratio and subclinical mastitis; % CD8+ lymphocytes and fertility; % CD335+ natural killer cells and lameness episodes; and serum haptoglobin levels and clinical mastitis. Importantly these traits were not associated with reduced productivity and, in the case of cellular immune traits, were highly repeatable. Moreover these immune traits displayed significant between-animal variation suggesting that they may be altered by genetic selection. This study represents the largest simultaneous analysis of multiple immune traits in dairy cattle to-date and demonstrates that a number of immune traits are associated with health events. These traits represent useful selection markers for future programmes aimed at improving animal health and fitness.

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples

Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.