Genetic Evaluation Programs Research Articles

330 A hybrid model for genomic selection using prioritized SNPs based on FST scores in the presence of non-genotyped animals

Abstract The dramatic advancement in genotyping technology has greatly reduced the complexity and cost of genotyping. The continuous increase in the density of marker panels is resulting in little to no improvement in the accuracy of genomic selection. Direct inversion of the genomic relationship matrix is infeasible for some livestock populations due to the excessive computational cost. In addition, most animals in genetic evaluation programs are non-genotyped. Including these animals in a genomic evaluation requires the imputation of the missing genotypes when using regression methods. To overcome these challenges, a hybrid approach is proposed. This approach fits a subset of SNP markers selected based on FST scores and a classical polygenic effect. The method was first tested using only genotyped animals and then extended to accommodate non-genotyped animals. The proposed approach was evaluated using simulated data for a trait with heritability of 0.1 and 0.4 and weaning weight in a crossbred beef cattle population. When all animals were genotyped, the hybrid approach using only 2.5% of prioritized SNPs exceeded the prediction accuracies of BayesB, BayesC, and GBLUP by more than 7%. When non-genotyped animals were incorporated, the proposed approach significantly outperformed ss-GBLUP method in terms of prediction accuracy under both simulated heritability scenarios. Although the results seem to depend on the genetic complexity of the trait, the proposed approach resulted in higher prediction accuracies than current methods. Furthermore, its computational costs in terms of CPU time and peak memory are substantially lower than the current methods.

216 Contribution of host gut microbiome in prediction of meat quality and carcass composition traits in swine

Abstract The objective of this study was to assess the improvement in predictive ability (PA) for meat quality and carcass composition traits by including the effect of host gut microbiome. Data were collected from Duroc sired three-way crossbred individuals (n = 1,123) genotyped from 60k SNP chips. Fecal 16S microbial sequences for all individuals were obtained at three different stages: weaning (WEAN: 18.64±1.09 days); week 15 (W_15: 118.2±1.18 days); and off test (OT: 196.4±7.80 days). A 4-fold cross validation was used, with animals grouped based on sire relatedness. Analysis was conducted in “BGLR” package in R. The first model included the fixed effect of dam line, contemporary group, and sex, as well as random pen and additive genetic effect (with genomic relationship matrix). The second model included same fixed and random effects with the addition of the microbiome effect (with microbiome relationship matrix). With the inclusion of microbiome, the PA increased for majority of traits. For carcass traits, the increase in PA was greatest for belly weight which changed from 0.22±0.06 to 0.32±0.06 at OT and lowest for loin depth and ham weight which changed from 0.14±0.06 to 0.15 ±0.06 and 0.12±0.02 to 0.13 ±0.03 at WEAN respectively. For meat quality traits, the increase in PA was greatest for subjective firmness score which changed from 0.16±0.04 to 0.19±0.04 at OT and lowest for marbling score and intramuscular fat which changed from 0.27±0.09 to 0.28±0.08 and 0.39±0.05 to 0.40±0.05 at WEAN respectively. Higher predictive ability was observed at OT rather than at WEAN and W_15 microbiome information. The results may lead to a newer approach to the genetic evaluation program of swine.

Expanding access to genetic evaluations in a large community oncology practice through a collaborative service delivery model.

123 Background: Identifying individuals with inherited cancer susceptibility is critical to cancer treatment and prevention in patients and families. While the identification and management of inherited susceptibility to cancer is the standard of care, genetic testing rates are low; 1.2 million women with breast and/or ovarian cancer who qualify have yet to undergo genetic testing (Childers et al 2017). The Genetic Risk Evaluation and Testing Program (GREAT) formed to improve access to genetic evaluations and testing in Texas Oncology, a large, state-wide community oncology practice. Methods: The GREAT program is a collaborative service delivery model, utilizing 4 certified genetic counselors (CGC) to lead advanced practice providers and physicians in offering pre and post-test evaluations to oncology patients in their own community. Training involves 8-12 weeks of didactic lectures, precepting, and ongoing education and support. GREAT-trained providers then offer comprehensive genetic evaluations and testing to established oncology patients as well as at-risk individuals from the surrounding community. Results: The GREAT program has trained 72 providers at 52 cancer centers. Rates of genetic evaluations increased each year from 2012 to 2018. Overall findings: 19,129 unique patients received an evaluation; 17,305 genetic tests were completed; 2,597 pathogenic/likely pathogenic variants (P/VLP) have been identified. Conclusions: Despite guidelines recommending genetic evaluations for hereditary cancer syndromes, most patients are not receiving this service. A hybrid service delivery model utilizing regional CGCs to train providers in community oncology offices can significantly increase access to genetic services. The model described is an effective and expansive mechanism for the delivery of high-quality cancer genetics care. The GREAT program plans to hire additional CGCs to train more providers across Texas Oncology with the goal of expanding access. [Table: see text]

Genetic improvement of canine hip dysplasia through sire selection across countries

Breeding against canine hip dysplasia (HD) may benefit from the importation of foreign sires. When foreign sires are evaluated on a different HD scale, this may diminish the efficacy. Using stochastic simulations, we evaluated genetic change and inbreeding levels for different scenarios of importing sires with high genetic merit for HD. Population size and genetic parameters (e.g. heritability, accuracy of selection, genetic correlation) were based on actual data for HD in Golden retrievers and Labrador retrievers in the UK and Sweden.For countries with different HD scales and an estimated breeding value (EBV) evaluation in place, the importation was useful if imported sires had EBV rankings in the top 50% and if genetic correlations between EBV systems were above 0.85. When importing sires with EBV rankings in the top 10%, moderate accuracies of EBVs (>0.40) and moderately strong genetic correlations (>0.70) were needed. Selection against HD without the importation of sires may increase inbreeding levels, while the importation of sires can decrease inbreeding levels. For national genetic evaluation and selection programmes, importing sires with high genetic merit can be an effective breeding strategy, but care is needed to estimate reliable EBVs.

Genotype x Environment Interaction for reproductive traits in brazilian Nellore breed cattle

SUMMARY The objective of this study was to evaluate the effect of the genotype-environment interaction (GEI) for scrotal circumference traits measured at different ages, 365 (SC365), 450 (SC450) and 550 (SC550) days of age, and age at first calving (AFC) for Nellore animals raised in different regions of Brazil. For the evaluation, the herds were grouped in the following regions of the country: North, Southeast and Central-west, using information from 26,619, 28,730, 14,476, 15,397 for the traits SC365, SC450, SC550 and AFC respectively. Genetic parameters, as well as the assessment of GEI were performed using Bayesian inference, using the programs of the BLUPF90. The estimated heritabilities were: 0.465 ± 0.021, 0.500 ± 0.022, 0.492 ± 0.026, 0.117 ± 0.017 for SC365, SC450, SC550 and AFC respectively. The results obtained in the analysis, indicated that this interaction was not significant for SC at different ages (genetic correlation, rg> 0.8). For AFC, significant effect of GEI was observed for combinations involving the Northern region (rg<0.8), indicating that this interaction should be considered by the genetic evaluation programs in this region.

Genetic correlations between meat quality traits and growth and carcass traits in Merino sheep1.

Genetic correlations between 16 meat quality and nutritional value traits and live weight at various ages, live ultrasound fat and muscle depth, carcass measures, and carcass dissection traits were estimated for Merino sheep in the Information Nucleus (IN). Genetic correlations between live weight at various ages and the carcass traits are also reported. The IN comprised 8 genetically linked flocks managed across a range of Australian sheep environments. Meat quality traits included between 1,200 and 1,300 records for progeny from over 170 sires for intramuscular fat (IMF), lean meat yield (LMY), shear force (SF5), pH, meat color, and meat nutritional value traits including iron and zinc levels and long-chain omega-3 and omega-6 polyunsaturated fatty acid levels. The genetic correlations indicated that selection of Merino sheep to either reduce fat or increase muscle using ultrasound assessments will result in little change in IMF and SF5. Myoglobin levels would tend to be reduced following selection for reduced ultrasound fat depth (0.35 ± 0.21, 0.43 ± 0.14), whereas increases in myoglobin levels would occur due to selection for increased ultrasound muscle depth (0.25 ± 0.24, 0.38 ± 0.15). Selection for increased live weight will result in favorable correlated responses in hot carcass weight (0.76 to 0.97), dressing percentage (0.13 to 0.47), and carcass muscle (0.37 to 0.95), but unfavorable responses of increases in carcass fatness (0.13 to 0.65) and possible small reductions in muscle oxidative activity (-0.13 ± 0.14 to -0.73 ± 0.33) and iron content (-0.14 ± 0.15 to -0.38 ± 0.16), and a possible deterioration of shear force from selection at later ages (0.15 ± 0.26, 0.27 ± 0.24). Negligible changes are generally expected for LMY and meat color traits following selection for increased live weight (most genetic correlations less than 0.20 in size). Selection for increased LMY would tend to result in unfavorable changes in several aspects of meat quality, including reduced IMF (-0.27 ± 0.18), meat tenderness (0.53 ± 0.26), and meat redness (-0.69 ± 0.40), as well as reduced iron levels (-0.25 ± 0.22). These genetic correlations are a first step in assisting the development of breeding values for new traits to be incorporated into genetic evaluation programs to improve meat production from Merino sheep and other dual-purpose sheep breeds.

Study of the effect of genotype-environment interaction on age at first calving and production traits in Nellore cattle using multi-trait reaction norms and Bayesian inference.

This study investigated the effects of genotype-environment interaction on yearling weight, age at first calving and post-weaning weight gain in Nellore cattle using multi-trait reaction norm models. The environmental gradient was defined as a function of the mean yearling weight of the contemporary groups. A first-order random regression sire model with four classes of residual variance was used in the analyses and Bayesian methods were applied to estimate the (co)variance components. The heritability estimates ranged from 0.284 to 0.547, 0.222 to 0.316 and 0.256 to 0.522 for yearling weight, age at first calving and post-weaning weight gain, respectively. The lowest genetic correlations between environment groups for each trait were 0.38, 0.02 and 0.04 for yearling weight, age at first calving and post-weaning weight gain, respectively. Differences in the correlation estimates were observed between traits in the same environments, with the magnitude of the estimates tending toward zero as the environment improved. The results highlight the importance of including genotype-environment interactions in genetic evaluation programs considering the differences observed between environmental groups not only in terms of heritability, but also of genetic correlations.

Genetic parameters of carcass and meat quality traits in different muscles (longissimus dorsi and semimembranosus) of Hanwoo (Korean cattle).

We estimated heritability () and genetic and phenotypic correlations for carcass and meat quality traits of longissimus dorsi (LD) and semimembranosus (SM) muscles in 30-mo-old Hanwoo steers. Variance and covariance components were estimated using REML procedures under univariate and bivariate models. The mean carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS) were 428.20 ± 46.30 kg, 87.38 ± 8.54 cm2, 13.00 ± 5.14 mm, and 5.21 ± 1.56, respectively. The mean CIE reflectance of meat lightness (L*), redness (a*), and yellowness (b*) were 40.01 ± 2.73, 22.37 ± 2.18, and 10.35 ± 1.46, respectively, in LD muscles and 36.33 ± 2.44, 22.91 ± 2.43, and 10.25 ± 1.65, respectively, in SM muscles. The mean Warner-Bratzler shear force (WBSF), intramuscular fat content (IMF), water-holding capacity (WHC), and protein and ash content in LD and SM muscles were 3.84 ± 0.96 and 6.52 ± 1.21 kg, 15.91 ± 4.39 and 5.10 ± 1.94%, 62.07 ± 3.38 and 71.61 ± 2.06%, 20.01 ± 1.39 and 21.34 ± 0.89%, and 0.80 ± 0.10 and 0.93 ± 0.07, respectively. The estimates of CWT, EMA, BFT, and MS were 0.51 ± 0.13, 0.45 ± 0.13, 0.29 ± 0.09, and 0.22 ± 0.08, respectively. The estimates were moderate for meat quality traits and were 0.37 ± 0.12, 0.40 ± 0.12, 0.33 ± 0.10, 0.33 ± 0.10, 0.30 ± 0.11, and 0.24 ± 0.09 for L*, WBSF, IMF, WHC, and protein and ash content, respectively, in LD muscle; estimates from SM muscle were comparatively low (0.08 ± 0.06 to 0.25 ± 0.09). Estimates of for a* and b* were also low (0.08 ± 0.06 to 0.13 ± 0.07). Carcass weight had a moderate, positive genetic correlation with EMA (0.60 ± 0.13) and a weak correlation with MS and BFT. The genetic correlations among the 3 colorimeter variants were strong and positive within and between muscles. Intramuscular fat content had moderate to strong and negative genetic correlations with WBSF (-0.49 ± 0.18), WHC (-0.99 ± 0.01), and protein (-0.93 ± 0.04) and ash content (-0.98 ± 0.06) in LD muscle, whereas the associations were less pronounced in SM muscle. In general, CWT and EMA had low genetic and phenotypic correlations with meat quality traits, which suggests that the traits are independent and have distinct genetic contributions in each muscle. Conversely, with few exceptions, meat quality traits had genetic and phenotypic correlations with MS and BFT. In conclusion, the estimated genetic parameters for carcass and meat quality traits could be used for genetic evaluation and breeding programs in Korean Hanwoo cattle populations.

Economic selection indexes for Hereford and Braford cattle raised in southern Brazil.

Economic selection indexes (EI) are considered the best way to select the most profitable animals for specific production systems. Nevertheless, in Brazil, few genetic evaluation programs deliver such indexes to their breeders. The aims of this study were to determine the breeding goals (BG) and economic values (EV, in US$) for typical beef cattle production systems in southern Brazil, to propose EI aimed to maximize profitability, and to compare the proposed EI with the currently used empirical index. Bioeconomic models were developed to characterize 3 typical production systems, identifying traits of economic impact and their respective EV. The first was called the calf-crop system and included the birth rate (BR), direct weaning weight (WWd), and mature cow weight (MCW) as selection goals. The second system was called the full-cycle system, and its breeding goals were BR, WWd, MCW, and carcass weight (CW). Finally, the third was called the stocking and finishing system, which had WWd and CW as breeding goals. To generate the EI, we adopted the selection criteria currently measured and used in the empirical index of PampaPlus, which is the genetic evaluation program of the Brazilian Hereford and Braford Association. The comparison between the EI and the current PampaPlus index was made by the aggregated genetic-economic gain per generation (Δ). Therefore, for each production system an index was developed using the derived economic weights, and it was compared with the current empirical index. The relative importance (RI) for BR, WWd, and MCW for the calf-crop system was 68.03%, 19.35%, and 12.62%, respectively. For the full-cycle system, the RI for BR, WWd, MCW, and CW were 69.63%, 7.31%, 5.01%, and 18.06%, respectively. For the stocking and finishing production system, the RI for WWd and CW was 34.20% and 65.80%, respectively. The Δ for the calf-crop system were US$6.12 and US$4.36, using the proposed economic and empirical indexes, respectively. Respective values were US$19.87 and US$18.22 for the full-cycle system and US$20.52 and US$18.52 in the stocking and finishing system. The efficiency of the proposed EI had low sensitivity to changes in the values of the economic and genetic parameters. The 3 EI generated higher Δ when using the proposed economic weight compared to the Δ provided by a PampaPlus index, suggesting the use of proposed EI to obtain greater economic profitability in relation to the current empirical PampaPlus index.

Milk yield, fat yield and fat percentage associations in a Thai multibreed dairy population

Milk yield (MY), fat yield (FY) and fat percentage (FP) are important traits for dairy cattle selection and dairy farm profitability in Thailand. Most dairy cattle in Thailand are multibreed, comprising multiple breeds (three from eight breeds per animal). This multibreed composition of dairy animals has generated a large amount of variation in dairy traits among cows raised under farm, tropical environmental conditions across the country. Effective genetic evaluation and selection programs for dairy traits in this population require reliable variance components and genetic parameters estimated under the management, nutritional, health, and climatic conditions in Thai dairy farms. Thus, the objective of this study was to estimate genetic parameters for MY, FY and FP in a Thai dairy multibreed dairy cattle population using farm-collected information. The dataset consisted of pedigree and phenotypic data for MY, FY and FP from 6596 first lactation cows from 687 farms. The data were analyzed using a three-trait (MY, FY and FP), animal mixed model. Fixed effects were herd-year-season, Holstein fraction, heterozygosity and age at first calving. Random effects were animal and residual. An average, information-restricted, maximum likelihood procedure was used to estimate variance components, which in turn were used to compute heritabilities and genetic correlations. Means (SD) were 4315.43 kg (1112 kg) for MY, 157.41 kg (50.42 kg) for FY and 3.59% (0.56%) for FP. Heritability estimates were 0.22 ± 0.06 for MY, 0.17 ± 0.06 for FY and 0.24 ± 0.07 for FP. Genetic correlations were 0.47 ± 0.16 between MY and FY, −0.30 ± 0.20 between MY and FP, and 0.30 ± 0.21 between FY and FP. These estimates of genetic parameters indicated that Thai dairy producers would achieve reasonable amounts of genetic progress if they selected dairy animals based on MY and either FY or FP.

Detecting selection signatures between Duroc and Duroc synthetic pig populations using high-density SNP chip.

The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D×Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the FST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation. These results could be a basis for investigating the underlying mutations associated with observed phenotypic variation. Validation using genome-wide association analysis would also facilitate the inclusion of some of these markers in genetic evaluation programs.

Index proposal for Nelore bulls classification using traits groups of weight, carcass and reproductive

Genetic breeding programs generally evaluate animals considering the same objectives, but the indices used in the selection criteria can vary. This can give rise to distinct bull rankings in each program. Thus, we aimed to create alternatives for the referral of bulls for mating through multivariate analyses. We used information from the summaries of two genetic evaluation programs (1 and 2) with Nellore bulls. Characteristics were separated into groups: weight, carcass and reproduction. Groups were formed using the mean Euclidean distance and the Tocher optimization method. The means of each trait among the animals allocated to the same group were used to compose the following subindexes: weight gain (siWG), carcass (siCG) and reproduction (siRG). Based on the mean of the group subindex classification, we calculated the average index of group classification (iAGc). When classifying the best groups by characteristics, we observed an increase (superiority of some bulls) in the estimated breeding values (EBVs) by comparison with the total number of bulls evaluated by the programs, selected animals and best 10 final indexes of the programs. There was a change in bull classification when using the iAGc in relation to the classification using the final indexes of the programs. The coefficient of simple coincidence showed that there was a change in bull classification between programs, both between deciles of the final indexes and groups of characteristics. The subindexes siWG, siCG and siRG are important for correcting specific problems in herds. The iAGc should be used instead of the final index of the programs, providing more options for the selection of bulls for mating.

Genetic parameters for hoof health traits estimated with linear and threshold models using alternative cohorts

A national genetic evaluation program for hoof health could be achieved by using hoof lesion data collected directly by hoof trimmers. However, not all cows in the herds during the trimming period are always presented to the hoof trimmer. This preselection process may not be completely random, leading to erroneous estimations of the prevalence of hoof lesions in the herd and inaccuracies in the genetic evaluation. The main objective of this study was to estimate genetic parameters for individual hoof lesions in Canadian Holsteins by using an alternative cohort to consider all cows in the herd during the period of the hoof trimming sessions, including those that were not examined by the trimmer over the entire lactation. A second objective was to compare the estimated heritabilities and breeding values for resistance to hoof lesions obtained with threshold and linear models. Data were recorded by 23 hoof trimmers serving 521 herds located in Alberta, British Columbia, and Ontario. A total of 73,559 hoof-trimming records from 53,654 cows were collected between 2009 and 2012. Hoof lesions included in the analysis were digital dermatitis, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, and white line disease. All variables were analyzed as binary traits, as the presence or the absence of the lesions, using a threshold and a linear animal model. Two different cohorts were created: Cohort 1, which included only cows presented to hoof trimmers, and Cohort 2, which included all cows present in the herd at the time of hoof trimmer visit. Using a threshold model, heritabilities on the observed scale ranged from 0.01 to 0.08 for Cohort 1 and from 0.01 to 0.06 for Cohort 2. Heritabilities estimated with the linear model ranged from 0.01 to 0.07 for Cohort 1 and from 0.01 to 0.05 for Cohort 2. Despite a low heritability, the distribution of the sire breeding values showed large and exploitable variation among sires. Higher breeding values for hoof lesion resistance corresponded to sires with a higher prevalence of healthy daughters. The rank correlations between estimated breeding values ranged from 0.96 to 0.99 when predicted using either one of the 2 cohorts and from 0.94 to 0.99 when predicted using either a threshold or a linear model.

Factors affecting fecal egg counts in periparturient Katahdin ewes and their lambs.

Selection for low fecal egg counts (FEC) can be used to genetically enhance resistance to gastrointestinal nematode parasites in growing lambs, thereby reducing the frequency of use of anthelmintics, facilitating marketing of organic lamb, and reducing the risk of development of anthelmintic resistance by the parasite. Recording of FEC in lambs has, therefore, been incorporated into several national sheep genetic evaluation programs. Ewes in late gestation and early lactation are also vulnerable to parasite infection and commonly experience a periparturient rise in FEC. This study was designed to assess factors associated with the periparturient rise in FEC in Katahdin ewes and associated changes in FEC in their lambs. Data came from 1,487 lambings by 931 Katahdin ewes from 11 farms in the Eastern United States. Fecal egg counts were measured in ewes at approximately 0, 30, and 60 d postpartum and in their lambs at approximately 60, 90, and 120 d of age. Approximately 1,400 lambs were evaluated at each measurement age. Data were analyzed separately for ewes and lambs and also initially analyzed separately for each measurement time. Repeated-measures analyses were then used to evaluate responses across measurement times. In ewes, FEC peaked at approximately 28 d postpartum, and we concluded that informative periparturient FEC could be obtained from 1 wk before until approximately 5 wk after lambing. Yearling ewes had higher FEC than adult ewes ( < 0.01), and ewes that nursed twin or triplet lambs had higher FEC than ewes that nursed single lambs ( < 0.01). In lambs, FEC increased through approximately 120 d of age. Lambs from yearling ewes and lambs nursed in larger litters were, like their dams, at greater risk of parasitism ( < 0.05). Ewes and lambs in these groups would benefit from enhanced monitoring of parasite loads at lambing and in early lactation. Correlations () between FEC in lambs at 90 d of age and FEC in ewes at 0, 30, and 60 d postpartum of 0.05 to 0.09 ( ≤ 0.05) support the presence of a genetic relationship between these 2 indicators of parasite resistance.

Breeding efficiency of Crossbred cattle and Murrahbuffaloes at organized dairy farm

A total of 1474 and 1935 production and reproduction records of crossbred cattle and Murrah buffaloes from the year 1992 to 2012 were utilized in the present study to investigate breeding efficiency (BE) and various performance traits. Breeding efficiency was calculated using Wilcox and Tomar methods and Least –squares of Harvey model was used to study the effects of various non-genetic factors (period, season) on breeding efficiency. Average breeding efficiency of Crossbred cattle was 82.31 ± 0.97% ranging from 75% to 85% by Wilcox method and 98.14 ± 1.09% ranging from 95% to 99% by Tomar method. Average breeding efficiency of buffaloes was 78.03 ± 1.01% ranging from 69% to 84% by Wilcox method and 78.39 ± 0.39% ranging from 74% to 80% by Tomar method under the management conditions. Breeding efficiency correlated positively with weight at calving, milk yield 305 days and milk yield complete in Crossbred cattle and Murrah buffaloes by both methods. The effect of period was significant(less than 0.01) on the breeding efficiency by Wilcox method and non-significant by Tomar method in Crossbred cattle. The effect of season was non-significant on breeding efficiency by both methods in crossbred cattle. In Murrah buffaloes the effect of period was significant(less than 0.01) on the breeding efficiency by both methods while the effect season was significant(less than 0.05) on breeding efficiency by Tomar method and non significant by Wilcox method. Therefore it is imperative to emphasis improvement in the husbandry practices and the introduction of genetic evaluation programmes at the same time.

Genetic relationship between heifers and cows fertility and milk yield traits in first-parity Iranian Holstein dairy cows

Relationship between reproductive characteristics of heifers and cows and milk production traits in Iranian primiparous Holstein dairy cows were investigated under a Bayesian approach using data collected from 1995 to 2014. The studied reproductive traits in heifers were success or failure at first insemination (SFH), number of inseminations for conception (INSH), and days to calving (DC). Considered reproductive traits in cows were success or failure at first insemination (SFC), number of insemination for conception (INSC) and days open (DO). Milk production traits were included 305-day adjusted milk yield (MY), fat yield (FY) and protein yield (PY). Linear models were used for the analysis of INSH, DC, INSC and DO, while threshold models were used for SFH and SFC. Direct heritability estimates were0.012, 0.029, 0.049, 0.006, 0.010, 0.039, 0.252, 0.167 and 0.214 for INSH, INSC, OD, DC, SFH, SFC, MY, FY and PY, respectively. Genetic correlation estimates between reproductive traits were high and negative for SFH and SFC with INSH, INSC, OD and DC; varying between −0.991 for INSC-SFC and −0.627 for OD-SFH. Genetic correlation estimates between INSC, INSH, OD and DC were high and positive, varying from 0.638 for INSH-OD to 0.932 for INSC-DC. A positive estimate of 0.613 was obtained for the genetic correlation between SFC and SFH. Genetic and phenotypic correlations between milk production traits were positive and high. Unfavorable genetic correlations were obtained between MY, FY and PY with reproductive traits, varying from −0.617 for SFC-PY to 0.593 for OD-MY. High genetic correlations were found for SFH-SFC (0.613) and INSH-INSC (0.862). The reproductive traits considered in heifers (except for DC) had medium to high genetic correlations with milk production and cow's reproduction traits. Furthermore, reproductive traits of heifers can be measured relatively early in the life. Therefore, it can be concluded that including reproductive traits of heifers in genetic evaluation programs can be useful of Iranian Holsteins.

Pediatric cancer and Li-Fraumeni/Li-Fraumeni-like syndromes: a review for the pediatrician.

cancer is the second leading cause of death in children between the ages of 0 and 14 years, corresponding to approximately 3% of all cases diagnosed in Brazil. A significant percentage (5-10%) of pediatric cancers are associated with hereditary cancer syndromes, including Li-Fraumeni/Li-Fraumeni-like syndromes (LFS/LFL), both of which are caused by TP53 germline mutations. Recent studies have shown that a specific TP53 mutation, known as p.R337H, is present in 1 in 300 newborns in Southern and Southeast Brazil. In addition, a significant percentage of children with LFS/LFL spectrum tumors in the region have a family history compatible with LFS/LFL. to review clinical relevant aspects of LFS/LFL by our multidisciplinary team with focus on pediatric cancer. the NCBI (PubMed) and SciELO databases were consulted using the keywords Li-Fraumeni syndrome, Li-Fraumeni-like syndrome and pediatric cancer; and all manuscripts published between 1990 and 2014 using these keywords were retrieved and reviewed. although LFS/LFL is considered a rare disease, it appears to be substantially more common in certain geographic regions. Recognition of population- specific risks for the syndrome is important for adequate management of hereditary cancer patients and families. In Southern and Southeastern Brazil, LFS/ LFL should be considered in the differential diagnosis of children with cancer, especially if within the spectrum of the syndrome. Due to the complexities of these syndromes, a multidisciplinary approach should be sought for the counseling, diagnosis and management of patients and families affected by these disorders. Pediatricians and pediatric oncologists in areas with high prevalence of hereditary cancer syndromes have a central role in the recognition and proper referral of patients and families to genetic cancer risk evaluation and management programs.

Economic values for milk production and quality traits in south and southeast regions of Brazil

The objective of this study was to calculate economic values for milk (MY), protein (PY) and fat productions (FY) and somatic cell count (SCC) which could be used to compose an economic index to rank animals involved in an international genetic evaluation program of Holstein cattle used in the commercial dairy population in Brazil. The main milk production systems (MPS) prevailing in the South and Southeast were defined based on the feeding management and production level of herds. To calculate feeding costs, energy requirements for the production of one kg of milk with the respective average protein and fat contents of each MPS were calculated. Feeding costs were obtained based on the regional prices of the diets' components. To calculate revenues, milk prices were obtained from the payment tables practiced by seven milk industries. Economic values were calculated from the marginal differences between revenues and costs, for the interest of maximizing the profit, assuming a fixed number of animals in the herd. The average economic values (R$) for MY, PY and FY were 0.51, 6.41 and 1.94, respectively. The economic impact of increasing the original SCC values in the individual records of cows in the population by 1% was -R$ 1.40 per cow, per year. Due to changes observed in the last years in the milk market in Brazil, selection for milk components became economically advantageous. As a result, the calculation of economic values and the proposition of an economic index based on these traits became feasible. Somatic cell count does have an economic impact on the final price of milk and consequently on the annual profit of herds. It has also been used in breeding programs as an indicator of mastitis resistance and should not be neglected in breeding programs of dairy cattle.

Whole exome sequencing for cancer &amp;ndash; is there evidence of clinical utility?

Whole exome sequencing for cancer &ndash; is there evidence of clinical utility? Alka Malhotra, Susan Levine, Diane Allingham-Hawkins Genetic Test Evaluation Program, Winifred S Hayes, Inc., Lansdale, PA, USA Background: In recent years, whole exome sequencing (WES), which allows detection of 85% of disease-causing variants, has been used to compare tumor and normal DNA to allow the identification of variants specific to the tumor. Genetic changes in cancer are increasingly used for diagnosis and may guide treatment decisions. In this paper, we explore whether there is evidence that WES improves outcomes for patients with cancer. Methods: Published evidence was evaluated using a methodology that combines the analytical validity, clinical validity, clinical utility and ethical, legal, and social implications (ACCE) model for genetic test evaluations with internationally accepted health technology assessment methodology. Conclusions were based on peer-reviewed published studies of &gt;10 patients, with &ge;3 studies for a given phenotype. Results: WES has been conducted most extensively (seven studies to date) in breast cancer patients, with fewer studies of other types of cancers (eg, leukemia, prostate cancer, and ovarian cancer). Studies evaluating somatic alterations showed high intratumor and intertumor heterogeneity. In addition, both novel and previously implicated variants were identified. However, only three studies with &gt;10 individuals have shown potential for clinical utility of WES; whereby, variants identified through WES may determine response to drug treatment. Conclusion: Despite evidence for clinical validity of WES in cancers, clinical utility is very limited and needs to be further evaluated in large clinical studies. Keywords: next-generation sequencing, exons, evidence-based, ACCE model, health technology assessment

Growth, carcass traits and palatability: Can the influence of the feeding regimes explain the variability found on those attributes in different Uruguayan genotypes?

It is well known what genetic and nutritional factors affect growth and meat quality, but there is less information related to interactive importance of them during the productive process. These systems are mainly based on rangelands affecting animal growth in early stages of life thus producing smaller cattle and reduced retail yield comparing with well grown calves. During the last ten years, Uruguayan livestock production systems have been intensified using improved pastures, concentrates and better genetic. The main breeds in Uruguay are Hereford, Angus and their crosses. These British breeds are under genetic evaluation programs which consider carcass trait parameters. It is important for beef industry to know if interactions between genotype and nutrition during growth and fattening phases are influencing production, efficiency, carcass weight and meat quality attributes. The aim of this article is to present information obtained under different feeding strategies during the post weaning and fattening and their influence on those attributes.