A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle

Analysis of data on 1000 Holstein-Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy-Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05-0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of > or =3 SNPs were identified. The average block length was 69.7 +/- 7.7 kb, which is approximately 5-10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000-100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require approximately 250,000 SNPs in the discovery phase.     

Understanding the reproductive performance of a dairy cattle herd by using both analytical and systemic approaches: a case study based on a system experiment

Reproductive performance has recently been a growing concern in cattle dairy systems, but few research methodologies are available to address it as a complex problem in a livestock farming system. The aim of this paper is to propose a methodology that combines both systemic and analytical approaches in order to better understand and improve reproductive performance in a cattle dairy system. The first phase of our methodology consists in a systemic approach to build the terms of the problem. It results in formalising a set of potential risk factors relevant for the particular system under consideration. The second phase is based on an analytical approach that involves both analysing the shapes of the individual lactation curves and carrying out logistic regression procedures to study the links between reproductive performance and the previously identified potential risk factors. It makes it possible to formulate hypotheses about the biotechnical phenomena underpinning reproductive performance. The last phase is another systemic approach that aims at suggesting new practices to improve the situation. It pays particular attention to the consistency of those suggestions with the farmer's general objectives. This methodology was applied to a French system experiment based on an organic low-input grazing system. It finally suggested to slightly modify the dates of the breeding period so as to improve reproductive performance. The formulated hypotheses leading to this suggestion involved both the breed (Holstein or Montbéliarde cows), the parity, the year and the calving date with regard to the turnout date as the identified risk factors of impaired performance. Possible use of such a methodology in any commercial farm encountering a biotechnical problem is discussed.     

Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

Background

The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations.

Methods

Twenty QTL for rear leg set side view were mapped using Bayes C. Marker effects estimated during QTL mapping were used to infer the QTL status for each individual. Subsequently, polymorphisms present in the QTL regions were extracted from the whole-genome sequences of 71 Holstein bulls. Only polymorphisms for which the status was concordant with the QTL status were kept as candidate causative mutations.

Results

QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in the QTL region. For some QTL, the concordance analysis was efficient and narrowed down to a limited number of candidate mutations located in one or two genes, while for other QTL a large number of genes contained concordant polymorphisms.

Conclusions

For regions for which the concordance analysis could be performed, we were able to reduce the number of candidate mutations. For part of the QTL, the concordant analyses narrowed QTL regions down to a limited number of genes, of which some are known for their role in limb or skeletal development in humans and mice. Mutations in these genes are good candidates for QTN (quantitative trait nucleotides) influencing rear leg set side view.     

Effect of genotyped cows in the reference population on the genomic evaluation of Holstein cattle

This study evaluated the dependence of reliability and prediction bias on the prediction method, the contribution of including animals (bulls or cows), and the genetic relatedness, when including genotyped cows in the progeny-tested bull reference population. We performed genomic evaluation using a Japanese Holstein population, and assessed the accuracy of genomic enhanced breeding value (GEBV) for three production traits and 13 linear conformation traits. A total of 4564 animals for production traits and 4172 animals for conformation traits were genotyped using Illumina BovineSNP50 array. Single- and multi-step methods were compared for predicting GEBV in genotyped bull-only and genotyped bull-cow reference populations. No large differences in realized reliability and regression coefficient were found between the two reference populations; however, a slight difference was found between the two methods for production traits. The accuracy of GEBV determined by single-step method increased slightly when genotyped cows were included in the bull reference population, but decreased slightly by multi-step method. A validation study was used to evaluate the accuracy of GEBV when 800 additional genotyped bulls (POPbull) or cows (POPcow) were included in the base reference population composed of 2000 genotyped bulls. The realized reliabilities of POPbull were higher than those of POPcow for all traits. For the gain of realized reliability over the base reference population, the average ratios of POPbull gain to POPcow gain for production traits and conformation traits were 2.6 and 7.2, respectively, and the ratios depended on heritabilities of the traits. For regression coefficient, no large differences were found between the results for POPbull and POPcow. Another validation study was performed to investigate the effect of genetic relatedness between cows and bulls in the reference and test populations. The effect of genetic relationship among bulls in the reference population was also assessed. The results showed that it is important to account for relatedness among bulls in the reference population. Our studies indicate that the prediction method, the contribution ratio of including animals, and genetic relatedness could affect the prediction accuracy in genomic evaluation of Holstein cattle, when including genotyped cows in the reference population.     

Problems in assessing multiple cutaneous melanoma. A review on the accuracy of a population based cancer registry

Databases with information on malignant tumors are of great value for epidemiologic studies. From the Regional South Swedish Tumour Registry, which is of documented high quality, 24 patients out of 8008 with reported melanoma diagnosis 1973–2003 were reported as having multiple (≥3) primary, invasive cutaneous malignant melanomas (CMM). Of the 76 tumours identified in these patients, 7 (9%) were found not to be invasive melanomas. Additional cases could be put into question since the lesions could be interpreted as epidermotropic metastases, a diagnosis which can be difficult to establish reliably by microscopic examination. Among the 24 patients we could also identify 8 (10%) additional lesions representing invasive CMM, not included in the Tumour Registry database. Thorough information concerning an earlier melanoma diagnosis and its site of presentation is needed from the clinician and the pathologist for optimal assessment of the histology and the prognostication of the patient, as well as proper reporting to a tumour registry. Identifying multiple primary malignant melanomas is also of special importance for counselling patients belonging to families with hereditary disease. In this study it is shown that diagnosing and reporting multiple malignant melanomas can be problematic due to insufficient communication and to the rare and deceptive capability of cutaneous metastases to imitate primary tumours.     

Study of the genetic structure of dairy cattle based on polymorphism within the aromatase gene

The study included 1083 Polish Holstein-Friesian strain Black-and-White cows. The genetic structure of the herd was determined on the basis of polymorphism within the aromatase gene (CYP 19/Cfr13I and CYP 19/PvuII). Genotypes were identified by the PCR-RELP method. The (CYP 19/Cfr13I allele frequencies were as follows: A-0.86 and B-0.14. The CYP 19/PvuII allele frequencies were as follows: A-0.91, B-0.09. The highest average heterozygosity rate was found in herd A (0.2108). The largest genetic distance eas between cows kept in farms A and C (0.00103). The article is published in the original.     

The frequency of endemic fetal loss in dairy cattle: a review

Estimates of the frequency of endemic fetal loss range from 0.4 to 10.6%, a 26-fold difference, in 26 studies of dairy herds over 5 decades. Sources of this difference include breed, geographic, study population, case definition and procedural differences. The definition of fetal loss was inconsistent among the studies and was often not clearly stated. Twelve of the studies cited only visually observed losses, while the remainder reported losses of all known pregnancies but using different gestational at-risk periods. Definitions of the resulting frequency measure and methods of computation varied widely among the studies. Fetal loss frequencies have been reported as ratios, proportions, incidence rates and cumulative incidence rates. Denominators used in frequency calculations have included the number of pregnant cows, number of cows in the breeding herd, number of cows that calved before or after the risk period and number of calves born. These procedural differences make comparisons among studies and an overall estimate of an expected frequency of endemic fetal loss in dairy cattle difficult at best. Procedural and definition differences aside, the median frequency of fetal loss from studies enumerating only observed abortions was 1.95% and from the studies that included both observed and unobserved abortions 6.5%. Based on this difference, approximately only 30% of endemic fetal losses are observed visually.     

Automatic recording of individual oestrus vocalisation in group-housed dairy cattle: development of a cattle call monitor

Oestrus detection remains a problem in the dairy cattle industry. Therefore, automatic detection systems have been developed to detect specific behavioural changes at oestrus. Vocal behaviour has not been considered in such automatic oestrus detection systems in cattle, though the vocalisation rate is known to increase during oestrus. The main challenge in using vocalisation to detect oestrus is correctly identifying the calling individual when animals are moving freely in large groups, as oestrus needs to be detected at an individual level. Therefore, we aimed to automate vocalisation recording and caller identification in group-housed dairy cows. This paper first presents the details of such a system and then presents the results of a pilot study validating its functionality, in which the automatic detection of calls from individual heifers was compared to video-based assessment of these calls by a trained human observer, a technique that has, until now, been considered the ‘gold standard’. We developed a collar-based cattle call monitor (CCM) with structure-borne and airborne sound microphones and a recording unit and developed a postprocessing algorithm to identify the caller by matching the information from both microphones. Five group-housed heifers, each in the perioestrus or oestrus period, were equipped with a CCM prototype for 5 days. The recorded audio data were subsequently analysed and compared with audiovisual recordings. Overall, 1404 vocalisations from the focus heifers and 721 vocalisations from group mates were obtained. Vocalisations during collar changes or malfunctions of the CCM were omitted from the evaluation. The results showed that the CCM had a sensitivity of 87% and a specificity of 94%. The negative and positive predictive values were 80% and 96%, respectively. These results show that the detection of individual vocalisations and the correct identification of callers are possible, even in freely moving group-housed cattle. The results are promising for the future use of vocalisation in automatic oestrus detection systems.     

Aetiology and pathogenesis of cystic ovarian follicles in dairy cattle: a review

Cystic ovarian follicles (COF) are an important ovarian dysfunction and a major cause of reproductive failure in dairy cattle. Due to the complexity of the disorder and the heterogeneity of the clinical signs, a clear definition is lacking. A follicle becomes cystic when it fails to ovulate and persists on the ovary. Despite an abundance of literature on the subject, the exact pathogenesis of COF is unclear. It is generally accepted that disruption of the hypothalamo-pituitary-gonadal axis, by endogenous and/or exogenous factors, causes cyst formation. Secretion of GnRH/LH from the hypothalamus-pituitary is aberrant, which is attributed to insensitivity of the hypothalamus-pituitary to the positive feedback effect of oestrogens. In addition, several factors can influence GnRH/LH release at the hypothalamo-pituitary level. At the ovarian level, cellular and molecular changes in the growing follicle may contribute to anovulation and cyst formation, but studying follicular changes prior to cyst formation remains extremely difficult. Differences in receptor expression between COF and dominant follicles may be an indication of the pathways involved in cyst formation. The genotypic and phenotypic link of COF with milk yield may be attributed to negative energy balance and the associated metabolic and hormonal adaptations. Altered metabolite and hormone concentrations may influence follicle growth and cyst development, both at the level of the hypothalamus-pituitary and the ovarian level.     

Development of a dairy cattle drinking water quality index (DCWQI) based on fuzzy inference systems

The critical role of water quality for all animals, and especially dairy cattle, the dairy products of which are consumed by humans, raises the need for an index which represents well the quality of water consumed by dairy cattle. Noting the high subjectivity and inappropriate classifications that traditional methods apply to development an index, we aimed to develop a better index that measures the quality of drinking water supplied to dairy cattle (DCWQI¹) based on fuzzy logic. Using fuzzy logic enabled us to capture experts’ knowledge and to simulate the human's way of thinking in the design of the index. Our approach avoided the shortcomings of the previous models. We selected 20 parameters that available literature determined were critical to assessing the quality of water for dairy cattle to drink due mainly to their potential impacts both on dairy cattle and human health. These parameters were: dissolved oxygen (DO), biochemical oxygen demand (BOD), pH, temperature, total dissolved solids (TDS), turbidity, fecal coliform, heterotrophic plate count, hardness, alkalinity, arsenic, lead, mercury, nickel, cadmium, chromium, total phosphorous, H₂S, nitrate, and fluoride. We used trapezoidal membership functions and the final ruleset consisted of 550 rules. Mamdani inference system captured experts’ knowledge and experience; center-of-gravity method was used to defuzzify the results. To evaluate the index performance, we conducted a case study of Karun River employing the water quality data from six sampling stations along the river over the period of 2007–2010 and compared the results to those from the National Sanitation Foundation (NSF) water quality index (WQI). Our study found that the water quality of Karun River lies in the low to medium range (annual mean index values of 38–55). In addition, the values from the fuzzy DCWQI were generally lower than the values from the NSF WQI, mainly because the DCWQI included heavy metals in its index, while the NSF WQI did not. Results of the present study suggest that DCWQI can be considered as a comprehensive tool for assessing the quality of water for dairy cattle drinking purposes and can be reliably used for that objective.     

Optimizing the accuracy of detecting a functional corpus luteum in dairy cows

The objectives were to evaluate the accuracy of detecting a functional CL by transrectal palpation and ultrasonography, and to optimize the accuracy of detecting a functional CL by ultrasonography in Holstein cows. In Experiment 1, four veterinarians performed transrectal palpation in 1250 cows at 37 d in milk (DIM), two veterinarians repeated transrectal palpation in 823 cows at 58 DIM, and one veterinarian performed 206 ultrasonographic examinations at 37 DIM. In Experiment 2, 987 and 983 ultrasonographic examinations were performed at 21 and 24 d after AI by one veterinarian for detection and measurement of CL. Cows with a blood progesterone concentration > or =1ng/mL were assumed to have a functional CL. Sensitivity and specificity were optimized using receiver operating characteristic analysis. In Experiment 1, sensitivity of transrectal palpation for diagnosing a functional CL ranged from 33.3 to 59.9% at 37 DIM and from 48.3 to 68.4% at 58 DIM, whereas specificity ranged from 76.7 to 93.2% at 37 DIM and from 73.3 to 86.7% at 58 DIM. Sensitivity and specificity for ultrasonography were 89.4 and 45.7%, respectively. In Experiment 2, the sensitivity and specificity of ultrasonography were 97.3 and 38.1% at 21 d after AI, and were 97.9 and 51.0% at 24 d after AI. Sensitivity and specificity were optimized using a cutoff diameter of 23mm at 21 d and 22mm at 24 d, which resulted in sensitivity and specificity of 87.2 and 83.0% at 21 d, and 89.5 and 89.4% at 24 d after AI, respectively. Sensitivity was low and specificity was high for transrectal palpation, whereas ultrasonography resulted in high sensitivity and low specificity. Using a cutoff diameter during ultrasonography improved accuracy of detection of a functional CL compared with either ultrasonography without cutoff or transrectal palpation.     

Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals

Amplified fragment length polymorphisms (AFLP) are dominant markers frequently used to build linkage maps where heterozygosity could be inferred by a backcross breeding strategy. In the present study, we describe the utilization of an unmanipulated great reed warbler, Acrocephalus arundinaceus pedigree to infer heterozygous genotypes of AFLP markers in order to map these markers to a partial linkage map previously based on microsatellites. In total, 50 of the 83 autosomal AFLPs (60%) and 4 of 5 Z-linked AFLPs (80%) were mapped. For each marker, on average, 88% of the expected number of heterozygote parents was detected. The likelihood of map assignment was to a large extent due to the number and density of microsatellite markers already in the map. The 'parsimonious linkage map', that is the map based on the most parsimonious location of all significantly linked markers, consisted of 21 autosomal linkage groups with 2 to 15 markers and had a total map size of 552 cM in males and 858 cM in females. The Z-chromosome linkage group with 12 markers had a size of 155 cM. The autosomal 'framework linkage map', that is the map based only on markers with an unambiguous position, had a total size of 237 cM in males and 440 cM in females, respectively. The inclusion of AFLPs enlarged the previous map substantially (e.g. the autosomal parsimonious linkage map became 441 cM and 621 cM larger for male and female recombination, respectively). The probability that an AFLP became mapped increased with increasing level of heterozygosity, whereas the probability of mapping into a framework position increased with both heterozygosity and number of genotyped individuals. Our results suggest that AFLP provides a fast and inexpensive means of enlarging genetic maps already composed of markers with high polymorphism, also in wild populations with unmanipulated pedigrees.     

核糖体RNA二级结构对拓扑结构准确性的影响

探讨了核糖体小亚基二级结构对真菌系统发育分析的影响。对用不同方法构建的系统发育树进行比较,结果表明结合二级结构信息的分析方法较传统方法产生了更为合理的拓扑结构。二级结构信息除用于优化序列比对外,还需整合到核酸替代模型中;恰当的序列比对方法、进化模型和建树运算法则有助于更加准确地揭示类群之间的亲缘关系。     

Effect of pregnancy on the genetic evaluation of dairy cattle

We investigated the effect of stage of pregnancy on estimates of breeding values for milk yield and milk persistency in Gyr and Holstein dairy cattle in Brazil. Test-day milk yield records were analyzed using random regression models with or without the effect of pregnancy. Models were compared using residual variances, heritabilities, rank correlations of estimated breeding values of bulls and cows, and number of nonpregnant cows in the top 200 for milk yield and milk persistency. The estimates of residual variance and heritabilities obtained with the models with or without the effect of pregnancy were similar for the two breeds. Inclusion of the effect of pregnancy in genetic evaluation models for these populations did not affect the ranking of cows and sires based on their predicted breeding values for 305-day cumulative milk yield. In contrast, when we examined persistency of milk yield, lack of adjustment for the effect of pregnancy overestimated breeding values of nonpregnant cows and cows with a long days open period and underestimated breeding values of cows with a short days open period. We recommend that models include the effect of days of pregnancy for estimation of adjustment factors for the effect of pregnancy in genetic evaluations of Dairy Gyr and Holstein cattle.     

Path-finding in real and simulated rats: assessing the influence of path characteristics on navigation learning

A large body of experimental evidence suggests that the hippocampal place field system is involved in reward based navigation learning in rodents. Reinforcement learning (RL) mechanisms have been used to model this, associating the state space in an RL-algorithm to the place-field map in a rat. The convergence properties of RL-algorithms are affected by the exploration patterns of the learner. Therefore, we first analyzed the path characteristics of freely exploring rats in a test arena. We found that straight path segments with mean length 23 cm up to a maximal length of 80 cm take up a significant proportion of the total paths. Thus, rat paths are biased as compared to random exploration. Next we designed a RL system that reproduces these specific path characteristics. Our model arena is covered by overlapping, probabilistically firing place fields (PF) of realistic size and coverage. Because convergence of RL-algorithms is also influenced by the state space characteristics, different PF-sizes and densities, leading to a different degree of overlap, were also investigated. The model rat learns finding a reward opposite to its starting point. We observed that the combination of biased straight exploration, overlapping coverage and probabilistic firing will strongly impair the convergence of learning. When the degree of randomness in the exploration is increased, convergence improves, but the distribution of straight path segments becomes unrealistic and paths become 'wiggly'. To mend this situation without affecting the path characteristic two additional mechanisms are implemented: a gradual drop of the learned weights (weight decay) and path length limitation, which prevents learning if the reward is not found after some expected time. Both mechanisms limit the memory of the system and thereby counteract effects of getting trapped on a wrong path. When using these strategies individually divergent cases get substantially reduced and for some parameter settings no divergence was found anymore at all. Using weight decay and path length limitation at the same time, convergence is not much improved but instead time to convergence increases as the memory limiting effect is getting too strong. The degree of improvement relies also on the size and degree of overlap (coverage density) in the place field system. The used combination of these two parameters leads to a trade-off between convergence and speed to convergence. Thus, this study suggests that the role of the PF-system in navigation learning cannot be considered independently from the animals' exploration pattern.     

Competitive order as a measure of social dominance in dairy cattle

Three experiments were used to examine competitive orders as measures of the social hierarchy in dairy cattle. A least squares procedure, which regressed for numbers of observations, was used for obtaining dominance values, from observations of agonistic behaviour. Behavioural data were quantified by time-lapse photography at 1-min intervals. Dominance value was of little importance relative to production variables in describing the amount of time spent eating a limited amount of grain, concentrate, or hay. Likewise, production oriented variables were more important in describing time spent in free stalls or at the feed trough at five levels of competition. Individual feed intakes of group fed dairy cattle at two levels of competition were described predominantly by production variables. From these data, competitive orders are not measures of social dominance in dairy cattle. Dominance values did not describe a priority of access to feed or resting sites.