Breeding and Genetics Symposium: really big data: processing and analysis of very large data sets

Modern animal breeding data sets are large and getting larger, due in part to recent availability of high-density SNP arrays and cheap sequencing technology. High-performance computing methods for efficient data warehousing and analysis are under development. Financial and security considerations are important when using shared clusters. Sound software engineering practices are needed, and it is better to use existing solutions when possible. Storage requirements for genotypes are modest, although full-sequence data will require greater storage capacity. Storage requirements for intermediate and results files for genetic evaluations are much greater, particularly when multiple runs must be stored for research and validation studies. The greatest gains in accuracy from genomic selection have been realized for traits of low heritability, and there is increasing interest in new health and management traits. The collection of sufficient phenotypes to produce accurate evaluations may take many years, and high-reliability proofs for older bulls are needed to estimate marker effects. Data mining algorithms applied to large data sets may help identify unexpected relationships in the data, and improved visualization tools will provide insights. Genomic selection using large data requires a lot of computing power, particularly when large fractions of the population are genotyped. Theoretical improvements have made possible the inversion of large numerator relationship matrices, permitted the solving of large systems of equations, and produced fast algorithms for variance component estimation. Recent work shows that single-step approaches combining BLUP with a genomic relationship (G) matrix have similar computational requirements to traditional BLUP, and the limiting factor is the construction and inversion of G for many genotypes. A na?ve algorithm for creating G for 14,000 individuals required almost 24 h to run, but custom libraries and parallel computing reduced that to 15 m. Large data sets also create challenges for the delivery of genetic evaluations that must be overcome in a way that does not disrupt the transition from conventional to genomic evaluations. Processing time is important, especially as real-time systems for on-farm decisions are developed. The ultimate value of these systems is to decrease time-to-results in research, increase accuracy in genomic evaluations, and accelerate rates of genetic improvement.     

Laboratory rearing of <Emphasis Type="Italic">Halyomorpha halys</Emphasis>: methods to optimize survival and fitness of adults during and after diapause

Laboratory colonies are necessary to conduct year-round research on the invasive brown marmorated stink bug, Halyomorpha halys (Stål), a severe agricultural and nuisance pest in the USA. When adults are collected in the fall to either start or supplement colonies, they require a period of cold storage before they resume sexual development and egg production. There is a lack of understanding of how to collect and store diapause-triggered adults in the laboratory. A series of experiments in 2013–2015 assessed survival and fecundity of stink bugs collected from different locations and stored under different temperatures and durations. We found that a minimum of 7 weeks is necessary to break diapause and that a substantial proportion of adults can survive when stored at constant 9 °C, even for periods longer than needed to terminate diapause. Adults survived significantly better at 6 and 9 °C than at 3 °C in storage for 7 weeks. Longer durations up to 34 weeks in storage reduced adult survival and significantly affected survival rates, timing of first egg laying, and overall fecundity. Location where adults were collected at overwintering sites in the fall had a significant impact on survival in cold storage and colony performance. Adults collected from soybean fields in mid-September and fed in the laboratory for 2 weeks before storage had lower survival than adults collected in October at aggregation sites and stored immediately. The food sources available to H. halys adults at collection locations for nutrition and sequestration of sufficient energy reserves going into diapause are discussed.     

The influence of pregnancy and source of supplemental protein on intake, digestive kinetics and amino acid absorption by ewes

Three experiments were conducted with ewes to determine the effects of pregnancy and(or) supplemental protein source on amino acid absorption and digestive criteria. In Exp. 1, four mated and five nonmated ewes fitted with abomasal and ileal cannulas were offered 272 g of cracked corn/d and ad libitum alfalfa hay (22% CP). Mated ewes absorbed greater quantities (P less than .10) and percentages (P less than .05) of amino acids presented to the abomasum than did nonmated ewes between d 121 and 124 of gestation. In Exp. 2, three nonmated ewes were used in a latin square design experiment to compare amino acid absorption when timothy hay (6% CP; 67% NDF) was offered alone or with supplements of corn plus either alfalfa hay (ALF) or soybean meal (SBM). Supplementation increased total, essential and nonessential amino acid flow to the abomasum and amino acid disappearance. In Exp. 3, 12 mated and 12 nonmated ewes were assigned to treatments in a 2 x 2 factorial arrangement to compare the effects of production status (gestation followed by lactation vs nonmated) and supplemented protein source (ALF vs SBM) on voluntary intake and digestive criteria. Ewes were pulse-dosed with Yb-marked NDF from hay on d 124 and 137 of gestation and d 26 of lactation. During lactation (d 7 to 28), dietary DM intakes were greater (P less than .05) by ewes consuming ALF compared with SBM and by lactating ewes compared with nonmated ewes. Flow rates were greater (P less than .05) from mated ewes throughout the experiment. It appears that pregnant ewes met their increased nutrient demands by increasing flow rates and by more efficient apparent absorption of amino acids.     

A Screening for the Occurrence of Autoreactive Antibodies in Sera of Pregnant and Non-pregnant Bitches

Sera of healthy pregnant (group I, n = 11) and non-pregnant (group II, n = 11) bitches were screened for autoantibodies (AAb). In both groups, blood samples were drawn every fifth day between days 5 and 55 after mating. Serum was analysed via indirect immunofluorescence (IIF) with the Canine ANA HEp-2 Screening Kit. In all animals, anticytoplasmic AAb were detected. Utilizing primate-heart substrate slides AAb against contractile proteins of the cytoplasm could be observed. The predominating fluorescence pattern in pregnant animals resembled above all desmin, which was proven via Western blot. The sera were then pre-incubated with tropomyosin, actin, vimentin, vinculin and keratin solutions, and assessed on HEp-2 slides and on human and canine fibroblasts as well. The latter substrate was used to verify whether the detected Ab were in fact AAb. Utilizing tropomyosin, revealed elimination of the cytoplasmic fluorescences on all three substrates. It is therefore assumed, that in sera of healthy dogs, AAb against contractile structure proteins of the cytoplasm are present regularly. The majority of pregnant bitches presented with higher end-point titres (EPT), than to be found in non-pregnant dogs. AAb against desmin played the key role in those patterns. In addition, sera were screened for thyroid specific AAb, namely thyroglobulin, thyroid peroxidase (TPO), T3 and T4, and for AAb against insulin by ELISA or Western blot (TPO). Only in two of the pregnant bitches a weak positive reaction (1:100) for T3-AAb was detected.     

Ostertagiasis in calves. II. infection parameters and body weight gains following housing

The performance of six groups of six calves each from a previous field experiment was followed from the beginning of housing until turning out seven months later. When housed the groups harboured different levels of infection with Ostertagia ostertagi and had corresponding weight and gain reductions. The most heavily infected groups improved rapidly following housing. Elevated serum pepsinogen levels decreased markedly, and approached normal values at eight weeks. Differences in serum pepsinogen levels between groups diminished considerably, but remained significant over the entire stabling period. The serum albumin level was low in the most seriously affected animals at the time of housing, but normal levels were restored within the first twelve weeks. In general, the number of parasite eggs in the faeces of the animals decreased, but there was considerable fluctuation. Apart from a single sampling date, no significant difference in egg per gram (EPG) could be demonstrated between the experimental groups during the stabling period.The calves were fed according to their age. The live weight differences between most and least affected groups diminished from 64 kg at the time of housing to 37 kg at the end of the stabling period. The reduction took place particularly during the first four weeks of housing.Considering both the grazing and stabling periods, it appeared that anthelmintic treatment twice during the period had no effect on the final live weight, whereas remeated treatments at three-week intervals resulted in an increase of 24 kg. Similarly, moving the animals to a clean pasture in mid-July resulted in an increase of 39 kg at the end of the stabling period when compared to calves which were not moved. Treatment of moved animals did not result in further body weight gain after seven months of housing.No significant correlation was found between parasite EPG of faeces and growth rate during the stabling period. However, a positive correlation was found between serum pepsinogen during the first eight weeks of housing and the weight gain over the entire stabling period. This was in contrast to the correlation experienced during the grazing period.     

微量Bradford法测定提纯禽结核菌素蛋白含量

研究用96孔微量板Bradford法测定提纯禽结核菌素蛋白含量。通过不同浓度的待测禽结核菌素与考马斯亮蓝G-250溶液混合后，在595nm光波下测定各孔样品的OD值。微量Bradford法检测禽结核菌素的线性范围是50—1000μg／mL，相关系数为0．999，最低定量限为50μg／mL。试验用3支禽结核菌素国际参照品，分别配制成125、250、500μg／mL三种不同浓度，每支每种浓度测定4次，计算实际测得的蛋白质浓度。结果显示，批内相对标准偏差为1．6％～4．4％；批间相对标准偏差0．7％-2．2％。研究结果表明微量Bradford法可作为测定禽结核菌素蛋白含量的一种方法。     

Diurnal variation in fecal concentrations of acid-detergent insoluble ash and alkaline-peroxide lignin from cattle fed bermudagrass hays of varying nutrient content

Background

The effect of time of fecal sampling on the accuracy of acid-detergent insoluble ash (ADIA) and alkaline-peroxide lignin (APL) for the prediction of fecal output (FO) in cattle was evaluated. Eight ruminally cannulated cows (594 ± 35.5 kg) were allocated randomly to 4 bermudagrass [Cynodon dactylon (L.) Pers.] hay diets markedly different in crude protein concentration (79–164 g/kg) with 2 replicates per diet for 3 periods. Cows were offered hay individually at 20 g DM/kg of body weight daily in equal feedings at 08:00 and 16:00 h for a 10-d adaptation period followed by 5-d of total fecal collection. Fecal grab samples also were taken each day during the fecal collection period at 06:00, 12:00, 18:00, and 24:00 h either directly from the rectum or from freshly voided feces. Samples were composited within cow and time across the 5 d total fecal collection period. Additionally, forage, ort, and fecal samples were analyzed for concentrations of APL and ADIA.

Results

Fecal concentrations of ADIA and APL were not affected by sampling time (P ≥ 0.22), even though diet affected (P < 0.01) fecal ADIA and APL concentrations. There were no diet × sampling time interactions (P ≥ 0.60). Estimates of FO and dry matter digestibility (DMD) from ADIA and APL were not affected (P ≥ 0.16) by sampling time or the diet × sampling time interaction (P ≥ 0.74). Estimates of FO and DMD from markers from different sampling times or all different combinations of sampling time were not different (P ≥ 0.72) from those of total collection among internal markers.

Conclusion

Little variation in concentrations of ADIA and APL in daily fecal excretion across time increases flexibility in fecal grab sampling schedules for predicting FO and DMD.     

D-optimal designs for mixed discrete and continuous outcomes analyzed using nonlinear models

Many dose-response experiments in toxicology and other biological sciences are designed to measure multiple outcomes. Unfortunately, most of these studies are powered or designed for a single response, and the inference on the under-powered endpoints is limited. As additional design challenges, the outcomes may have different regions and shapes of activity or have different response types. As a new application to the traditional D-optimality criterion, we have developed optimal designs for mixed discrete and continuous outcomes that are analyzed with nonlinear models. These designs use a numerical algorithm to choose the location of the dose groups and proportion of total sample size allocated to each group that minimize the generalized variance of a model-based covariance matrix that incorporates the correlation between outcomes. Using this methodology, we designed a dose-response experiment with binary, count, and continuous outcomes to evaluate neurotoxicity. In this example, the optimal designs placed dose groups at the predicted dose thresholds and throughout the active range. The designs were generally robust to different correlation structures. In addition, when the expected correlation was moderate or large, we observed a substantial gain in efficiency compared to optimal designs created for each outcome separately.     

Effects of bovine cytochrome P450 single-nucleotide polymorphism, forage type and body condition on production traits in cattle

Relating single-nucleotide polymorphisms (SNP) to cows with acceptable productivity could benefit cattle breeders in areas where tall fescue is the predominant forage. This study aimed to (i) identify SNPs in bovine cytochrome P450 3A28 (CYP3A28) and (ii) determine the associations between SNP genotype, forage and cow body condition (BC). Genotype (CC, CG or GG) and forage [Kentucky-31 wild-type endophyte-infected tall fescue (KY+) vs. bermudagrass] effects on milk volume and quality were determined in Herd 1 cows (123 cows); in Herd 2 (99 cows), genotype and BC (low vs. moderate) effects on ovarian follicle size, calving date and calving per cent were determined; and in Herd 3 (114 cows), effects of genotype and fescue cultivar [KY+ vs. non-toxic endophyte-infected tall fescue (HiMag4)] were related to calving per cent, calving date and weaning weights of both cow and her calf. A cytosine (C) to guanine (G) transversion at base 994 (C994G) in CYP3A28 was identified. There was a genotype × forage type interaction (p < 0.05) on milk protein in Herd 1 cows; CC cows grazing bermudagrass had greater milk protein percentage in relation to other cows in the herd. In Herd 2, BC and genotype × BC tended (p < 0.10) to influence follicle size and Julian calving date respectively. Diameter of the largest follicle tended to be larger in moderate BC than in low-BC cows; whereas, CC and CG cows in moderate BC and homozygous (CC and GG) cows in low BC tended to calve 14 days earlier in relation to CG cows in low BC. In Herd 3, there was a genotype × forage type interaction (p < 0.05) on calving per cent, Julian calving date and calf weaning weight. In this study, genetic alterations (G allele at C994G) coupled with nutritional factors (low BC and toxic tall fescue) resulted in overall lower productivity in cows.