Genomic selection is arguably the most promising tool for improving genetic gain in domestic animals to emerge in the last few decades, but is an expensive process. The aim of this study was to evaluate the economic impact related to the implementation of genomic selection in a simulated dairy cattle population. The software QMSim was used to simulate genomic and phenotypic data. The simulated genome contained 30 chromosomes with 100 cm each, 1666 SNPs markers equally spread and 266 QTLs randomly designated for each chromosome. The numbers of markers and QTLs were designated according to information available from Animal QTL (http://www.animalgenome.org/QTLdb) and Bovine QTL (http://bovineqtl.tamu.edu/). The allelic frequency changes were assigned in a gamma distribution with alpha parameters equal to 0·4. Recurrent mutation rates of 1·0e−4 were assumed to apply to markers and QTLs. A historic population of 1000 individuals was generated and the total number of animals was reduced gradually along 850 generations until we obtained a number of 200 animals in the last generation, characterizing a bottleneck effect. Progenies were created along generations from random mating of the male and female gametes, assuming the same proportion of both genders. Than the population was extended for another 150 generations until we obtained 17 000 animals, with only 320 male individuals in the last generation. After this period a 25 year of selection was simulated taking into account a trait limited by sex with heritability of 0·30 (i.e. milk yield), one progeny/cow/year and variance equal to 1·0. Annually, 320 bulls were mated with 16 000 dams, assuming a replacement rate of 60 and 40% for males and females, respectively. Selection and discard criteria were based in four strategies to obtain the EBVs assuming as breeding objective to maximize milk yield. The progeny replaced the discarded animals creating an overlapping generation structure. The selection strategies were: RS is selection based on random values; PS is selection based on phenotypic values; Blup is selection based on EBVs estimated by BLUP; and GEBV is selection based on genomic estimated breeding values in one step, using high (GBlup) and low (GBlupi) density panels. Results indicated that the genetic evaluation using the aid of genomic information could provide better genetic gain rates in dairy cattle breeding programs as well as reduce the average inbreeding coefficient in the population. The economic viability indicators showed that only Blup and GBlup/GBlupi strategies, the ones that used milk control and genetic evaluation were economic viable, considering a discount rate of 6·32% per year.

Feeding livestock with n-3 fatty acid (FA) sources (linseed, for example) is a common strategy to improve lipid quality of meat and milk products. However, in monogastric animals, linseed tegument decreases digestibility and alphalinolenic acid (ALA) uptake, while the whole linseed is well used by ruminants. In a context of increasing sustainability of feeding systems, providing monogastric animals and ruminants with linseed products adapted to their digestive systems is an important issue. This research paper addresses the hypotheses: (i) sieved extruded linseed (SEL) specific for ruminants is as or more effective than standard extruded linseed (ii) microalgae DHA Gold® is an interesting source of docosahexaenoic acid (DHA) in feedstuff and (iii) the effects of SEL and microalgae on milk characteristics are complementary and additive. Thirty-two cows were divided into 4 groups with different dietary n-3 fatty acid sources using a continuous design. All the diets were fed as mixed rations based on maize silage, energy concentrate and soybean meal. The first group received a control diet (CTRL) with no additional fat. The 3 other groups received SEL, microalgae DHA Gold® (ALG) and a mixture of microalgae DHA Gold® and SEL (SEL/ALG). Milk was collected from morning milkings after six weeks of dietary treatment. In SEL and SEL/ALG, ALA increased (+0·32 and +0·26% unit, respectively), and DHA increased in ALG and SEL/ALG (+0·43 and +0·15% unit, respectively) compared to CTRL, as a consequence of the initial composition of the n-3 FA sources. In SEL, milk yield, fat and protein contents, milk fat globule size and spontaneous lipolysis (measured to evaluate suitability for milk processing) were not different compared with CTRL. In ALG and SEL/ALG, milk yield decreased (−2·8 and −6·0 kg/d, respectively), fat content was halved, and fat globule size was reduced (−1·46 and −1·31 µm, respectively) compared to CTRL. Spontaneous lipolysis increased in ALG (+0·12 mEq/kg of milk) compared to CTRL. Protected microalgae and the doses of microalgae in the diet need further investigation to prevent FA modification in the rumen and the consequent deleterious effects on milk fat.

The aim of this research communication was to identify chromosome regions and genes that could be related to milk yield (MY), milk fat (%F) and protein percentage (%P) in Brazilian buffalo cows using information from genotyped and non-genotyped animals. We used the 90 K Axiom® Buffalo Genotyping array. A repeatability model was used. An iterative process was performed to calculate the weights of markers as a function of the squared effects of Single Nucleotide Polymorphism (SNP) and allele frequencies. The 10 SNPs with the largest effects for MY, %F and %P were studied and they explained 7·48, 9·94 and 6·56% of the genetic variance, respectively. These regions harbor genes with biological functions that could be related to the traits analyzed. The identification of such regions and genes will contribute to a better understanding of their influence on milk production and milk quality traits of buffaloes.

Local zebu cattle breeds in Indian villages are crossbred with exotic breeds at an unprecedented rate without utilising the full potential of genomic technologies. In addition to agriculture produce, livestock, particularly cattle, constitute a vital source of livelihood for farmers in India. Age-old agricultural practices, errant monsoon, and frequent crop failures have resulted in Maharashtra having the highest number of farmer suicides in the country. Local cattle breeds are considered low-yield breeds and thus are primarily used as beasts of burden. Information on functional gene variants in Indian cattle breeds is scant and limited to PCR-RFLP study in few breeds. In this study, 32 samples from 8 cattle breeds were obtained from remote villages of Maharashtra state. By using the re-sequencing technology, we sequenced 403 bp of the exon IV CSN3 allele and inferred its haplotypes. From 32 samples, 14 genotypes (G1–G14) defined by 7 single-nucleotide polymorphisms (SNP's) were identified. From these 14 genotypes, we reconstructed 3 haplotypes (H01, H02, and H03) and estimated their frequencies. Of the 3 haplotypes, two (H01 and H03) corresponded to CSN3*B4 and CSN3*B and CSN3*H and CSN3*G alleles, respectively. The third haplotype H02 was identified as a new allele and differed from CSN3*B4 and CSN3*B and CSN3*H and CSN3*G alleles by one nonsynonymous mutation at the position C5306T-Ile100Thr. The neighbour-joining tree reconstruction revealed haplotype sharing or hybridisation between B. t. indicus and B. t. taurus because the 3 haplotypes originated in this study clustered with A1, B2, B4, B, G, and H alleles, which were reported previously in both the subspecies of B. taurus. The occurrence of one new allele in a small sample size highlights the urgency to screen local zebu cattle breeds by using genomic tools for circumventing genetic erosion that is widespread in Indian villages in India.

The research reported in this Research Communication aimed to describe the influence of Toll-like receptor 4 gene polymorphisms on milk production traits in Chinese Holstein cows. Toll-like receptor 4 (TLR4) is an important member of the toll-like receptor gene family that is widely found in various organisms. Since TLR4 can identify molecular patterns from various pathogenic microorganisms and induce natural and acquired immunity, it plays an important role in disease resistance in dairy cows. Two single nucleotide polymorphisms (SNPs) of TLR4 (c.−226 G > C and c.2021 C > T) that were previously found to be associated with health traits were genotyped using Sequenom MassARRAY (Sequenom Inc., San Diego, CA) for Chinese Holstein cows (n = 866). The associations between SNPs or their haplotypes and milk production traits and somatic cell count were analyzed by the generalized linear model procedure of Statistics Analysis System software (SAS). The c.−226 G > C and c.2021 C > T showed low linkage disequilibrium (r2 = 0·192). There was no association between these two SNPs and SCC, but significant effects were found for SNP c.−226 G > C on test-day milk yield, fat content, protein content, and total solid and milk urea nitrogen (P < 0·05), and SNP c.2021 C > T and the SNP haplotypes on test-day milk yield, fat content, protein content, lactose content and total solids (P < 0·05). The software MatInspector revealed that c.−226 G > C was located within several potential transcription factor binding sites, including transcription factor AP-2. The polymorphisms c.−226 G > C and c.2021 C > T had significant effects on the milk production for Chinese Holstein, and these SNP could be used for molecular marker-assisted selection of milk production.

This Research Communication describes an investigation of the nutritional depletion of total mixed rations (TMR) by pest birds. We hypothesized that species-specific bird depredation of TMR can alter the nutritional composition of the ration and that these changes can negatively impact the performance of dairy cows. Blackbirds selected the high energy fraction of the TMR (i.e., flaked corn) and reduced starch, crude fat and total digestible nutrients during controlled feeding experiments. For Holsteins producing 37·1 kg of milk/d, dairy production modeling illustrated that total required net energy intake (NEI) was 35·8 Mcal/d. For the reference TMR unexposed to blackbirds and the blackbird-consumed TMR, NEI supplied was 41·2 and 37·8 Mcal/d, and the resulting energy balance was 5·4 and 2·0 Mcal/d, respectively. Thus, Holsteins fed the reference and blackbird-consumed TMR were estimated to gain one body condition score in 96 and 254 d, and experience daily weight change due to reserves of 1·1 and 0·4 kg/d, respectively. We discuss these results in context of an integrated pest management program for mitigating the depredation caused by pest birds at commercial dairies.

The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffalo SCAP gene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed the SCAP gene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile of SCAP gene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffalo SCAP gene were identified, six of them (g.1717600A>G, g.1757922C>T, g.1758953G>A, g.1759142C>T, g.1760740G>A, and g.1766036T>C) were found to be significantly associated with 305-day milk yield. Thus, buffalo SCAP could sever as a candidate gene affecting milk production traits in buffalo and the identified SNPs might potentially be genetic markers.

Bovine spongiform encephalopathy (BSE) involves insertion/deletion (in/del) polymorphisms in the prion protein gene (PRNP) promoter region that are associated with vulnerability to disease progression. Recently, a second member of the prion gene family, prion-like protein gene (PRND), has been reported to show the PRND R132Q polymorphism, which is associated with the susceptibility to BSE in German Fleckvieh breeds. The objective of this study was to examine the genotype, allele, and haplotype frequencies of PRND gene in Korean cattle and evaluate their susceptibility to BSE. We did this in 277 Korean native cattle (Hanwoo) and 124 Korean dairy cattle (Holstein) by direct sequencing and compared the R132Q genotype frequency between BSE-affected German cattle and Korean cattle. The results indicated a total of 5 single nucleotide polymorphisms (SNPs) including PRND c.149G > A (p.50Arg > His; R50H), PRND c.285C > T (C4819T), PRND c.395G > A (p.132Arg > Gln; R132Q) and PRND c.528T > A (T5063A) in the open reading frame (ORF) and c.602C > G in the 3′ untranslated region (UTR) of exon 2 in Korean Holstein and Hanwoo cattle. Except for c.149G > A, the remaining 4 SNPs showed significantly different genotype and allele frequencies between the Korean Holstein and Hanwoo (P < 0·01). There were no significant differences in genotype distribution of c.395G > A SNP between BSE-affected German and Korean Holstein cattle (P = 0·6778), but a significant difference was detected between BSE-affected German cattle and Hanwoo cattle (P = 0·0028). The results suggest that Hanwoo cattle may possess a relatively more BSE-resistant genotype than Korean Holstein cattle.

This Research Communication describes the polymorphisms in the coding region of DGAT1 gene in Riverine buffalo, Swamp buffalo and crossbred buffalo, and associations between polymorphisms and milk production performance in Riverine buffalo. Two polymorphisms of DGAT1were identified, located in exon 13 and exon 17, respectively. The distribution of the genotypes of the two SNP loci in different buffalo population varied, especially the polymorphism located in exon 13 which was not found in the Swamp buffalo. Moreover, SNP located in exon 17 was a nonsynonymous switch resulting in the animo acid sequence changed from an arginine (Arg) to a histidine (His) at position 484. Both SNPs were in Hardy–Weinberg equilibrium, and the polymorphism of g.8330T>C in the exon 13 was significantly associated with peak milk yield, total milk yield and protein percentage. The C variant was associated with an increase in milk yield and peak yield but less in protein percentage compared with the T variant. The polymorphisms of g.9046T>C in exon 17 were significantly associated with fat percentage, in that the buffaloes with TT genotype had a significantly higher fat percentage than those with CC genotype. These findings reveal the difference in the genetic evolution of the DGAT1 between Riverine buffalo and Swamp buffalo, and provide evidence that the DGAT1 gene has potential effects for Riverine buffalo milk production traits, which can be used as a candidate gene for marker-assisted selection in buffalo breeding.

The aims of the study reported in the Research Communication were to evaluate changes of macrominerals and major calcitropic hormone concentrations in 51 healthy dairy cows over the peripartum period, and to compare those cows with 51 cows subject to subclinical hypocalcaemia (SCH) on calving day. The results showed that serum calcium (Ca) and potassium (K) concentrations were lowest in the healthy periparturient dairy cows at parturition, while sodium (Na) and parathyroid hormone (PTH) concentrations were highest. Serum magnesium (Mg), chloride (Cl) and phosphorus (P) concentrations were highest 1 wk prepartum, however, the concentration of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] was highest 1 wk postpartum. The dairy cows with subclinical hypocalcaemia (SCH) had significantly lower serum levels of Ca, K, Na, Mg, Cl, 1,25(OH)2D3 and glucose and had significantly higher levels of serum P, non-esterified fatty acids (NEFA) and β-hydroxybutyrate (BHBA) than their healthy counterparts on calving day. However, the serum calcitonin and PTH concentrations were not significantly different between the two groups. These data demonstrated that the concentrations of macrominerals and major calcium regulating hormones of cows change dramatically over the peripartum period. Furthermore, SCH was associated with a risk of the development of ketosis and fatty liver.

The objective of the study reported in this Research Communication was to investigate the association of polymorphisms in the insulin-like growth factor receptor 2 (IGF2R) gene with milk traits in 283 Polish Holstein-Friesian (PHF) cows from the IGAB PAS farm in Jastrzębiec. IGF2R regulates the availability of biologically active IGF2 which is considered as a genetic marker for milk or meat production in farm animals. Two novel genetic polymorphisms were identified in the bovine IGF2R gene: a polymorphic TG-repeat in intron 23 (g.72389 (TG)15-67), and a g.72479 G > A SNP RFLP-StyI in exon 24. The following milk traits were investigated: milk yield, protein and fat yield, SCC and lactose content. To determine the influence of the IGF2R STR and SNP genotypes on the milk traits, we used the AI-REML (average information restricted maximum likelihood) method with repeatability, multi-trait animal model based on test-day information using DMU package. Statistical analysis revealed that the G/A genotype (P ≤ 0·01) was associated with milk and protein yield, lactose content and somatic cell count (SCC) in Polish HF cows. TGn (29/22, 28/29, 28/22, 28/28) genotypes were associated with high values for milk, (28/22, 28/23) with protein and fat yield, (25/20) with lactose content, and (29/33, 28/28) with low SCC. We suggest that the IGF2R gene polymorphisms could be useful genetic markers for dairy production traits in cattle.

The experiment reported in this Research Communication aimed to determine the combined effects of early weaning and post-weaning feeding level on growth, reproductive parameters and milk yield in Alpine goats. Sixty-four Alpine goat kids were weaned abruptly at either 12·2 (±1·40) kg (40 d of age, E) or 17·7 (±2·30) kg (60 d of age, No). After weaning, E and No goats were subjected to 2 feeding strategies (n = 16): ad libitum concentrate until 130 d of age and then 620 g DM/d/goat until 200 d of age (EC and NoC) or ad libitum concentrate until 200 d of age (EAL and NoAL). Goats were weighed twice a month until 200 d of age. Pregnancy rate and litter size were recorded. Daily milk yield was measured by milk meter during the first lactation. Up to 60 d of age, average daily gain (ADG) of E kids was significantly lower than No kids. From 60 to 130 d of age, ADG of the four treatments were not different. After 130 d of age, EC and NoC kids had lower ADG than EAL and NoAL kids. Pregnancy rates of EAL and NoAL goats were lower than those of EC and NoC. Milk yield was not modified by weaning weight or feeding management. Milk quality was not affected by any treatment. To conclude, the age at weaning as well as the feeding level after weaning did not negatively impact growth and milk yield. We hypothesise that the establishment of the lactation function is not impacted by rearing management. Hence, decreasing the age at weaning could be an interesting way to reduce the cost of the rearing period in goat kids.

This research paper addresses the hypothesis that dietary pioglitazone (PGT), as synthetic and specific ligand for PPAR-γ or walnut meal (WM) as a natural ligand for PPAR-γ, affect plasma metabolites and reduce the oxidative status in high body condition score (BCS) dairy cows (≥4 BCS). Total of 36 multiparous Holstein cows were randomly assigned to one of the dietary treatments: 1- Control (basal diet; CTR), 2- Walnut meal (9·45% walnut meal of DMI; WM), and 3- Pioglitazone (6 mg/kg BW; PGT). The experimental diets were fed from parturition time to 21 d postpartum. Results showed that the PGT supplementation increased dry matter intake (DMI) (22·95 kg/d) compared to the CTR (21·45 kg/d) and WM (21·78 kg/d) groups. Results showed that milk yield and milk composition were not affected by the experimental diets. Body condition score losses tended to be higher in the CTR group compared to the PGT and WM cows. The PGT group had higher plasma insulin compared to the CTR group (11·84 vs. 10·68 mIU/l), and WM cows had intermediate plasma insulin. The PGT cows had lower plasma non esterified fatty acid (NEFA) and tended to have lower β-hydroxy butyric acid (BHBA) than the CTR group. Feeding pioglitazone decreased plasma malondialdehyde (MDA) and increased plasma total antioxidant capacity (TAC) and superoxide dismutase (SOD) compared to the CTR and WM groups. It was concluded that dietary pioglitazone had positive effects on DMI, BCS change, blood metabolites and oxidative status in fresh dairy cows with high pre-calving BCS. The anti-oxidant effects of walnut meal were not supported by the present data.

The majority of the work today regarding the effects of extended milking intervals has focused on dairy cattle and only to a limited extent on dairy goats and sheep. The aim of this study was to investigate the effect of different non-milking intervals on milk yield and composition, mammary physiology and welfare indices in dairy ewes. Thirty-six multiparous ewes in late lactation were allocated to one of four groups of nine and subjected to 24, 48 or 72 h of non-milking or normal milking interval (12 h) (group A, B, C and D, respectively). Data showed that there were no significant differences in milk yield among the experimental groups during the third day after re-milking. Furthermore, no significant differences in milk lactose, protein and fat concentration among the experimental groups were observed after 7, 14 and 21 d of re-milking, respectively. Non-milking for 72 h resulted in a temporary increase of sodium concentration, Na + /K + ratio and enzymatic activities of plasmin (PL), plasminogen (PG) and plasminogen activator (PA) in milk. However, these parameters had similar values among the experimental groups on day 5 after re-milking. The concentration of lactose in blood was also significantly increased as a result of the 72 h non-milking interval and returned to its initial levels the second day after re-milking. These data, taken together, suggest that early involution events that occurred as an effect of non-milking were fully reversible within a short period of time. Finally, no significant signs of welfare impairment were observed in ewes due to extended milking intervals. In conclusion, non-milking up to 72 h had no negative effects on milk yield and composition, mammary physiology and welfare parameters in dairy ewes.

The objective of this study was to demonstrate the usefulness of an immunomagnetic method to purify subpopulations of milk somatic cells. The experiment was conducted on milk samples collected from healthy cows (n = 17) and from cows with clinical mastitis (n = 24) due to a Staphylococcus aureus natural infection. A two-step immunomagnetic purification was applied to simultaneously separate three somatic cell subpopulations from the same milk sample. Total RNA was extracted and qPCR was performed to determinate mRNA levels of innate immunity target genes in purified somatic cell subpopulations. Good quality and quantity of RNA allowed the reference gene analysis in each cell subpopulation. An up-regulation of the main genes involved in innate immune defence was detected in separated polymorphonuclear neutrophilic leucocytes-monocytes and lymphocytes of mastitic milk. These results and flow cytometric analysis suggest that the immunomagnetic purification is an efficient method for the isolation of the three populations from milk, allowing the cells to be studied separately.

The experiments reported in this Research Paper aimed to study the effects of mustard and cumin seeds inclusion on feed utilisation, milk production, composition, and profile of milk fatty acids in lactating Damascus goats. The study was a completely randomised design with repeated measurements in time using fifteen goats (6 ± 2 d of lactation) divided into 3 treatments (5 goats per treatment). Goats were offered a control diet of berseem clover and concentrates (1 : 1 dry matter (DM) basis) or the control diet supplemented with either 10 g/d of dried mustard seeds (mustard treatment) or 10 g/d of cumin seeds (cumin treatment) for 12 weeks. Treatments had no effect (P > 0·05) on feed intake, but enhanced (P < 0·05) digestibility of DM, organic matter, non-structural carbohydrates, and fibre fractions. Digestibility was greater (P < 0·001) with cumin treatment compared with mustard treatment. Mustard and cumin seeds had greater (P < 0·05) ruminal total short chain fatty acids (SCFA) production, and molar proportion of propionate, with greater (P < 0·001) SCFA production for cumin vs. mustard treatment. Mustard and cumin seeds increased (P < 0·05) concentrations of serum total proteins, globulin, and glucose and lowered (P < 0·05) serum cholesterol concentration. Mustard and cumin seeds inclusion elevated milk production (P = 0·007), while cumin increased milk contents (P < 0·05) of fat and lactose. Cumin treatment lowered (P < 0·05) milk saturated fatty acids (SFA) and had greater total unsaturated fatty acids (UFA) and total conjugated linoleic acid (CLA) contents. Overall, supplementing diets of Damascus goats with mustard or cumin seeds at 10 g/daily enhanced feed digestion, ruminal fermentation, milk yield (actual production by 6·8 and 11·1%, and energy corrected milk yield by 10·1 and 15·4%, respectively) and positively modified milk fatty acid profile with a 3·9% decrease in milk individual and total SFA, and an increase in individual and total UFA by about 9·7%, and total CLA by about 23·1%.