Breeding Index Research Articles

Characterization of malaria vectors in Huye District, Southern Rwanda

Background: Effective control of malaria requires knowledge of vector species, their feeding and resting behaviour as well as breeding habitats. The objective of this study was to determine malaria vector species abundance and identify their larval habitats in Huye district, southern Rwanda.Methods: Adult mosquitoes were collected indoors using light trap and pyrethrum spray catch techniques, and outdoors using light traps. Female Anopheles mosquitoes were identified to species level by morphological characteristics. Enzyme-linked Immunosorbent Assay (ELISA) was used to screen for Plasmodium falciparum circumsporozoite protein and host blood meal sources. Anopheles larvae were sampled using dippers and raised into adult mosquitoes which were identified morphologically.Results: Anopheles gambiae sensu lato comprised of 70% of the 567 Anopheles collected. Other Anopheles species identified were An. funestus 4%, An. squamosus 16.5%, An. maculipalpis 6.5%, An. ziemanni 1.7%, An. pharoensis 1.2 % and An. coustani 0.1%. The majority, 63.5% of the collected mosquitoes were from indoors collections. The overall human blood index was 0.509. The P. falciparum circumsporozoite protein was found in 11 mosquitos including 8 Anopheles gambiae s.l. and 3 secondary vectors out of the 567 tested. The overall sporozoite rate was 1.9%. A total of 661 Anopheline larvae from 22 larval habitats were collected. They comprised of An. gambiae s.l. (89%) and An. ziemanni (11%). The absolute breeding index was 86.4%. The most common larval habitats were in full sunlight with still water like rice paddies and pools of stagnant water.Conclusion: These findings show that Anopheles gambiae s.l. is the dominant malaria vector in the area with other vectors playing a secondary role in malaria transmission. Malaria interventions need to be strengthened to reduce even further the malaria transmission in the area.

Evaluation of collection samples of spring durum wheat for yielding capacity and breeding indices

Evaluation of collection samples of spring durum wheat for yielding capacity and breeding indices

Optimising the proportion of selection candidates measured for feed intake for a beef cattle breeding objective that includes methane emissions.

Reducing daily methane production (DMP) via selection for lower estimated daily (pasture) feed intake (DFI) has the potential to be more cost effective than direct selection for DMP. Daily feed intake has a high heritability and high genetic correlation to DMP and has a potential lower cost of measurement. This study's main aim was to determine for a breeding nucleus the optimal proportion of randomly selected young male and female cattle in which to estimate DFI. This optimum proportion was determined by modeling the measurement costs and response to selection of Angus cattle on a (standard industry) Angus breeding index (ABI) augmented with DFI and DMP in a combined breeding objective (BO), but without DMP being measured. For the assumed herd structure and considering a 20 yr planning horizon, the highest net present value (NPV) occurred when 64% of males and no females were measured for DFI. The highest breakeven DFI test cost (A$41.51/head) and highest returns on investment (ROI) occurred when 36% of males and no females had DFI estimates. Higher ROI were achieved when all males had DFI estimates before any females had DFI estimates. There was a diminishing increase in rate of genetic gain when moving from 36% to 64% of males with DFI estimates, thus ROI decreased from 29.7% to 23.1%. When 36% of males had DFI estimates (and no females), herd DMP genetic gain was slightly positive as the DMP reduction per generation from male selection (-0.086) was more than offset by the DMP increase per generation from female selection (+0.110). The selection response for DMP only became negative when at least 40% of males had DFI estimates. Having 64% of males with DFI estimates resulted in a predicted genetic decrease in DMP (-0.018 kgCOe/head per yr), compared to an increase of 0.052 kgCOe/head per yr when no animals had DFI estimates. The optimum proportion of males with DFI estimates (36 to 64%) depends on the breeders attitude toward ROI and the value of genetic change for DMP. Sensitivity analysis showed that the economic value (EV), heritability and genetic variance of DFI had a higher impact on the NPV and ROI outcomes than parameters related to ABI and DMP, so future work should focus on obtaining robust estimates for DFI parameters. Higher EV for feed intake and DMP would result in higher percentages of animals being profitably measured for DFI, leading to larger reductions in DMP.

Maize Stalk Lodging: Morphological Determinants of Stalk Strength

An incomplete understanding of stalk strength and stalk lodging impedes efforts to improve maize (Zea mays L.) production. To develop a more complete understanding of stalk strength, the current study examined the effect of stalk morphology on stalk bending strength. A detailed geometric analysis was conducted on five varieties of dent corn sown at five planting densities in two replicates at each of two locations near Greenville, IA, in 2013. Stalks were imaged using high‐resolution X‐ray computed tomography, and morphological features of the stalk were quantified using customized computer code. After scanning, stalks were subjected to mechanical tests to determine stalk bending strength and rind penetration resistance. The section modulus of the stalk (a morphological quantity derived from engineering beam theory) was found to be highly predictive of stalk strength, and its predictions appear to be largely unaffected by common confounding factors such as hybrid and planting density. By assuming the stalk cross section to be a hollow ellipse, the section modulus of the stalk can be estimated using measurements of stalk diameter and rind thickness (which does not require computerized tomography scanning). The elliptical section modulus is highly predictive of stalk strength, does not appear to be confounded by experimental variables, and can be obtained using a pair of calipers. Thus, it demonstrates potential as a selective breeding index to improve lodging resistance. In the current study, the elliptical section modulus predicted stalk strength with four times the accuracy of rind penetration resistance (a more common method used in breeding studies).

132 OVERVIEW OF FERTILITY TRAITS IN RUSSIAN HOLSTEIN BULLS USING GENOME-WIDE ASSOCIATION

Holsteins are the most widely distributed cattle breed in Russia. To achieve improvement of both milk production and fertility traits, principles were elaborated to use genomic approaches together with breeding strategies to develop a common breeding index. Combining semen-quality measures for sires with the cows’ reproduction records makes it possible to resolve the problems with decreased conception rates and semen production. Our objective was to search the genomic regions and associated markers for bulls’ fertility traits in Russian Holstein cattle. For the first step, 282 bulls were genotyped using the Bovine SNP50 BeadChip (Illumina Inc., San Diego, CA, USA). The data set originated from the Moscow AI station including records for semen volume (SV), sperm concentration (SC), average SV for multiple ejaculates collected from one sire (ASV), motility (Mt), and number of spermatozoa (NS). The data set consisted of 14,490 records, which varied between 10 and 328 per animal, with 104 sires in the data set. The average age of sires was 80.1 ± 0.3 months. For sires with own records, the deregressed estimated breeding values were calculated using BLUP AM, whereas for the sires without records direct genomic values (DGV) were calculated through GBLUP. The DGV values were used as the animal’s pseudo-phenotypes for a common data set. After quality check in Plink 1.07, 41,435 SNP were taken. Bonferroni correction test for detection of significant associations was applied as P < 1.21 × 10−6. The values for the heritability were 0.322, 0.202, 0.366, 0.014, and 0.169 for SV, SC, ASV, Mt, and NS, respectively. The SNP with a direct significant effect on SV and ASV were identified: ARS-BFGL-NGS-100206 (P = 1.5 × 10−7), BTA-89872-no-rs (P = 6.0 × 10−8), ARS-BFGL-NGS-33119 (P = 2.7 × 10−7), Hapmap26947-BTA-133787 (P = 5.0 × 10−7), BTA-30092-no-rs (P = 9.8 × 10−7), ARS-BFGL-BAC-6515 (P = 1.0 × 10−7), and BTB-01625220 (P = 4.2 × 10−8). For SC and NS traits, the polymorphisms ARS-BFGL-NGS-57433 (P = 7.4 × 10−7) and ARS-BFGL-NGS-12662 (P = 5.1 × 10−7) were found. Two QTL for Mt including 11 SNP were detected on BTA1 (146.3–146.9 Mb) and BTA9 (76.9–77.1 Mb). The DGV effect of SNP (R2) ranged from 8.0 to 10.4% of additive genetic variance. The genes SOX5 (BTA12), PERP (BTA9), and EPT1 (BTA11) were associated with embryonic development, cell death, or apoptosis and synthesis of selenoproteins. Our results may be used to select donor cows for oocytes or embryo collection in the focus of genomic selection. Supported by the Federal Agency for Scientific Organizations #0600–2014–0007.6 and by the Russian Ministry of Education and Science #RFMEFI60414X0062.

Factors associated with intramammary infection in dairy cows caused by coagulase-negative staphylococci, Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Corynebacterium bovis, or Escherichia coli

The aim of this study was to determine risk factors for bovine intramammary infection (IMI) associated with the most common bacterial species in Finland. Large databases of the Finnish milk-recording system and results of microbiological analyses of mastitic milk samples from Valio Ltd. (Helsinki, Finland) were analyzed. The study group comprised 29,969 cows with IMI from 4,173 dairy herds. A cow with a quarter milk sample in which DNA of target species was detected in the PathoProof Mastitis PCR Assay (Thermo Fisher Scientific, Waltham, MA) was determined to have IMI. Only cows with IMI caused by the 6 most common pathogens or groups of pathogens, coagulase-negative staphylococci (CNS), Staphylococcus aureus, Streptococcus uberis, Streptococcus dysgalactiae, Corynebacterium bovis, and Escherichia coli, were included. The control group comprised 160,176 IMI-free cows from the same herds as the study group. A multilevel logistic regression model was used to study herd- and cow-specific risk factors for incidence of IMI. Pathogen-specific results confirmed those of earlier studies, specifically that increasing parity increases prevalence of IMI regardless of causative pathogen. Holsteins were more susceptible to IMI than Nordic Reds except when the causative pathogen was CNS. Occurrence of IMI caused by C. bovis was not related to milk yield, in contrast to IMI caused by all other pathogens investigated. Organic milk production was associated with IMI only when the causative pathogen of IMI was Staph. aureus; Staph. aureus IMI was more likely to occur in conventional than in organic production. Cows in older freestall barns with parlor milking had an increased probability of contracting an IMI compared with cows in tiestall barns or in new freestall barns with automatic milking. This was the case for all IMI, except those caused by CNS, the prevalence of which was not associated with the milking system, and IMI caused by Staph. aureus, which was most common in cows housed in tiestall barns. A better breeding index for milk somatic cell count was associated with decreased occurrence of IMI, indicating that breeding for improved udder health has been successful in reducing the incidence of IMI caused by the most common pathogens in Finland. In the Finnish dairy sector, the importance of other measures to control IMI will increase as the Holstein breed progressively takes the place of the Nordic Red breed. Attention should be paid to hygiene and cleanliness, especially in old freestall barns. Based on our results, the increasing prevalence of automatic milking is not a reason for special concern.

Breeding systems in Angiosperms: novel inferences from a new analytical approach

A novel analytical approach to classify breeding systems in Angiosperms combining statistical and conceptual criteria is proposed, which will allow to describe and compare available mating system data in an unified form. Four breeding system indexes (BSI) were combined: Index of Agamospermy, Index of Spontaneous Self-Pollination (ISSP), Index of Self-Fertility (ISF), and Index of Self-incompatibility. Their values, ranging from 0 to ∞, were analyzed using t tests to discriminate experimental breeding index values from 0 and 1.0. For each index, five discrete categories were described. The composite of the four BSI assigned to a species represents an integrated characterization of its reproductive system. A magnitude measure (M) describes the strength of each BSI assigned to a species. Indexes of inbreeding and outbreeding depression were also examined for each species. Published data from 1908 taxa were used to determine composite breeding systems. Frequencies of breeding index categories across the four BSI for the entire data set were determined. Non-agamospermous species dominated. Non-spontaneous self-pollinating and xenogamous species were the most frequent categories observed for ISSP and ISF indexes, respectively. The largest group of species examined was partially self-incompatible. Actual number of composite breeding systems inferred based on our analysis represents a small fraction (8.9 %) of all mathematically possible ones. Similarly, the observed combinations between results obtained from the four pollination tests and estimates of natural reproductive efficiency were only 22.1 % of all mathematically possible combinations. Within Angiosperms, there is a marked trend toward evolution of partial self-incompatibility with significant inbreeding depression.

Uterine disease and its effect on subsequent reproductive performance of dairy cattle: a comparison of two cow-side diagnostic methods

The aim of this study was to compare vaginal mucus scoring and ultrasonographic assessment of uterine content as predictors of future reproductive performance of dairy cows. Holstein-Friesian cows (n = 493) from seven commercial dairy farms were enrolled in this study. All cows received one prebreeding examination (PBE) between 21 and 38 days after parturition. During the PBE, vaginal mucus was scored (MS) and the transrectal ultrasonographic examination of the uterus to assess content (UTS) took place. The MS was scored on a scale of 0 to 3 using a Metricheck device and appearance of the uterus on transrectal ultrasound was scored on a scale of 0 to 4 based on the presence and consistency of intraluminal fluid. Other data collected from each cow included the farm ID (F_ID), conception rate to first service, length of breeding window, lactation number, calving month, body condition score (BCS) at calving, BCS loss after calving, BCS at PBE, days in milk at PBE, 305 day milk yield, economic breeding index (EBI), EBI fertility subindex and EBI health subindex. For each cow these parameters were analyzed using univariate Cox proportional hazard model to evaluate the effect of variables on the reproductive performance, measured as positive pregnancy status (PS) at the end of the breeding season. Receiver-operating characteristic analysis of the diagnostic tests compared with each other took place as well. Cows with positive UTS were 7.75 times more likely to have a positive MS as well (P < 0.01). The PS hazard ratios for cows with UTS0, 1, 2, 3, and 4 were 1; 0.84; 0.53; 0.78; 0.28, respectively (P < 0.001). For the cows with MS0, 1, 2, and 3, the PR hazard ratios were 1; 1.02; 0.51; 0.75; respectively (P = 0.01). Conception rate to first service, breeding window, and PS were significantly better for the cows with UTS0, 1 and 2 compared with the cows with UTS3–4 and MS2+3 (68%; 18%, [P = 0.020]; 29; 75 days, [P = 0.001]; 95%; 55%; [P = 0.010], respectively). There was a significant effect of days in milk at PBE in relation to the subsequent PS (P = 0.04). Cows in lactation number 5 or more were less likely (r = 0.69) to get in calf before the end of the breeding season than cows in their first lactation. Cows that calved later in the season were less likely to become pregnant before the end of the breeding season (P < 0.03). Younger cows (lactation <5) and cows with MS and UTS scores of 0 and −1 had significantly better reproductive performance (P < 0.04). Receiver-operating characteristic analysis showed that MS did not always reflect UTS, but cows with positive UTS were 7.75 times more likely to have a positive MS (P < 0.01) and a high UTS had a larger negative effect on time to PS than a high MS (P < 0.05). In conclusion, both prebreeding vaginal mucus evaluation with the Metricheck device and an ultrasound scan of the uterus serve as a good predictor of the subsequent PS. There is overlap between the two systems, but the best predictor for future reproductive outcome of the cow is a combination of both.

Production and diseases of dairy cows: Viewpoint for discussion regarding the significance of genetics (cause) and management (effect)

The milk production of dairy cows has been increased during recent decades through animal-husbandry, improved feeding regime, extensive veterinary service and proper management. It can be assumed that this tendency will be continued in the future. However, the incidence of diseases (production diseases), including ketosis, fat liver, mastitis, lameness, metritis and disturbed fertility, has also increased and exhibits a close genetic correlation with milk yield. The pathogenesis of these diseases is - more or less - causally related to the negative energy balance and hence, is a consequence of selection for high milk yield. The genetic disposition and health risks are modulated by the management of dairy cows and both factors contribute to the large variation of diseases in practice. An analysis of production diseases must therefore distinguish between the genetic disposition (cause) and the management (effect). An effective improvement of the complex of production diseases includes the critical discussion of the current breeding index for dairy cows.

71 CIRCULATING microRNAs AS POTENTIAL BIOMARKERS OF EARLY PREGNANCY IN HIGH-PRODUCING DAIRY COWS

Lactation induces changes in the metabolic status of postpartum dairy cows that negatively affects the likelihood of pregnancy establishment. At present, pregnancy diagnosis with confidence is only possible after the third week of gestation. Earlier diagnosis could facilitate earlier re-breeding, reduce calving intervals, and improve profits for the industry. MicroRNAs (miRNAs) released in body fluids have been identified as minimally invasive biomarkers of several diseases. In addition, distinct miRNA profiles have been directly related to specific stages of human pregnancy. The aim of this study was to profile circulating miRNAs in the blood of high-producing dairy cows in order to identify biomarkers of early pregnancy. In-calf primiparous Holstein-Friesian cows (n = 22) with a similar economic breeding index were used. At calving, cows were randomly assigned to one of two groups: (1) lactating (n = 11; milked twice per day) or (2) non-lactating (n = 11; dried off immediately). Around 65 to 75 days postpartum (dpp), oestrous cycles were synchronized and a single embryo from a superovulated Holstein-Friesian donor was transferred at Day 7 post-oestrus. Plasma samples were analysed at Day 13 (initiation of conceptus elongation) and at Day 19 (initiation of implantation). Pregnancy rate, established by the presence of conceptus at Day 19, was 5/11 (45%) for lactating and 8/11 (73%) for non-lactating cows, respectively. Circulating miRNA levels were profiled in 4 animals per group in non-lactating pregnant, and lactating pregnant and nonpregnant cows at selected timepoints using Illumina HiSEqn 2000 (Illumina Inc., San Diego, CA, USA) for smallRNA sequencing. Annotation and discovery of miRNAs were done using MirDeep2, and read counts were analysed using edgeR to identify differentially expressed miRNAs. Target genes analysis was run with miRWalk and pathways interactions were built using Cytoscape (P ≤ 0.05). Differentially abundant miRNAs between lactating and non-lactating cows were found at both time points (FDR ≤ 0.05). At Day 13, non-lactating cows had a distinct miRNA profile compared with lactating cows showing 8 differentially expressed miRNA (6 v. pregnant and 2 v. nonpregnant cows). At Day 19, no significant differences were found within pregnant cows, but 5 differentially expressed miRNAs were identified between pregnant and nonpregnant cows, regardless of metabolic status. Interestingly, one miRNA, bta-mir140, was up-regulated in non-lactating pregnant cows from Day 13 onwards compared with nonpregnant cows. Furthermore, the same miRNA was up-regulated in lactating pregnant v. nonpregnant at Day 19. Among bta-mir140 target genes, CD274, SLC44A4, CXCL12, and SIRPA were strictly associated with immune tolerance. In conclusion, the maternal plasma miRNome may represent an early indicator of pregnancy status. In particular, the up-regulation of bta-mir140 in pregnant cows suggests that this miRNA may be a good candidate as an early biomarker of fertility. Furthermore, the positive correlation between this miRNA and pathways involved in T-cell response may indicate a role of immune tolerance in preventing rejection at the initiation of implantation.

Reproductive Indices of Rainbow Trout (Oncorhynchus mykiss) Females from a Trout Farm

Rainbow Trout (Oncorhynchus mykiss) breeding females have been studied from the standpoint of phenotypic characteristics and breeding indices for establishing future protocols of selection and improvement. The relative fecundation (RF) has been determined to a medium value of 335.88 ± 17.723 g and a variability coefficient of 52.77%. The high value of the variability coefficient is due to the fact that this is the first breeding generation of trout nursery and has not been submitted to any selection and improvement activities up to the present. From the breeding performance standpoint, the medium value of the number of eggs (TNE) obtained has been of 8127.44 ± 478.532, the medium egg weight (EW) has been of 0.06 ± 0.001g, the medium diameter of one egg (ED) = 4.16 ± 0.029 mm and the medium volume of one egg (EV) has been of 65.63 ± 1.223 mm3. The following breeding indices have also been calculated: gonadosomatic report (GR), Behning fertilizing coefficient (BFC) and the Williams absolute fecundity indices (WAFI). The outcome results have been the following: GR = 14.82 ± 0.587; BFC = 16.82 ± 0.563; WAFI = 5.77 ± 0.333. The values of the correlations point out the necessity of breeding selection work in order to improve the breeding performances.

Differential gene expression in the endometrium reveals cytoskeletal and immunological genes in lactating dairy cows genetically divergent for fertility traits.

Profitable milk production in dairy cows requires good reproductive performance. Calving interval is a trait used to measure reproductive efficiency. Herein we used a novel lactating Holstein cow model of fertility that displayed genetic and phenotypic divergence in calving interval, a trait used to define reproductive performance using a national breeding index in Ireland. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility (Fert+; n=7) or very poor genetic merit for fertility (Fert-; n=6). We tested the hypothesis that Fert+ cows would have a corresponding detectable difference in endometrial gene expression compared with the Fert- cows. To do this, we sequenced the transcriptome of endometrial biopsies collected on Day 7 of the oestrous cycle (non-pregnant). This is an important stage for uterine remodelling and initiation of histotroph secretion. Significant differential expression (false discovery rate-adjusted P<0.1) of 403 genes between Fert+ and Fert- cows was found. A novel network-based functional analysis highlighted 123 genes from three physiologically relevant networks of the endometrium: (1) actin and cytoskeletal components; (2) immune function; and (3) ion transportation. In particular, our results indicate an overall downregulation of inflammation-related genes and an upregulation of multiple ion transporters and gated-voltage channels and cytoskeletal genes in Fert+ cows. These three topics, which are discussed in terms of the uterus and in the context of fertility, provide molecular evidence for an association between gene expression in the uterine environment and genetic merit for fertility in dairy cows.

The effect of Lameness before and during the breeding season on fertility in 10 pasture-based Irish dairy herds.

BackgroundThe effects of lameness on fertility have been documented frequently but few data are available from seasonally breeding, pasture-based herds (such as those used in Ireland) where cows are housed during the winter months but managed at pasture for the remainder of the year. This study determined the prevalence of lameness in a group of 786 cows in 10 pasture-based Irish dairy herds before, during and after the breeding season and assessed the relationship between lameness and the reproductive performance in these herds through serial locomotion scoring during the grazing period.ResultsLameness prevalences of 11.6 % before, 14.6 % during and 11.6 % after the breeding season were found and these compared favourably to results from housed cattle and are similar to other studies carried out in grazing herds. A Cox proportional hazards model with locomotion score as time varying covariate was used. After controlling for the effect of farm, month of calving, body condition score at calving, body condition score loss after calving and economic breeding index, cows identified as lame during the study were less likely to become pregnant. Cows lame before the earliest serve date but no longer lame during the breeding season, cows becoming lame after the earliest serve date and cows identified lame both before and after this date were respectively 12 %, 35 % and 38 % less likely to become pregnant compared to cows never observed lame during the study. However, these findings were only significant for cows becoming lame after the earliest serve date and cows lame both before and after the start of breeding.ConclusionsThis study found that the reproductive efficiency was significantly (p < 0.05) lower in cows becoming lame during the breeding season and cows lame before and during the breeding season compared to non-lame cows. Cows no longer lame during the breeding season had a lower Submission Rate to first serve within 3 weeks of earliest serve date. However, the Pregnancy Rate was not significantly (p > 0.05) lower in these animals compared to cows never diagnosed as lame. In addition to lameness status, nutritional status and genetics were found to influence the reproductive performance in pasture-based Irish dairy herds.

Genomic evaluation of a relatively small dairy cattle population by combination with a larger population

The objectives were to investigate the accuracy of genomic evaluations obtained for a small dairy cattle population (Israeli Holsteins) via joint evaluation with a larger population (Dutch Holsteins), and to evaluate the use of pedigree data from foreign bulls computed by Interbull without daughter records in Israel. The training population included 4,010 Dutch bulls and 713 Israeli bulls. The validation population included 185 Israeli bulls with daughter records for milk production traits and slightly fewer bulls for the nonproduction traits. Milk, fat, and protein yields, somatic cell score, longevity, female fertility, direct and maternal calving ease, direct and maternal stillbirth, and the Israeli breeding index were analyzed. The genomic prediction model was based on the Bayesian multi-QTL model of Meuwissen and Goddard, where the effects of dense single nucleotide polymorphisms across the whole genome are fitted directly, without the use of haplotypes or identical-by-descent probabilities. Correlations of May 2014 estimated breeding values (EBV14) with genomic EBV (GEBV) were higher than the correlations of EBV14 with parent averages (PA) computed from the June 2009 evaluation for all traits. For the Israel selection index, the difference between EBV14 and GEBV correlation on the one hand and EBV14 and PA computed using Interbull data on the other hand was 15 percentage points. For protein, the difference between the corresponding correlations was 14 percentage points. Generally, correlations of EBV14 with PA based on Israeli EBV only were similar to correlations of EBV14 with PA including Interbull evaluations. Relative to EBV14, milk production traits were biased upwards for both GEBV and PA, but the bias was greater for PA. The Y-intercepts of regressions of EBV14 were significantly different from zero for regression on GEBV for all 3 milk production traits and the Israeli selection index. This was not the case for regression of EBV14 on PA. The regression line intersected with the line of unbiased estimation near the EBV of the bulls with highest values. Because only bulls with high evaluations are of interest for selection, GEBV for these bulls were less biased compared with that of bulls with lower evaluations. The difference in mean EBV14 between bulls born during 2007–2008 selected by GEBV and PA was 65 units. If half of all inseminations are by young bulls, then the annual genetic gain obtained by implementation of genomic evaluation will be 8 units per year (65/8). Because annual gain is currently 107 units, this is a gain of 7%.

Development of an index to rank dairy females on expected lifetime profit

The objective of this study was to develop an index to rank dairy females on expected profit for the remainder of their lifetime, taking cognizance of both additive and nonadditive genetic merit, permanent environmental effects, and current states of the animal including the most recent calving date and cow parity. The cow own worth (COW) index is intended to be used for culling the expected least profitable females in a herd, as well as inform purchase and pricing decisions for trading of females. The framework of the COW index consisted of the profit accruing from (1) the current lactation, (2) future lactations, and (3) net replacement cost differential. The COW index was generated from estimated performance values (sum of additive genetic merit, nonadditive genetic merit, and permanent environmental effects) of traits, their respective net margin values, and transition probability matrices for month of calving, survival, and somatic cell count; the transition matrices were to account for predicted change in a cow’s state in the future. Transition matrices were generated from 3,156,109 lactation records from the Irish national database between the years 2010 and 2013. Phenotypic performance records for 162,981 cows in the year 2012 were used to validate the COW index. Genetic and permanent environmental effects (where applicable) were available for these cows from the 2011 national genetic evaluations and used to calculate the COW index and their national breeding index values (includes only additive genetic effects). Cows were stratified per quartile within herd, based on their COW index value and national breeding index value. The correlation between individual animal COW index value and national breeding index value was 0.65. Month of calving of the cow in her current lactation explained 18% of the variation in the COW index, with the parity of the cow explaining an additional 3 percentage units of the variance in the COW index. Females ranking higher on the COW index yielded more milk and milk solids and calved earlier in the calving season than their lower ranking contemporaries. The difference in phenotypic performance between the best and worst quartiles was larger for cows ranked on COW index than cows ranked on the national breeding index. The COW index is useful to rank females before culling or purchasing decisions on expected profit and is complementary to the national breeding index, which identifies the most suitable females for breeding replacements.

Genome-wide association study identifies QTLs for EBV of backfat thickness and average daily gain in Duroc pigs.

Backfat thickness (BFT) and average daily gain (ADG) are two important economic traits in commercial swine production. Identifying QTLs and uncovering the molecular mechanism for BFT and ADG would greatly help to speed up the breeding progress. In current breeding program, EBV for these two traits are calculated and formulated a comprehensive breeding index, which then be used to improve pig performance. Using Illumina PorcineSNP60 BeadChip, a pilot genomewide association studies (GWAS) for BFT and ADG in 83 Duroc pigs were performed. A total of 31 genome-wise significant SN Ps were detected to be associated with BFT on SSC 4, 9, 11, 12 and 14, ten of which were coincident with previously reported QTL regions. There are two genome-wise loci prominently associated with ADG on SSC2 and SSC13, respectively. The two loci on SSC2 are well overlapped with the QTL regions previously reported. All the 31 significant SNPs associated with BFT are verified on 219 outbreed pigs, six SN Ps reach an extreme significant level and seven SNP reaches a significant level, CACNA1E and ACBD6 are chosen as positional candidate genes. Our findings not only confirmed previously findings, but also revealed a number of novel SNPs associated with BFT and ADG. Two positional candidate genes CACNA1E and ACBD6 were identified for further study. These results would facilitate the identification of causative genes for BFT and ADG.

Environmental and genetic factors affecting cow survival of Israeli Holsteins

The objectives were to investigate the effects of various environmental factors that may affect herd-life of Israeli Holsteins, including first-calving age and season, calving ease, number of progeny born, and service sire for first calving in complete and truncated records; and to estimate heritabilities and genetic correlations between herd-life and the other traits included in the Israeli breeding index. The basic data set consisted of 590,869 cows in milk recording herds with first freshening day between 1985 and at least 8 yr before the cut-off date of September 15, 2013. Herd-life was measured as days from first calving to culling. The phenotypic and genetic trends for herd-life were 5.7 and 16.8d/yr. The genetic trend was almost linear, whereas the phenotypic trend showed 4 peaks and 3 valleys. Cows born in February and March had the shortest herd-life, whereas cows born in September had the longest herd-life. Herd-life was maximal with calving age of 23mo, which is 1mo less than the mean calving age, and minimal at 19 and 31mo of calving age. Dystocia and twinning on first-parity calving reduced herd-life by approximately180 and 120d, but the interaction effect increased herd-life by 140d. Heritability for herd-life was 0.14. Despite the fact that the service sire effect was significant in the fixed model analysis, service sire effect accounted for <0.05% of the total variance. In the analysis of 1,431,938 truncated records, the effects of dystocia and twinning rate were very similar but less than 50% of the effects found in the analysis of complete records. Pregnancy at the truncation date increased expected herd-life by 432d. The correlation between actual herd-life and predicted herd-life based on truncated records was 0.44. Genetic correlations between the truncated records and actual herd-life were 0.75 for records truncated after 6mo but approached unity for records truncated after 3 yr. The genetic correlations of herd-life with first-parity milk, fat, and protein production, somatic cell score (SCS), and female fertility were all positive, except for SCS, in which negative values are economically favorable. The highest correlations with herd-life in absolute value were with female fertility and SCS.

Significance of ossificated ungular cartilages regarding the performance of cold-blooded trotters.

BackgroundOssification of the ungular cartilages (OUC) in the foot of horses has been studied for more than 100 years. There is a high heritability of this condition but its clinical relevance has remained questionable. Nevertheless, modern equine orthopedic literature ranks OUC as one of top 10 causes of lameness in cold-blooded trotters and stallions of these breeds are excluded from breeding if they have more than mild levels of side bones. Cold-blooded trotters have been used for racing for many decades and official sports data have been available since 1923. A decreased performance is often the only obvious clinical sign noticed by trainers and owners motivating them to seek professional help from veterinarians and farriers. By comparing various performance parameters in Swedish-Norwegian cold-blooded trotters without and with different grades of OUC, we aimed to determine the clinical relevance of ossified hoof cartilages in a population of high-performance horses.Front hooves from 649 Swedish-Norwegian cold-blooded trotters were evaluated radiologically regarding OUC. Breeding index and official sports data originating from strict protocols kept by groups of officials in trotting associations was used for comparison of performance of these horses that together had competed in more than 23,000 races between 1973 and 2009. Generalized linear mixed models were used for the statistical analyses. The response variable was modeled using ordinal logistic models with a multinomial distribution and a cumulative logit link function. The horse was used as a random factor.ResultsSignificant effects of gender on performance were demonstrated, but no correlations were found between different positions nor grades of ossified ungular cartilage and number of starts, running pace, race winnings, number of races completed in a regular gait.ConclusionsOssification of the ungular cartilages does not cause decreased performance in cold-blooded trotters and is therefore most likely not a cause of clinical or subclinical lameness in this breed. Results from this study can assist equine professionals in evaluating and interpreting the clinical relevance of radiological findings on ossified hoof cartilage among heavy and high-performing horses.

Effects of Amount of Intensive Training on VLa4 in 3‐Year Old Standardbred Horses

IntroductionThe effects of different amounts of training on performance of young horses have not yet been studied in a long term perspective. The aim of this study was therefore to assess the effect on VLa4 of two training programs performed from the age of 2 to 3 in Standardbred horses.MethodsFourteen horses were in March as 2‐year olds divided into two groups; one was randomized to a training program including intensive exercise (control) and the other to a training program with reduced amount of intensive exercise (distance −30% compared to control). Group division was partly based on breeding index (means: control 110, reduced 109) and gluteus medius fiber type ratio (IIA/IIB, both groups mean 1.34). Horses were trained ∼2 times/week. After 14 months, a VLa4‐test was performed on a track (4 x 1000 m). Speed was measured by GPS and increased by ∼3 s/1000 m for every interval. Blood samples were collected after each interval and lactate concentration was determined using Lactate Pro. Exponential regression analysis of speed and lactate concentration were used to estimate individual VLa4. ANOVA and Tukey's test were used to analyse differences between groups.ResultsThere was no difference in VLa4 between the control and reduced exercise group (10.6 ± 0.1 and 10.8 ± 0.1 m/s).ConclusionsThe study indicates that it might be possible to reduce the amount of intensive training by ≤30% without impairing performance of 3 year old Standardbred horses.Ethical Animal ResearchThe study was approved by the local ethics committee in Umeå. Sources of funding: Swedish University of Agricultural Sciences, Swedish National Trotting School at Wången, Swedish Trotting Association, Swedish Horse Council Foundation, Swedish Horse Racing Totalisator Board (ATG), Trioplast AB, Dow Chemicals, Polar Sverige AB, and Scandivet AB. Competing interests: none.

A genome-wide association study of immune response traits in Canadian Holstein cattle

BackgroundBreeding for enhanced immune response (IR) has been suggested as a tool to improve inherent animal health. Dairy cows with superior antibody-mediated (AMIR) and cell-mediated immune responses (CMIR) have been demonstrated to have a lower occurrence of many diseases including mastitis. Adaptive immune response traits are heritable, and it is, therefore, possible to breed for improved IR, decreasing the occurrence of disease. The objective of this study was to perform genome-wide association studies to determine differences in genetic profiles among Holstein cows classified as High or Low for AMIR and CMIR. From a total of 680 cows with immune response phenotypes, 163 cows for AMIR (81 High and 82 Low) and 140 for CMIR (75 High and 65 Low) were selectively genotyped using the Illumina Bovine SNP50 BeadChip. Results were validated using an unrelated population of 164 Holstein bulls IR phenotyped for AMIR and 146 for CMIR.ResultsA generalized quasi likelihood score method was used to determine single nucleotide polymorphisms (SNP) and chromosomal regions associated with immune response. After applying a 5% chromosomal false discovery rate, 186 SNPs were significantly associated with AMIR. The majority (93%) of significant markers were on chromosome 23, with a similar peak found in the bull population. For CMIR, 21 SNP markers remained significant. Candidate genes within 250,000 base pairs of significant SNPs were identified to determine biological pathways associated with AMIR and CMIR. Various pathways were identified, including the antigen processing and presentation pathway, important in host defense. Candidate genes included those within the bovine Major Histocompatability Complex such as BoLA-DQ, BoLA-DR and the non-classical BoLA-NC1 for AMIR and BoLA-DQ for CMIR, the complement system including C2 and C4 for AMIR and C1q for CMIR, and cytokines including IL-17A, IL17F for AMIR and IL-17RA for CMIR and tumor necrosis factor for both AMIR and CMIR. Additional genes associated with CMIR included galectins 1, 2 and 3, BCL2 and β-defensin.ConclusionsThe significant genetic variation associated with AMIR and CMIR in this study may imply feasibility to include immune response in genomic breeding indices as an approach to improve inherent animal health.