A transgenerational study on the effect of great-granddam birth month on granddaughter EBV for production traits in Italian Simmental cattle.

Heat tolerance is a key feature of resilient animals. Offspring of animals that suffer environmental stress during pregnancy could show physiological, morphological, and metabolic modifications. This is due to a dynamic reprogramming of the epigenetics of the mammalian genome that occurs in the early life cycle. Thus, the aim of this study was to investigate the extent of the transgenerational effect of heat stress during the pregnancy of Italian Simmental cows. The effects of dam and granddam birth months (as indicator of pregnancy period) on their daughter and granddaughter estimated breeding values (EBV) for some dairy traits as well as of the temperature-humidity index (THI) during the pregnancy were tested. A total of 128,437 EBV (milk, fat, and protein yields, and somatic cell score) were provided by the Italian Association of Simmental Breeders. The best birth months (of both dam and granddam) for milk yield and protein yield were May and June, whereas the worst were January and March. Great-granddam pregnancies developed during the winter and spring seasons positively affected the EBV for milk and protein yields of their great-granddaughters; in contrast, pregnancies during summer and autumn had negative effects. These findings were confirmed by the effects of maximum and minimum THI in different parts of the great-granddam pregnancy on the performances of their great-granddaughters. Thus, a negative effect of high temperatures during the pregnancy of female ancestors was observed. Results of the present study suggest a transgenerational epigenetic inheritance in Italian Simmental cattle due to environmental stressors.

Analysis of runs of homozygosity of cattle living in different climate zones.

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.

Domestication and evolution of cattle originated different modern breeds in different places worldwide. The interaction between natural and artificial selection and the adaptation to environment shaped the genome, and the three different types of cattle here considered (taurus, indicus, and composite) may harbor different selection signatures. To study the difference among types and region of origin (tropics, temperate, and continental zones), Regions of Homozygosity (ROH) were used. ROH are continuous homozygous chromosomal segments identical by descendent, which characteristics can give information about inbreeding occurrence and natural and artificial selection. Moreover, it had been investigated which genes were mapped in these regions, and if interesting differences pertaining to environmental adaptation or fitness in general, could be observed.

Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds.

The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (FPED ), or runs of homozygosity (ROH; FROH ) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of FROH . The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.

Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity.

Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity. A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by both the altitude and temperature of the place where the flock was located. The highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest one for mountain. A total of 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. These markers mapped in eight chromosomes and they clustered into 17 ROH islands, where 80 candidate genes were mapped. Results of this study highlighted differences in the ROH distribution and features among sheep farmed in flocks located at different levels of altitude, confirming the role of environmental adaptability in shaping the genome of this breed.

Investigation of ß-hydroxybutyrate in early lactation of Simmental cows: Genetic parameters and genomic predictions.

Genomic information allows for a more accurate calculation of relationships among animals than the pedigree information, leading to an increase in accuracy of breeding values. Here, we used pedigree-based and single-step genomic approaches to estimate variance components and breeding values for ß-hydroxybutyrate milk content (BHB). Additionally, we performed a genome-wide association study (GWAS) to depict its genetic architecture. BHB concentrations within the first 90 days of lactation, estimated from milk medium infrared spectra, were available for 30,461 cows (70,984 records). Genotypes at 42,152 loci were available for 9,123 animals. Low heritabilities were found for BHB using pedigree-based (0.09 ± 0.01) and genomic (0.10 ± 0.01) approaches. Genetic correlation between BHB and milk traits ranged from -0.27 ± 0.06 (BHB and protein percentage) to 0.13 ± 0.07 (BHB and fat-to-protein ratio) using pedigree and from -0.26 ± 0.05 (BHB and protein percentage) to 0.13 ± 0.06 (BHB and fat-to-protein ratio) using genomics. Breeding values were validated for 344 genotyped cows using linear regression method. The genomic EBV (GEBV) had greater accuracy (0.51 vs. 0.45) and regression coefficient (0.98 vs. 0.95) compared to EBV. The correlation between two subsequent evaluations, without and with phenotypes for validation cows, was 0.85 for GEBV and 0.82 for EBV. Predictive ability (correlation between (G)EBV and adjusted phenotypes) was greater when genomic information was used (0.38) than in the pedigree-based approach (0.31). Validation statistics in the pairwise two-trait models (milk yield, fat and protein percentage, urea, fat/protein ratio, lactose and logarithmic transformation of somatic cells count) were very similar to the ones highlighted for the single-trait model. The GWAS allowed discovering four significant markers located on BTA20 (57.5-58.2 Mb), where the ANKH gene is mapped. This gene has been associated with lactose, alpha-lactalbumin and BHB. Results of this study confirmed the usefulness of genomic information to provide more accurate variance components and breeding values, and important insights about the genomic determination of BHB milk content.

The Nero Lucano Pig Breed: Recovery and Variability.

The Nero Lucano (NL) pig is a black coat colored breed characterized by a remarkable ability to adapt to the difficult territory and climatic conditions of Basilicata region in Southern Italy. In the second half of the twentieth century, technological innovation, agricultural evolution, new breeding methods and the demand for increasingly lean meat brought the breed almost to extinction. Only in 2001, thanks to local institutions such as: the Basilicata Region, the University of Basilicata, the Regional Breeders Association and the Medio Basento mountain community, the NL pig returned to populate the area with the consequent possibility to appreciate again its specific cured meat products. We analyzed the pedigrees recorded by the breeders and the Illumina Porcine SNP60 BeadChip genotypes in order to obtain the genetic structure of the NL pig. Results evidenced that this population is characterized by long mean generation intervals (up to 3.5 yr), low effective population size (down to 7.2) and high mean inbreeding coefficients (FMOL = 0.53, FROH = 0.39). This picture highlights the low level of genetic variability and the critical issues to be faced for the complete recovery of this population.

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events.

BACKGROUND: Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types. RESULTS: The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction. CONCLUSIONS: Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

Genome-wide analysis of homozygosity regions in european simmental bulls.

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH-based coefficient of inbreeding (FROH ) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) FROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome-wide ROH-traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.

Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed.

Arthrogryposis and macroglossia are congenital pathologies known in several cattle breeds, including Piemontese. As variations in single genes were identified as responsible for arthrogryposis in some breeds, we decided: (i) to test the hypothesis of a similar genetic determinism for arthrogryposis in the Piemontese breed by genotyping affected and healthy animals with a high-density chip and applying genome-wide association study (GWAS), FST and canonical discriminant analysis (CDA) procedures, and (ii) to investigate with the same approach the genetic background of macroglossia, for which no genetic studies exist so far. The study included 125 animals (63 healthy, 30 with arthrogryposis, and 32 with macroglossia). Differently from what reported for other breeds, the analysis did not evidence a single strong association with the two pathologies. Rather, 23 significant markers on different chromosomes were found (7 associated to arthrogryposis, 11 to macroglossia, and 5 to both pathologies), suggesting a multifactorial genetic mechanism underlying both diseases in the Piemontese breed. In the 100-kb interval surrounding the significant SNPs, 20 and 26 genes were identified for arthrogryposis and macroglossia, respectively, with 12 genes in common to both diseases. For some genes (NTN3, KCNH1, KCNH2, and KANK3), a possible role in the pathologies can be hypothesized, being involved in processes related to muscular or nervous tissue development. The real involvement of these genes needs to be further investigated and validated.

Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle.

Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations. To partially overcome these problems, a multivariate statistical algorithm was proposed. The basic idea was that animals with different phenotypic values of a specific trait share different allelic combinations for genes involved in its determinism. Three multivariate techniques were used to highlight the differences between the individuals assembled in high and low phenotype groups: the canonical discriminant analysis, the discriminant analysis and the stepwise discriminant analysis. The multivariate method was tested both on simulated and on real data. The results from the simulation study highlighted that the multivariate GWAS detected a greater number of true associated single nucleotide polymorphisms (SNPs) and Quantitative trait loci (QTLs) than the single marker model and the Bayesian approach. For example, with 3000 animals, the traditional GWAS highlighted only 29 significantly associated markers and 13 QTLs, whereas the multivariate method found 127 associated SNPs and 65 QTLs. The gap between the two approaches slowly decreased as the number of animals increased. The Bayesian method gave worse results than the other two. On average, with the real data, the multivariate GWAS found 108 associated markers for each trait under study and among them, around 63% SNPs were also found in the single marker approach. Among the top 118 associated markers, 76 SNPs harbored putative candidate genes.

Variance components using genomic information for 2 functional traits in Italian Simmental cattle: Calving interval and lactation persistency.

Functional traits, such as fertility and lactation persistency, are becoming relevant breeding goals for dairy cattle. Fertility is a key element for herd profitability and animal welfare; in particular, calving interval (CIN) is an indicator of female fertility that can be easily recorded. Lactation persistency (LPE; i.e., the ability of a cow to maintain a high milk yield after the lactation peak) is economically important and is related to several other traits, such as feed efficiency, health, and reproduction. The selection of these functional traits is constrained by their low heritability. In this study, variance components for CIN and LPE in the Italian Simmental cattle breed were estimated using genomic and pedigree information under the single-step genomic framework. A data set of 594,257 CIN records (from 275,399 cows) and 285,213 LPE records (from 1563,389 cows) was considered. Phenotypes were limited up to the third parity. The pedigree contained about 2 million animals, and 7,246 genotypes were available. Lactation persistency was estimated using principal component analysis on test day records, with higher values of the second extracted principal component (PC2) values associated with lower LPE, and lower PC2 values associated with higher LPE. Heritability of CIN and LPE were estimated using single-trait repeatability models. A multiple-trait analysis using CIN and production traits (milk, fat, and protein yields) was performed to estimate genetic correlations among these traits. Heritability for CIN in the single-trait model was low (0.06 ± 0.002). Unfavorable genetic correlations were found between CIN and production traits. A measure of LPE was derived using principal component analysis on test day records. The heritability and repeatability of LPE were 0.11 ± 0.004 and 0.20 ± 0.02, respectively. Genetic correlation between CIN and LPE was weak but had a favorable direction. Despite the low heritability estimates, results of the present work suggest the possibility of including these traits in the Italian Simmental breeding program. The use of a single-step approach may provide better results for young genotyped animals without their own phenotypes.

Bias in heritability estimates from genomic restricted maximum likelihood methods under different genotyping strategies.

We investigated the effects of different strategies for genotyping populations on variance components and heritabilities estimated with an animal model under restricted maximum likelihood (REML), genomic REML (GREML), and single-step GREML (ssGREML). A population with 10 generations was simulated. Animals from the last one, two or three generations were genotyped with 45,116 SNP evenly distributed on 27 chromosomes. Animals to be genotyped were chosen randomly or based on EBV. Each scenario was replicated five times. A single trait was simulated with three heritability levels (low, moderate, high). Phenotypes were simulated for only females to mimic dairy sheep and also for both sexes to mimic meat sheep. Variance component estimates from genomic data and phenotypes for one or two generations were more biased than from three generations. Estimates in the scenario without selection were the most accurate across heritability levels and methods. When selection was present in the simulations, the best option was to use genotypes of randomly selected animals. For selective genotyping, heritabilities from GREML were more biased compared to those estimated by ssGREML, because ssGREML was less affected by selective or limited genotyping.

Conservation status and historical relatedness of Italian cattle breeds.

BACKGROUND: In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. RESULTS: After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. CONCLUSIONS: This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.

A novel polymorphism in the oxytocin receptor encoding gene (OXTR) affects milk fatty acid composition in Italian Mediterranean river buffalo.

The oxytocin receptor, also known as OXTR, is a protein which functions as receptor for the hormone and neurotransmitter oxytocin and the complex oxytocin-oxytocin receptor plays an important role in the uterus during calving. A characterisation of the river buffalo OXTR gene, amino acid sequences and phylogenetic analysis is presented. The DNA regions of the OXTR gene spanning exons 1, 2 and 3 of ten Mediterranean river buffalo DNA samples were analysed and 7 single nucleotide polymorphisms were found. We focused on the g.129C > T SNP detected in exon 3 and responsible for the amino acid replacement CGCArg > TGCCys in position 353. The relative frequency of T allele was of 0·257. An association study between this detected polymorphism and milk fatty acids composition in Italian Mediterranean river buffalo was carried out. The fatty acid composition traits, fatty acid classes and fat percentage of 306 individual milk samples were determined. Associations between OXTR g.129C > T genotype and milk fatty acids composition were tested using a mixed linear model. The OXTR CC genotype was found significantly associated with higher contents of odd branched-chain fatty acids (OBCFA) (P < 0·0006), polyunsaturated FA (PUFA n 3 and n 6) (P < 0·0032 and P < 0·0006, respectively), stearic acid (C18) (P < 0·02) and lower level of palmitic acid (C16) (P < 0·02). The results of this study suggest that the OXTR CC animals might be useful in selection toward the improvement of milk fatty acid composition.

Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy.

Increased inbreeding is an inevitable consequence of selection in livestock populations. The analysis of high-density single nucleotide polymorphisms (SNPs) facilitates the identification of long and uninterrupted runs of homozygosity (ROH) that can be used to identify chromosomal regions that are identical by descent. In this work, the distribution of ROH of different lengths in five Italian cattle breeds is described. A total of 4095 bulls from five cattle breeds (2093 Italian Holstein, 749 Italian Brown, 364 Piedmontese, 410 Marchigiana and 479 Italian Simmental) were genotyped at 54K SNP loci. ROH were identified and used to estimate molecular inbreeding coefficients (FROH ), which were compared with inbreeding coefficients estimated from pedigree information (FPED ) and using the genomic relationship matrix (FGRM ). The average number of ROH per animal ranged from 54 ± 7.2 in Piedmontese to 94.6 ± 11.6 in Italian Brown. The highest number of short ROH (related to ancient consanguinity) was found in Piedmontese, followed by Simmental. The Italian Brown and Holstein had a higher proportion of longer ROH distributed across the whole genome, revealing recent inbreeding. The FPED were moderately correlated with FROH > 1 Mb (0.662, 0.700 and 0.669 in Italian Brown, Italian Holstein and Italian Simmental respectively) but poorly correlated with FGRM (0.134, 0.128 and 0.448 for Italian Brown, Italian Holstein and Italian Simmental respectively). The inclusion of ROH > 8 Mb in the inbreeding calculation improved the correlation of FROH with FPED and FGRM . ROH are a direct measure of autozygosity at the DNA level and can overcome approximations and errors resulting from incomplete pedigree data. In populations with high linkage disequilibrium (LD) and recent inbreeding (e.g. Italian Holstein and Italian Brown), a medium-density marker panel, such as the one used here, may provide a good estimate of inbreeding. However, in populations with low LD and ancient inbreeding, marker density would have to be increased to identify short ROH that are identical by descent more precisely.

Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures in Piedmontese and Italian Brown cattle breeds.

Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected.

Use of partial least squares regression to impute SNP genotypes in Italian cattle breeds.

BACKGROUND: The objective of the present study was to test the ability of the partial least squares regression technique to impute genotypes from low density single nucleotide polymorphisms (SNP) panels i.e. 3K or 7K to a high density panel with 50K SNP. No pedigree information was used. METHODS: Data consisted of 2093 Holstein, 749 Brown Swiss and 479 Simmental bulls genotyped with the Illumina 50K Beadchip. First, a single-breed approach was applied by using only data from Holstein animals. Then, to enlarge the training population, data from the three breeds were combined and a multi-breed analysis was performed. Accuracies of genotypes imputed using the partial least squares regression method were compared with those obtained by using the Beagle software. The impact of genotype imputation on breeding value prediction was evaluated for milk yield, fat content and protein content. RESULTS: In the single-breed approach, the accuracy of imputation using partial least squares regression was around 90 and 94% for the 3K and 7K platforms, respectively; corresponding accuracies obtained with Beagle were around 85% and 90%. Moreover, computing time required by the partial least squares regression method was on average around 10 times lower than computing time required by Beagle. Using the partial least squares regression method in the multi-breed resulted in lower imputation accuracies than using single-breed data. The impact of the SNP-genotype imputation on the accuracy of direct genomic breeding values was small. The correlation between estimates of genetic merit obtained by using imputed versus actual genotypes was around 0.96 for the 7K chip. CONCLUSIONS: Results of the present work suggested that the partial least squares regression imputation method could be useful to impute SNP genotypes when pedigree information is not available.

A single nucleotide polymorphism in the promoter region of river buffalo stearoyl CoA desaturase gene (SCD) is associated with milk yield.

An association study between the milk yield trait and the stearoyl-CoA desaturase (SCD) polymorphism (g.133A > C) in Italian Mediterranean river buffalo was carried out. A full characterization of the river buffalo SCD promoter region was presented. Genotyping information was provided and a quick method for allelic discrimination was developed. The frequency of the C allele was 0·16. Test-day (TD) records (43 510) of milk production belonging to 226 lactations of 169 buffalo cows were analysed with a mixed linear model in order to estimate the effect of g.133A > C genotype, as well as the effect of parity and calving season. The SCD genotype was significantly associated with milk yield (P = 0·02). The genotype AC showed an over-dominance effect with an average daily milk yield approximately 2 kg/d higher than CC buffaloes. Such a difference represents about 28% more milk/d. The effect of the genotype was constant across lactation stages. The contribution of SCD genotype (r(2)SCD) to the total phenotypic variance in milk yield was equal to 0·12. This report is among the first indications of genetic association between a trait of economic importance in river buffalo. Although such results need to be confirmed with large-scale studies in the same and other buffalo populations, they might offer useful indications for the application of MAS programmes in river buffalo and in the future they might be of great economic interest for the river buffalo dairy industry.

An association analysis between OXT genotype and milk yield and flow in Italian Mediterranean river buffalo.

The aim of this study was to evaluate possible associations between three SNPs at the oxytocin locus (AM234538: g.28C>T; g.204A>G and g.1627G>T) and two productive traits, milk yield and milkability, in Italian Mediterranean river buffaloes. Effects of parity, calving season and month of production were also evaluated. A total of 41 980 test-day records belonging to 219 lactations of 163 buffalo cows were investigated. The allele call rate was 98·8% and the major allele frequency for all the investigated loci was 0·76. The OXT genotype was significantly associated with milk yield (P=0·029). The TT genotype showed an average daily milk yield approximately 1·7 kg higher than GT buffaloes. Such a difference represents about 23% more milk/d. A large dominance effect (-1·17±0·43 kg) was estimated, whereas the contribution of OXT genotype (r(2)(OXT)) to the total phenotypic variance in milk yield was equal to 0·06. The TT genotype showed higher values also for the milk flow, even though the estimated difference did not reach a level of statistical significance (P=0·07). Such an association, among the first reported for the oxytocin locus in ruminants, should be tested on a population scale and possible effects on milk composition traits should be evaluated in order to supply useful indications for the application of marker-assisted selection programmes in river buffaloes.

Brain renin-angiotensin system modifies the blood pressure response to intracerebroventricular cadmium in rats.

In order to elucidate the involvement of the brain renin-angiotensin system (RAS) in cadmium intracerebroventricular (ICV) hypertension, we evaluated the effects of a pretreatment with different drugs: clonidine, an alpha(2) adrenergic agonist, enalapril and captopril, both ACE inhibitors, and saralasin, a competitive nonselective AT(1) and AT(2) receptor antagonist. We used a rat strain with low levels of kallikrein (LKR) that was more sensitive to ICV cadmium hypertension, compared with normal kallikrein rats (NKRs), the control strain. The interplay between the kallikrein-kinin system and the RAS in the LKR strain caused various hemodynamic alterations, which we believe were the result of elevated RAS activity in these animals. Moreover, we suggest that the defective kallikrein-kinin system in LKR may also cause an alteration in the activation of brain RAS in these animals. The LKR displayed elevated concentrations of plasma AII, hypertrophy of the myocardium, and initial alterations in the renal glomerulotubular system. With the exception of clonidine, all of the other drugs showed greater antihypertensive effects of differing statistical significance in LKR, compared with NKR. Both ACE inhibitors were able to significantly reduce pressor response to cadmium ICV in LKR throughout the experiment, whereas in NKR, they were only able to reduce the hypertensive peak of cadmium. A significant protective effect was also observed in LKR pretreated with saralasin, while no effect was observed in NKR. These findings confirm the presence of brain RAS activation in LKR and its contribution to the central control of pressor response to cadmium ICV.