Relatedness between numerically small Dutch Red dairy cattle populations and possibilities for multibreed genomic prediction

Red dairy breeds are a valuable cultural and historical asset, and often a source of unique genetic diversity. However, they have difficulties competing with other, more productive, dairy breeds. Improving competitiveness of Red dairy breeds, by accelerating their genetic improvement using genomic selection, may be a promising strategy to secure their long-term future. For many Red dairy breeds, establishing a sufficiently large breed-specific reference population for genomic prediction is often not possible, but may be overcome by adding individuals from another breed. Relatedness between breeds strongly decides the benefit of adding another breed to the reference population. To prioritize among available breeds, the effective number of chromosome segments (M_e) can be used as an indicator of relatedness between individuals from different breeds. The M_e is also an important parameter in determining the accuracy of genomic prediction. The M_e can be estimated both within a population and between 2 populations or breeds, as the reciprocal of the variance of genomic relationships. We investigated relatedness between 6 Dutch Red cattle breeds, Groningen White Headed (GWH), Dutch Friesian (DF), Meuse-Rhine-Yssel (MRY), Dutch Belted (DB), Deep Red (DR), and Improved Red (IR), focusing primarily on the M_e, to predict which of those breeds may benefit from including reference animals of the other breeds. All of these breeds, except MRY, are under high risk of extinction. Our results indicated high variability of M_e, especially between M_e ranging from ～3,500 to ～17,400, indicating different levels of relatedness between the breeds. Two clusters are especially important, one formed by MRY, DR, and IR, and the other comprising DF and DB. Although relatedness between breeds within each of these 2 clusters is high, across-breed genomic prediction is still limited by the current number of genotyped individuals, which for many breeds is low. However, adding MRY individuals would increase the reference population of DR substantially. We estimated that between 11 and 133 individuals from other breeds are needed to achieve accuracy of genomic prediction equivalent to using one additional individual from the same breed. Given the variation in size of the breeds in this study, the benefit of a multibreed reference population is expected to be lower for larger breeds than for the smaller ones.     

Inbreeding and effective population size in French dairy sheep: Comparison between genomic and pedigree estimates

Before availability of dense SNP data, genetic diversity was characterized and managed with pedigree-based information. Besides this classical approach, 2 methodologies have been proposed in recent years to characterize and manage diversity from dense SNP data: the SNP-by-SNP approach and the alternative based on runs of homozygosity (ROH). The establishment of criteria to identify ROH is a current constraint in the literature dealing with ROH. The objective of this study was, using a medium-density SNP chip, to quantify by 3 methods (pedigree, SNP-by-SNP, and ROH) the genetic diversity on 5 selected French dairy sheep subpopulations and breeds and to assess the effect of the definition of ROH on these estimates. The data set available included individuals from the breeds Basco-Béarnaise, Manech Tête Noire, Manech Tête Rousse, and 2 subpopulations of Lacaune: Lacaune Confederation and Lacaune Ovitest. Animals were genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA). After filtering, the genomic data included 38,287 autosomal SNP and 8,700 individuals, which comprised 72,803 animals in the pedigree. The results indicated that no significant differences were observed in effective population size estimates obtained from pedigree or genomic (SNP-by-SNP or ROH) information. In general, estimates of effective population size were above 200 in Lacaune Confederation and Lacaune Ovitest subpopulations and below 200 in Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse breeds. The minimum length that constituted a ROH, the minimum number of SNP that constituted a ROH, as well as the minimum density and the maximum distance allowed between 2 homozygous SNP are ROH-defining factors with important implications in the estimation of the rate of inbreeding. The ROH-based rates of inbreeding in concordance with those obtained from pedigree information require a specific set of values. This particular set of values is different from that identified to obtain ROH-based rates of inbreeding similar to those obtained on a SNP-by-SNP basis. Factors to define ROH do not change the results much unless extreme values are considered, although further research on ROH-based inbreeding is still required.     

Inbreeding in Danish dairy cattle breeds

The purpose of this study was to monitor current and predict future rates of inbreeding in the Danish dairy breeds. Calves born from 1999 until 2003 and registered as Danish Holstein (1,883,983), Danish Jersey (336,966), or Danish Red (261,047) were reference populations. Average complete generation equivalent was approximately 7. For calves born in 2003, average inbreeding was 3.9, 3.4, and 1.4% for Holstein, Jersey, and Danish Red, respectively. In recent years, effective population sizes were 49, 53, and 47, respectively. Based on coancestry statistics, future effective population sizes will be 43, 42, and 51, respectively. The effective number of founders, effective number of ancestors, and effective number of founder genomes were calculated. These measures of genetic diversity were all low for Holstein and Jersey and somewhat larger for Danish Red. The most important ancestors of Danish Holstein were Elevation (13.8%), Chief (10.9%), and Bell (8.5%). The most important ancestor of Danish Red was Momentum (9.4%), a Red Holstein-Friesian. The most important ancestor for Danish Jersey was FYN Lemvig (12.1%) with a large number of progeny in the reference population. The results of this study indicate the necessity for active management of the rate of inbreeding in the future.     

Production and reproduction of Fleckvieh,Brown Swiss,and 2 strains of Holstein-Friesian cows in a pasture-based,seasonal-calving dairy system

The first objective of this study was to compare the productive and reproductive performance of Holstein-Friesian (CH HF), Fleckvieh (CH FV), and Brown Swiss (CH BS) cows of Swiss origin with New Zealand Holstein-Friesian (NZ HF) cows in pasture-based compact-calving systems; NZ HF cows were chosen as the reference population for such grazing systems. The second objective was to analyze the relationships within and between breeds regarding reproductive performance, milk yield, and body condition score (BCS) dynamics. On 15 commercial Swiss farms, NZ HF cows were paired with Swiss cows over 3 yr. Overall, the study involved 259 complete lactations from 134 cows: 131 from 58 NZ HF, 40 from 24 CH HF, 43 from 27 CH FV, and 45 from 25 CH BS cows. All production parameters were affected by cow breed. Milk and energy-corrected milk yield over 270 d of lactation differed by 1,000 kg between the 2 extreme groups; CH HF having the highest yield and CH BS the lowest. The NZ HF cows had the greatest milk fat and protein concentrations over the lactation and exhibited the highest lactation persistency. Body weight differed by 90 kg between extreme groups; NZ HF and CH BS being the lightest and CH HF and CH FV the heaviest. As a result, the 2 HF strains achieved the highest milk production efficiency (270-d energy-corrected milk/body weight^0.75). Although less efficient at milk production, CH FV had a high 21-d submission rate (86%) and a high conception rate within 2 inseminations (89%), achieving high pregnancy rates within the first 3 and 6 wk of the breeding period (65 and 81%, respectively). Conversely, poorer reproductive performance was recorded for CH HF cows, with NZ HF and CH BS being intermediate. Both BCS at nadir and at 100 d postpartum had a positive effect on the 6-wk pregnancy rate, even when breed was included in the model. The BCS at 100 d of lactation also positively affected first service conception rate. In conclusion, despite their high milk production efficiency, even in low-input systems, CH HF were not suited to pasture-based seasonal-calving production systems due to poor reproductive performance. On the contrary, CH FV fulfilled the compact-calving reproduction objectives and deserve further consideration in seasonal calving systems, despite their lower milk production potential.     

Investigations on merging breeds in genetic conservation schemes

Genetic diversity within livestock species is threatened by extinction of breeds and by genetic drift; the need to conserve genetic diversity by conservation schemes is widely accepted. To maintain the between-breed diversity, breeds are usually kept separately in live conservation schemes. However, in some cases it might be very difficult or even impossible to conserve a highly endangered breed in a closed population. If this breed is important for diversity, it might be beneficial to merge it with one or more breeds to conserve a part of the diversity that is contributed by this breed. The present study introduces a general framework that may enable one to decide when it is beneficial to form a synthetic breed that includes highly endangered breeds to maximize conserved diversity and when to keep the breeds separate. Expected future diversities were estimated using a kinship-based diversity measure together with extinction probabilities of the breeds. Using a small hypothetical data set, the pattern of diversity and its 2 components, within-breed and between-breed diversity, were analyzed in detail when forming a synthetic breed. The suggested approach was applied to a data set of 13 central European red and yellow cattle breeds. The results suggested forming a synthetic breed by combining a nonendangered breed with 1 of the 2 highly endangered breeds, which would result in a slight increase in conserved diversity.     

甜菜母根计算机优选软件的研制及应用

采用计算机程序软件对每组1000株甜菜母根进行群体优选的方法在国内属首创。文章介绍了以离散数学为基础建立的数学模型、双目标群体优选方法的原理及应用。该软件具有优选精度高,速度快,性能可靠,使用方便等特点,是替代几十年来一直沿用的传统相关表法和近年来采用的计算机画相关表法的最理想方法。软件为今后甜菜母根检糖化验实现微机管理自动化打下良好基础。     

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Genomic selection has been implemented over the years in several livestock species, due to the achievable higher genetic progress. The use of genomic information in evaluations provides better prediction accuracy than do pedigree-based evaluations, and the makeup of the genotyped population is a decisive point. The aim of this work is to compare the effect of different genotyping strategies (number and type of animals) on the prediction accuracy for dairy sheep Latxa breeds. A simulation study was designed based on the real data structure of each population, and the phenotypic and genotypic data obtained were used in genetic (BLUP) and genomic (single-step genomic BLUP) evaluations of different genotyping strategies. The genotyping of males was beneficial when they were genetically connected individuals and if they had daughters with phenotypic records. Genotyping females with their own lactation records increased prediction accuracy, and the connection level has less relevance. The differences in genotyping females were independent of their estimated breeding value. The combined genotyping of males and females provided intermediate accuracy results regardless of the female selection strategy. Therefore, assuming that genotyping rams is interesting, the incorporation of genotyped females would be beneficial and worthwhile. The benefits of genotyping individuals from various generations were highlighted, although it was also possible to gain prediction accuracy when historic individuals were not considered. Greater genotyped population sizes resulted in more accuracy, even if the increase seems to reach a plateau.     

Estimation of extinction probabilities of five german cattle breeds by population viability analysis

The estimation of the expected loss of genetic diversity and marginal diversities in a set of breeds within a defined future time horizon requires initial estimates of breed extinction probabilities. In this study, the extinction probabilities of 5 German dual-purpose cattle breeds were estimated by population viability analysis. Regression was used to estimate the infinitesimal mean and variance of the population growth and this was based on the diffusion approximation of the density independent population growth (also known as the Dennis regression model). The annual number of milk-recorded cows in each breed was used as census data. Based on the regression results, the extinction probabilities and their confidence intervals were estimated for a wide variety of future time horizons using Monte Carlo time series simulations. The estimates of extinction probabilities were sensible, but in 2 cases they depended heavily on the time horizon considered. Additionally, the confidence intervals became very wide with an increased time horizon. We recommend the estimation of extinction probabilities for a set of future time horizons rather than for a single future time and the selection of an upper bound for this set that is not too large to be meaningful. The validity of the use of the number of milk-recorded cows as census data and of the model assumptions is discussed in detail.     

Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls

Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10–15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.     

Production level,fertility, health traits,and longevity in local and commercial dairy breeds under organic production conditions in Austria,Switzerland, Poland,and Sweden

Our aim was to map the performance of local (native) dairy cattle breeds in Austria, Switzerland, Poland, and Sweden with regard to production, fertility, longevity, and health-associated traits and to compare them with commercial (modern) breeds. For this purpose, we analyzed test-day records (July 1, 2011, to June 30, 2014) and treatment records (Austria, Sweden) of cows managed on organic farms. We performed country-wise comparisons of 123,415 lactations from Original Braunvieh (OB) and Grey Cattle (AL) with Braunvieh (BV; Brown Swiss blood >60%) in Switzerland; AL with BV (Brown Swiss blood >50%) in Austria; Polish Black and White (ZB), Polish Red and White (ZR), and Polish Red (RP) with Polish Holstein Friesian (PHF) in Poland; and Swedish Red (SRB) with Swedish Holstein (SH) in Sweden. Average milk yields were substantially lower for local compared with commercial breeds in all countries; differences ranged from 750 kg (Sweden) to 1,822 kg (Austria), albeit on very different average levels. Local breeds showed a longer productive lifetime by 0.64, 0.83, 1.42, and 0.20 lactations in Switzerland, Austria, Poland, and Sweden, respectively, again on very different levels in each country. Regarding fertility traits, calving interval was shorter in local than in commercial breeds by 13 (Sweden), 14 (Switzerland), and 20 d (Austria, Poland). Insemination index was lower in certain local breeds by 0.15 (Switzerland), 0.14 (Austria), 0.21 (Poland), and 0.13 (Sweden). Several local breeds showed a lower proportion of cows with >100,000 somatic cells/mL. This was the case in Switzerland (OB 24.2%; BV 35.8%), Austria (AL 25.3%; BV 36.9%), and Sweden (SRB 42.4%; SH 43.4%). In contrast, the respective proportion in Poland exceeded 82% in all breeds except the commercial PHF (76.1%). In Sweden, lactations with veterinary treatments were considerably less prevalent in SRB (15.6%) than in SH (21.7%). In Austria, breeds differed only in treatments for udder disorders, which favored AL. In conclusion, the markedly lower milk yields of local breeds are partly counterbalanced by (somewhat inconsistent) advantages in longevity, fertility, and health traits across 4 European countries. This indicates that the robustness of local breeds can contribute to improved sustainability of organic dairy systems.     

Genetic evaluations of dairy bulls for daughter energy balance profiles using linear type scores and body condition score analyzed using random regression

The difference in body lipid between the start and end of lactation represents the body energy lost (or gained) in support of maintaining lactation including the nonproduction components of lactation. This source of energy is ignored in current genetic evaluations for production for dairy sires. The depletion and accretion of body tissue creates a pattern of body energy content over time that is, in part, under genetic control. Using random regression and field data, we modeled changes in body condition score (BCS) and liveweight, predicted from linear type traits, on first parity cows to produce daily breeding values of their sires for energy balance. These curves show that sires differ in the way their daughters lose and regain body energy throughout lactation. For all sires, the overall mean maximum daughter body energy loss was 1499 MJ (SD = 144 MJ) and occurred at d 99 (SD = 12.8 d) of lactation and the mean total daughter body energy loss at d 305 of lactation was 779 MJ (SD = 224 MJ). In this study, the profiles of body energy loss indicate that daughters of most sires lost body energy before d 150 and then recovered body energy, whereas the daughters of a few sires continued to lose body energy through to the end of lactation. Some sires with high merit for production may have daughters with body tissue mobilization profiles associated with poorer health and fertility leading to higher costs. A method of accounting for this cost could be to correct yield for body tissue mobilization. Deducting kilograms of milk from the breeding value for milk for each sire, equivalent in energy content to the body energy lost, resulted in a correlation of 0.98 between the ranking of sires for milk kilograms before and after adjustment. However, some sires changed rank bylarge amounts, the largest being +355 positions. Breeding values for energy balance can be calculated from single observations of BCS and linear type traits on daughters of a sire; data that can routinely be collected in national conformation assessment schemes.     

The impact of 3 strategies for incorporating polled genetics into a dairy cattle breeding program on the overall herd genetic merit

Dehorning in cattle has been associated with behavioral, physiological, and neuroendocrine responses indicative of pain. Unaddressed, the pain associated with a routine production procedure could contribute to a negative public perception of livestock production practices. Alternative considerations of dehorning include the selection of polled cattle within herds, thereby avoiding pain and production loss. As polledness results from an autosomal dominant pattern of inheritance, genetic selection for polled cattle could reduce the prevalence of the horned trait. Herein we discuss 3 strategies to incorporate polled genetics into a cow herd and the estimated impact on the overall genetic merit of the herd. Furthermore, the availability and genetic merit of polled artificial insemination bulls in the United States is summarized. Both Holstein and Jersey dairy bulls registered with the National Association of Animal Breeders from December 2010 through April 2013 were queried. Polled bulls were identified as either being homozygous (PP) or heterozygous (Pp) and the average net merit (NM) predicted transmitting ability (PTA) of each sire group was calculated. The percentage of polled calves born each year over a 10-yr period was calculated for the following 3 scenarios: (A) various percentages of horned cows were randomly mated to Pp bulls, (B) various percentages of horned cows were preferentially mated to Pp bulls, and (C) horned cows were selectively mated to PP bulls, heterozygous cows to Pp bulls, and homozygous polled cows to horned bulls. Additionally, the change in NM PTA of the cow herd was calculated over the same period. The highest percentage of polled animals (87%) was achieved in scenario C. An evaluation of the herd NM PTA highlights the trade-offs associated with increasing polled genetics. Given the current genetic merit of horned and polled bulls, increasing the percentage of polled calves will decrease the NM PTA in Holstein, but may have minimal impact in Jersey herds. Decisions regarding selective breeding to increase polled genetics will need to be evaluated in the context of production objectives, cost of dehorning, and impact on overall genetic merit.     

Symposium review: Novel strategies to genetically improve mastitis resistance in dairy cattle

Mastitis is a disease of major economic importance to the dairy cattle sector because of the high incidence of clinical mastitis and prevalence of subclinical mastitis and, consequently, the costs associated with treatment, production losses, and reduced animal welfare. Disease-recording systems compiling data from a large number of farms are still not widely implemented around the world; thus, selection for mastitis resistance is often based on genetically correlated indicator traits such as somatic cell count (SCC), udder depth, and fore udder attachment. However, in the past years, several countries have initiated collection systems of clinical mastitis, based on producers recording data in most cases. The large data sets generated have enabled researchers to assess incidence of this disease and to investigate the genetic background of clinical mastitis itself, as well as its relationships with other traits of interest to the dairy industry. The genetic correlations between clinical mastitis and its previous proxies were estimated more accurately and confirmed the strong relationship of clinical mastitis with SCC and udder depth. New traits deriving from SCC were also studied, with the most relevant findings being associated with mean somatic cell score (SCS) in early lactation, standard deviation of SCS, and excessive test-day SCC pattern. Genetic correlations between clinical mastitis and other economically important traits indicated that selection for mastitis resistance would also improve resistance against other diseases and enhance both fertility and longevity. However, milk yield remains negatively correlated with clinical mastitis, emphasizing the importance of including health traits in the breeding objectives to achieve genetic progress for all important traits. These studies enabled the establishment of new genetic and genomic evaluation models, which are more efficient for selection to mastitis resistance. Further studies that are potential keys for future improvement of mastitis resistance are deep investigation of the bacteriology of mastitis, identification of novel indicator traits and tools for selection, and development of a larger female reference population to improve reliability of genomic evaluations. These cutting-edge studies will result in a better understanding of the genetic background of mastitis resistance and enable a more accurate phenotyping and genetic selection to improve mastitis resistance, and consequently, animal welfare and industry profitability.     

Graduate Student Literature Review: Understanding the genetic mechanisms underlying mastitis

Mastitis is the costliest disease facing dairy producers today; consequently, it has been the subject of substantial research focus. Efforts have evolved from an initial focus on understanding the etiology of intramammary infections to the application of preventative measures, including attempts to breed cows that are resistant to infection. However, breeding for resistance to infection has proven difficult, given the complexity of the disease and the high expense associated with assembling high-quality genotypes and phenotypes. This review provides a brief background on mastitis; illustrates current understanding of the genetics influencing mastitis and the application of this knowledge; and discusses challenges and limitations in understanding these mechanisms and applying these findings to genetic improvement strategies.     

Genetic basis of thermotolerance in 2 local dairy sheep populations in the Iberian Peninsula

Sheep milk production in the Northern Mediterranean countries heavily relies on local breeds subject to selection schemes to improve milk production. Climate change may shift the range of thermal loads on the animals and challenge their adaptation to the new thermal gradient. The objective of this study was to characterize the genetic component of thermal tolerance of 2 local breeds from the Iberian Peninsula, Latxa and Manchega, belonging to different genetic types that have evolved under different climatic environments (Oceanic for Latxa and Continentalized Mediterranean for Manchega). A total of 79,243 and 2,388,853 test day monthly records of milk, fat and protein yields from 12,882 and 277,904 ewes of Latxa and Manchega breeds, respectively, along a 12-yr period, were matched with the value of the average temperature-humidity index (THI) on the day of milk recording of the closest weather station to the flocks. These data were used to fit individual reaction norms (Legendre polynomials) describing changes in yields along the THI gradient. Genetic values for thermal tolerance were obtained from the slopes of those reaction norms under cold or heat stress and variances and covariances between yield and thermal tolerance were derived from the (co)variance matrices of the polynomial random regression coefficients. Results showed differing patterns in the 2 breeds. The Latxa breed showed clearer signs of genotype by environment interaction than did Manchega. Estimated correlations between yields under extremes of cold and heat were always above 0.8 for Manchega and around 0.4 for Latxa for all traits. Estimates of correlations between comfort and thermal stress were again over 0.8 for Manchega and lower for the higher (hot end) values (down to 0.6) than for the lower (cold end) values (down to 0.84) of the THI gradient for Latxa, indicating greater thermal stress expected from high than from low temperatures in this breed. Substantial variability in thermal tolerance under the more extreme THI values was found in both breeds. Estimated genetic correlations between yield and thermal tolerance were close to 0 and 0.2 for Latxa and Manchega in the cold and down to ?0.6 and ?0.3 in the heat end, although small variation was observed for fat in Latxa. Estimated realized trends from the average estimated breeding value, by year of birth, showed a positive response for yields in both breeds [around 0.1 standard deviation (SD) unit], but a detrimental correlation for thermal tolerance (down to ?0.03 SD units for heat tolerance in Latxa). These results can be used to design optimal selection strategies for sustainable improvement of productivity under a rising-temperature scenario associated with climate change.     

广东青年女性内衣体型特征初探

通过近三年来对广东地区青年女性内衣体型调查研究所得到的数据进行统计分析,得出广东 青年女性内衣体型的基本特征,为进一步开展体型特征研究打下基础.