Multi-trait Animal Model Research Articles

On the trail of detecting genetic (co)variation between resistance to parasite infections (Diplectanum aequans and Lernanthropus kroyeri) and growth in European seabass (Dicentrarchus labrax)

The European seabass is one of the main commercial fish produced in Mediterranean marine aquaculture. Recently, its production has been negatively affected by losses due to frequent and recurring outbreaks of parasitic, bacterial and viral diseases. In recent years, the gill parasites Diplectanum aequans and Lernanthropus kroyeri are increasingly becoming more dominant and contributing more significantly to the observed losses. Genetic improvement for disease resistance represents an important strategy for controlling infectious diseases in farmed fish by increasing their robustness. In order to determine the possibility of including such trait in selective breeding programs, we need to comprehend whether additive genetic variation for resistance against Diplectanum aequans and Lernanthropus kroyeri exists. For this purpose, two open-sea parasite cohabitation trials (for two consecutive years) were performed in the commercial production sites of a private company (Nireus S.A), that had high infestation with Diplectanum aequans and Lernanthropus kroyeri. Juvenile European seabass (9425 offspring from 91 full-sib and half-sib families per year), originating from the company's breeding program were equally divided into two groups and transferred to two commercial farming sites located in the areas of Nafpactos and Sagiada, in western Greece, for the intended cohabitation studies. The parasite numbers on all the gill arches were counted and recorded at the end of the trials for the infestation levels. A third site (Palairos) without any parasite infestation was used as a control site. A multi-trait animal model was used to estimate the variance-covariance components and to evaluate the genetic parameters for Parasite Counts, recorded from all the gill arches of the fish, and their corresponding growth in sea cages. The estimated heritabilities for parasite count, using untransformed data, were 0.20 (D. aequans) and 0.28 (L. kroyeri) and for transformed data 0.29 and 0.26, respectively. The heritability estimates for body weight were 0.42−0.51 for D. aequans and 0.28−0.51 for L. kroyeri trials. Similarly, estimated heritabilities for the growth in sea cages were 0.43 and 0.29, respectively. Although parasite count has a low to medium unfavorable genetic correlation with body weight and growth (0.09−0.37), it seems that it is not significantly impairing selection for growth. Furthermore, the results of this study are very promising in terms of the existing potential for genetic improvement of parasite resistance, and provides a good basis for further genetic analysis using molecular markers.

Genetic associations between growth traits and age at first calving in Guzera cattle using random regression models

The aim of this study was to estimate genetic associations between body weight (BW), scrotal circumference (SC), and age at first calving (AFC) in Guzera cattle using random regression models. The analyses used 159,366 and 23,780 records of BW and SC obtained between 335 and 724 days of age and divided into classes at intervals of 10 days, as well as 63,596 records of AFC. A multitrait animal model via Gibbs sampling was adopted that included random direct additive genetic, permanent environmental (only for BW and SC), and residual effects. The fixed effects considered were the contemporary group, age of cow at calving (linear and quadratic effect), and the fixed curve to model the average trend of the population on the age classes of the animals. For BW and SC, four models were compared using the deviance information criterion, with Legendre polynomials ranging from one to four coefficients (intercept, linear, quadratic, and cubic) for additive genetic and permanent environmental effects. The model with three coefficients (quadratic) was considered the most appropriate to describe the (co)variance structure of the traits analyzed. The mean heritability estimates ranged from 0.17 to 0.31 for BW and from 0.19 to 0.28 for SC across age classes. The mean heritability for AFC was 0.07. The genetic correlations between BW and SC across age classes were always positive and favorable, ranging from 0.33 to 0.39. These findings indicate that selection for higher BW should result in animals with greater SC. The genetic correlations between BW at different ages and AFC ranged from -0.56 to -0.38, while those between SC at different ages and AFC ranged from -0.55 to 0.08. Except for some genetic correlations close to zero and positive between SC close to 365 days of age and AFC, in general the results showed that the selection for either higher BW or greater SC should result in a reduction of AFC in Guzera cattle. Calculation of the relative selection efficiency indicated a greater correlated response in AFC by selection for SC, especially after 634 days of age, compared to direct selection for AFC.

Estimation of Genetic Parameters and Correlation between Yearling Ultrasound Measurements and Carcass Traits in Hanwoo Cattle.

Simple SummaryKnowledge of genetic parameters is essential to obtain breeding values in order to increase the response to selection and incorporate novel traits in designing a breeding program. There is a growing demand for the genetic improvement of carcass traits in the Korean beef industry. The use of yearling ultrasound measurements as indicator traits can be an efficient way to evaluate carcass traits. To date, the assessment of genetic parameters for ultrasound measurements in Hanwoo cattle is still limited. Therefore, this study was conducted to estimate the heritability, and the genetic and phenotypic correlations of yearling ultrasonic and carcass traits in Hanwoo cattle. The results revealed moderate to high heritability estimates for the traits of interest, which indicate a probable increase in the response to selection for these traits. Moreover, high and favorable genetic correlations were observed between carcass traits and their corresponding ultrasound measurements. Our findings suggest that the inclusion of yearling ultrasound data on potential replacements would be suitable as a selection tool for genetic improvement of carcass traits in Hanwoo breeding programs.Genetic parameters have a significant role in designing a breeding program and are required to evaluate economically important traits. The objective of this study was to estimate heritability and genetic correlation between yearling ultrasound measurements, such as backfat thickness (UBFT), eye muscle area (UEMA), intramuscular fat content (UIMF), and carcass traits, such as backfat thickness (BFT), carcass weight (CW), eye muscle area (EMA), marbling score (MS) at approximately 24 months of age, as well as yearling weight (YW) in Hanwoo bulls (15,796) and steers (5682). The (co) variance components were estimated using a multi-trait animal model. Moderate to high heritability estimates were obtained and were 0.42, 0.50, 0.56, and 0.59 for CW, EMA, BFT, and MS, respectively. Heritability estimates for yearling measurements of YW, UEMA, UBFT, and UIMF were 0.31, 0.32, 0.30, and 0.19, respectively. Favorable and strong genetic correlations were observed between UIMF and MS (0.78), UBFT and BFT (0.63), and UEMA and EMA (0.65). Moreover, the estimated genetic correlation between YW and CW was high (0.84) and relatively moderate between YW and EMA (0.43). These results suggest that genetic improvement can be achieved for carcass traits when using yearling ultrasound measurements as selection criteria in ongoing Hanwoo breeding programs.

Estimation of (Co)Variance components and genetic parameters of fibre traits in Rambouillet sheep using multi-trait analysis.

The present study aimed to estimate the genetic parameters of different fibre traits, viz., greasy fleece weight, staple length, and fibre diameter in Rambouillet sheep population using a multi-trait animal model. Data, spanning over 10 years (1998-2007) and pertaining to fibre traits at first clip, were collected for a total of 4186 Rambouillet sheep maintained at an organized farm. (Co)Variance structure and genetic parameters were estimated using a multi-trait animal model. The genetic analysis of data was performed based on restricted maximum likelihood (REML) procedure using WOMBAT software. The model incorporated sex of lamb (i = 1, 2), year of birth (j = 1-10), season of birth (k = 1-2), and litter size (l = 1-2) as fixed effects while direct additive genetic and maternal genetic effects were included as random effects. The direct additive genetic heritability estimates were 0.120±0.034, 0.136±0.037, and 0.356±0.070 for greasy fleece weight, staple length, and fibre diameter, respectively. The maternal genetic heritability of all fibre traits under study was very low. Additive genetic correlation was positive and low between greasy fleece weight and staple length; and between staple length and fibre diameter. In conclusion, fibre diameter was moderately heritable which implies that selection may lead to moderate improvement in this trait. The results from the present study will help in formulating optimal breeding plans for improvement of fibre traits in Rambouillet sheep.

Genetic Parameters and Genome-Wide Association Studies of Eight Longevity Traits Representing Either Full or Partial Lifespan in Chinese Holsteins.

Due to the complexity of longevity trait in dairy cattle, two groups of trait definitions are widely used to measure longevity, either covering the full lifespan or representing only a part of it to achieve an early selection. Usually, only one group of longevity definition is used in breeding program for one population, and genetic studies on the comparisons of two groups of trait definitions are scarce. Based on the data of eight traits well representing the both groups of trait definitions, the current study investigated genetic parameters and genetic architectures of longevity in Holsteins. Heritabilities and correlations of eight longevity traits were estimated using single-trait and multi-trait animal models, with the data from 103,479 cows. Among the cows with phenotypes, 2,630 cows were genotyped with the 150K-SNP panel. A single-trait fixed and random Circuitous Probability Unification model was performed to detect candidate genes for eight longevity traits. Generally, all eight longevity traits had low heritabilities, ranging from 0.038 for total productive life and herd life to 0.090 for days from the first calving to the end of first lactation or culling. High genetic correlations were observed among the traits within the same definition group: from 0.946 to 0.997 for three traits reflecting full lifespan and from 0.666 to 0.997 for five traits reflecting partial productive life. Genetic correlations between two groups of traits ranged from 0.648 to 0.963, and increased gradually with the extension of lactations number regarding the partial productive life traits. A total of 55 SNPs located on 25 chromosomes were found genome-wide significantly associated with longevity, in which 12 SNPs were associated with more than one trait, even across traits of different definition groups. This is the first study to investigate the genetic architecture of longevity representing both full and the partial lifespan simultaneously, which will assist the selection of an appropriate trait definition for genetic improvement of longevity. Because of high genetic correlations with the full lifespan traits and higher heritability, the partial productive life trait measured as the days from the first calving to the end of the third lactation or culling could be a good alternative for early selection on longevity. The candidate genes identified by this study, such as RPRM, GRIA3, GTF2H5, CA5A, CACNA2D1, FGF10, and DNAJA3, could be used to pinpoint causative mutations for longevity and further benefit the genomic improvement of longevity in dairy cattle.

Impact of Interbeef on national beef cattle evaluations

International evaluation models for beef cattle allow to compare animals’ estimated breeding values (EBV) across different countries, thanks to sires having offspring in more than one country. In this study we aimed to provide an up-to-date picture of the Interbeef international beef cattle evaluations from a national perspective, considering both large and small populations. Limousin age-adjusted weaning weight (AWW) phenotypes were available for 3,115,598 animals from 10 European countries, born between 1972 and 2017. EBV and reliabilities were obtained using a multi-trait animal model including maternal effects where AWW from different countries are modelled as different traits. We investigated the country of origin of the sires with internationally publishable EBV and, among them, the country of origin of the top 100 sires for each country scale. All countries had 20 to 28,557 domestic sires whose EBV were publishable, according to Interbeef’s rules, on the scale of other countries. All countries, except one, had domestic sires that ranked among the top 100 sires on other country scales. Across countries, inclusion of information from relatives recorded in other countries increased the reliability of EBV for domestic animals on average by 9.6 percentage points for direct EBV, and 8.3 percentage points for maternal EBV. In conclusion, international evaluations provide small countries access to a panel of elite foreign sires with EBV on their country scale and a more accurate estimation of EBV of domestic animals, while large countries obtain EBV for their sires on the scale of different countries which helps to better promote them.

Genetic parameter estimates for milkability traits and their relationship with somatic cell score in South African Holstein cattle

Milkability is an important functional trait, which is directly related to milking costs and udder health. There are no milkability traits incorporated in the South African dairy cattle breeding objectives and genetic parameter estimates for these traits are not available in this population. The main objective of the study was, therefore, to estimate the genetic parameters for milkability traits and its correlation with somatic cell scores in South African Holstein cattle. Data consisted of production and milkability records of 2719 Holstein cows, from ten herds, collected from 2016 to 2018. Genetic parameters were estimated by a multi-trait animal model using the restricted maximum likelihood (REML) procedure. Means for milking time (MT), average milk flow (AMF), maximum milk flow (MMF), and somatic cell score (SCS) were 5.20min, 1.91kg/min, 2.99kg/min, and 2.06, respectively. The heritability estimates were low to moderate from 0.19 ± 0.07, 0.24 ± 0.06, 0.36 ± 0.11, and 0.41 ± 0.12, respectively, for SCS, AMF, MT, and MMF. The genetic correlations were significant (P < 0.05) among the three milkability traits ranged from - 0.31 ± 0.05 between AMF and MT to 0.85 ± 0.02 between AMF and MMF. Positive genetic correlations were observed between AMF and MMF, while the correlations for MT with the remaining milkability traits were negative. Genetic correlations of SCS with AMF, MMF, and MT were - 0.13 ± 0.04, 0.13 ± 0.04, and - 0.25 ± 0.12, respectively. The mean estimated breeding value (EBV) was estimated using cattle birth dates, and there was an increase in AMF of 0.0001kg/min EBV per year on cattle born during the period 2002 to 2014. Maximum milk flow also showed an increasing genetic trend of 0.0003kg/min per year over the same period. On the other hand, the genetic trend for MT was undesirable, as it increased by 0.0003kg/min per year. The moderate to high heritability estimates for milkability traits showed that selection for improvement was possible in South African Holstein cattle. High genetic correlation between AMF and MMF implied that these two may be regarded as the same trait. Milking time can contribute towards improving the accuracy of estimating EBVs for SCS in a multi-trait analysis, and vice versa, due to the moderate correlation between the two traits. The marginal genetic trend in milkability traits may be an interrelated response to selection of other traits already under selection in the population such as SCS. Results of the current study provided a basis for including milkability traits of South African Holstein cattle in the breeding objectives.

Genetic Parameters for Age at First Calving and First Calving Interval of Beef Cattle.

The objective of this study was to estimate genetic parameters for age at first calving (AFC) and first calving interval (FCI) for the entire beef cattle population and separately for the Charolais (CH) and Aberdeen Angus (AA) breeds in the Czech Republic. The database of performance testing between the years 1991 and 2019 was used. The total number of cows was 83,788 from 11 breeds. After editing, the data set contained 33,533 cows, including 9321 and 4419 CH and AA cows, respectively. The relationship matrix included 85,842 animals for the entire beef population and 24,248 and 11,406 animals for the CH and AA breeds, respectively. A multibreed multitrait animal model was applied. The estimated heritability was low to moderate. Genetic correlations between AFC and FCI varied depending on the breeds from positive to negative. Differences between variance components suggest that differences between breeds should be considered before selection and breeding strategy should be developed within a breed.

Multi-trait animal model based estimation of direct and correlated responses in Frieswal cattle

The study was undertaken to estimate the genetic parameters, direct and correlated responses for the test day and lactation milk yield in Frieswal cattle. Data on 9,955 daily milk yield records of 973 Frieswal cows calved during 2005 to 2014 at Ambala and Meerut dairy farms were utilized. The variance components, heritability estimates, genetic and phenotypic correlations for all the 11 traits were estimated simultaneously by fitting multi-trait animal model using the Wombat program of Meyer (2006) with contemporary groups as fixed effect, the additive genetic random effects, linear and quadratic regressions of covariate age at first calving and linear regression of covariate first lactation length. The expected genetic gain (DG), correlated response (CR) in cumulative 305-day yield and vice versa and the relative efficiency (RE %) of selection based on different test day yields were estimated. The results revealed lower additive genetic variance and heritability estimates for different test days and cumulative 305-day yield. The genetic correlations between the test days up to 225 and cumulative 305-days were higher which indicated the positive relationship between these traits. The higher correlated responses in cumulative 305- day yield estimated through the selection for TD135, TD165 and TD45, in that order indicated that early selection of sires using test day records would be efficient in genetic improvement for lactational milk yield in Frieswal breed of cattle.

Genetic parameters for production traits, resistance and resilience to Nematode parasites under different worm burden challenges in Corriedale sheep

Characterized as the most important gastrointestinal parasite (GIP) in the world, Haemonchus contortus is also the most predominant and pathogenic genus in Uruguay, causing high morbidity and mortality rates in sheep flocks. For approximately 26 years resistance to GIP has been included in the National Genetic Evaluation (NGE) of Corriedale and Merino breeds, using Faecal Egg Count (FEC) as the selection criterion. The aim of the present study was to estimate genetic parameters for FEC, post-weaning Body Weight (BW), Packed Cell Volume (PCV), FAMACHA© and Body Condition Score (BCS), to determine the possibility to include these traits in the NGE of GIP resistance and resilience, as complementary selection criteria and to investigate the sensitivity of breeding values to different environmental worm burden challenges. Data were collected on 19,510 lambs from 2000 to 2009 in 24 Corriedale studs that participated in the NGE of sheep in Uruguay. (Co)variances components were estimated using a multi-trait animal model performing a Bayesian analysis. Posterior means estimated for heritability (h2) were of low to moderate magnitude (between 0.10 and 0.33) for the traits analysed. Genetic correlations (rg) were not significantly different from zero for BW- Loge (FEC + 100), BW-FAMACHA©, BW-PCV, Loge (FEC + 100)-PCV, BCS-FAMACHA©, moderate favourable rg for Loge (FEC + 100)-FAMACHA and PCV-BCS (0.55, 0.41) and high favourable rg for BW-BCS (0.66). These results indicate the possibility to complement selection programs incorporating BW, Loge (FEC + 100), FAMACHA©, PCV and BCS in order to select resistant and resilient animal to GIP. Furthermore, genetic parameters for BW and Loge (FEC + 100) to different environmental worm burden challenge was investigated. Two contemporary groups of low worm environment (Loge (FEC + 100) below 6.40) and a high worm environment (Loge (FEC + 100) above 6.75) were considered. In this model, h2 estimated for BW and Loge (FEC + 100) were found to be not statistically different between low and high environmental worm burden, furthermore, high correlations between traits at both environments were also presented.

Multi trait genetic evaluation of growth traits in Nellore sheep raised on pasture in semi-arid regions of India using Bayesian approach

Abstract The main aim of this study is to estimate genetic parameters and (co) variance components for body weights at various ages in Nellore sheep born during the period from 1993 to 2016 (23 years). A total of 4822 lambs with pedigree descended from 144 sires and 1299 dams were included in this study. Bayesian analysis using Gibbs sampler multi trait animal model with and without maternal effects was studied. Traits included in this study were birth weight (BW), weaning weight (WW), six months body weight (6MW), nine months body weight (9 MW), Yearling weight (YW). Year-season of birth and sex of lamb (contemporary groups) were considered as fixed effects with ewe weight at lambing as a covariate. Estimates of direct heritability estimates for birth weight, WW, 6MW, 9MW and YW based on best model were 0.17, 0.28, 0.27, 26 and 0.23, respectively and the corresponding maternal heritability estimates were 0.12, 0.14, 0.14, 0.12 and 0.13, respectively. The direct-maternal genetic covariance was negative for all the studied traits. Strong and positive estimates of direct additive genetic correlations were observed in growth traits and they ranged from 0.16 to 0.83, whereas the direct-maternal genetic correlations were negative for all the traits and these estimates ranged from ˗0.89 to ˗0.08. Moderate estimates of heritability for the growth traits obtained in this study suggested the presence of better genetic variability and the possibility for genetic improvement of Nellore sheep through selection. Maternal genetic effects were significant in all the traits. Hence, it is recommended to incorporate these effects in the genetic analysis by including it as a genetic or environmental effect or both. The environmental variance obtained in the study suggested that the growth performance of Nellore sheep may be enhanced by improving the feeding and management aspects. Correlations among traits and effects should be considered while implementing breed improvement program.

Impact of sub-setting the data of the main Limousin beef cattle population on the estimates of across-country genetic correlations

BackgroundCattle international genetic evaluations allow the comparison of estimated breeding values (EBV) across different environments, i.e. countries. For international evaluations, across-country genetic correlations (rg) need to be estimated. However, lack of convergence of the estimated parameters and high standard errors of the rg are often experienced for beef cattle populations due to limited across-country genetic connections. Furthermore, using all available genetic connections to estimate rg is prohibitive due to computational constraints, thus sub-setting the data is necessary. Our objective was to investigate and compare the impact of strategies of data sub-setting on estimated across-country rg and their computational requirements.MethodsPhenotype and pedigree information for age-adjusted weaning weight was available for ten European countries and 3,128,338 Limousin beef cattle males and females. Using a Monte Carlo based expectation–maximization restricted maximum likelihood (MC EM REML) methodology, we estimated across-country rg by using a multi-trait animal model where countries are modelled as different correlated traits. Values of rg were estimated using the full data and four different sub-setting strategies that aimed at selecting the most connected herds from the largest population.ResultsUsing all available data, direct and maternal rg (standard errors in parentheses) were on average equal to 0.79 (0.14) and 0.71 (0.19), respectively. Direct-maternal within-country and between-country rg were on average equal to − 0.12 (0.09) and 0.00 (0.14), respectively. Data sub-setting scenarios gave similar results: on average, estimated rg were smaller compared to using all data for direct (0.02) and maternal (0.05) genetic effects. The largest differences were obtained for the direct-maternal within-country and between-country rg, which were, on average 0.13 and 0.12 smaller compared to values obtained by using all data. Standard errors always increased when reducing the data, by 0.02 to 0.06, on average. The proposed sub-setting strategies reduced the required computing time up to 22% compared to using all data.ConclusionsEstimating all 120 across-country rg that are required for beef cattle international evaluations, using a multi-trait MC EM REML approach, is feasible but involves long computing time. We propose four strategies to reduce computational requirements while keeping a multi-trait estimation approach. In all scenarios with data sub-setting, the estimated rg were consistently smaller (mainly for direct-maternal rg) and had larger standard errors.

Characterization of Friesian Heifer Fertility under Egyptian Conditions

Data from 3081 reproductive records of Friesian heifers covering the period from 1979 to 2013 belongs to Sakha and El-Karada experimental farms - Kafr-El-Sheikh Governorate, Animal Production Research Institute, Ministry of Agriculture, Egypt were analyzed. A multitrait animal model was used to estimate genetic parameters, genetic and phenotypic changes for age at first breeding (AFB), age at successful breeding (ASB), age at first calving (AFC), number of services per conception (NSC) and service period (SP). Heritabilities of AFB, ASB, AFC, NSC and SP were 0.15, 0.12, 0.11, 0.02 and 0.01, respectively. Genetic correlations between AFB, ASB and AFC were high and ranged from 0.97 to 0.99, however the phenotypic correlations were ranged from 0.78 to 0.99. Genetic correlations between NSC and both AFB, ASB and AFC were -0.12 to 0.16, however the corresponding phenotypic correlations were ranged from -0.04 to 0.46. The genetic correlations between SP and both AFB, ASB and AFC were ranged from 0.58 to 0.79, however that corresponding estimates of phenotypic correlations were ranged from 0.01 to 0.56. The genetic and phenotypic correlations between NSC and SP were 0.72 and 0.94, respectively. A linear regression analysis of estimated breeding values on year of birth of heifers showed favorable genetic improvement of all fertility traits, however the reverse phenotypic trend was observed for AFB, ASB and AFC.

Genetic Improvement of Some Productive Traits in Zaraibi Goats

The objective of this study was to evaluate the genetic improvement in Zaraibi goats herd raised on El-serw research station located in the north eastern part of Nile Delta, Egypt. The station belongs to Animal Production Research Institute (APRI). Some body weights at different ages were included in genetic and environmental trends. These weights were 4-month weight (4M), 6-month weight (6M), and 12-month weight (12M). Data and pedigree information were collected from 1988 until 2018. The least square means of body weights at 4M, 6M and 12M were 12.14±0.02, 15.49±0.02 and 24.08±0.04 kg, respectively. Year of birth, season, gender of kid, parity of dam and type of birth significantly (P<0.01) affect growth traits. Genetic parameters were estimated using a multi-trait animal model program (MTDFREML). The same previous fixed effects were included in this analysis regarding the animal as random effects. The heritability of the studied body weights tend to increase as age increases. That is inversely matched with the environmental proportion of total variance which was found to be 0.72, 0.66 and 0.62 for M4, M6 and M12, respectively. The heritability value was estimated as 0.28 for 4M. Genetic trends were obtained as the regression of the predicted breeding values on years of birth and Environmental trends were obtained as the regression of year constants on years of birth. The annual genetic change trends were positive and significant for 4M, 6M and 12M (0.091, 0.121 and 0.158 kg/year, respectively) and the annual phenotypic change trends were (0.020, 0.045, 0.117 kg/year, respectively). Genetic trends for M12 trait were higher than those for other traits in this study. Genetic and environment correlations between 4 month body weight and other growth traits were positive. Negative environmental trends indicates poor management system for the flock during studied period. Weight at 12 months of age has the highest heritability in studied body weights and suggested to be selection criteria to improve yearling weight for Zaraibi goat.

209 Genomic selection for multiple maternal and growth traits in large white pigs using Single-Step GBLUP

Abstract The objective of this study was to implement a multi-trait genomic evaluation for maternal and growth traits in a swine population. Phenotypes for preweaning mortality, litter size, weaning weight, and average daily gain were available for 282K Large White pigs. The pedigree included 314k individuals, of which 35,731 were genotyped for 45K SNPs. Variance components were estimated in a multi-trait animal model without genomic information by AIREMLF90. Genomic breeding values were estimated using the genomic information by single-step GBLUP. The algorithm for proven and young (APY) was used to reduce computing time. Genetic correlation between proportion and the total number of preweaning deaths was 0.95. A strong, positive genetic correlation was also observed between weaning weight and average daily gain (r = 0.94). Conversely, the genetic correlations between mortality and growth traits were negative, with an average of -0.7. To avoid computations by expensive threshold models, preweaning mortality was transformed from a binary trait to two linear dam traits: proportion and a total number of piglets dead before weaning. Because of the high genetic correlations within groups of traits, inclusion of only one growth and one mortality trait in the model decreases computing time and allows for the inclusion of other traits. Reduction in computing time for the evaluation using APY was up to 20x, and no differences in EPD ranking were observed. The algorithm for proven and young improves the efficiency of genomic evaluation in swine without harming the quality of predictions. For this population, a binary trait of mortality can be replaced by a linear trait of the dam, resulting in a similar ranking for the selection candidates.

Genetic parameters for litter traits at different parities in purebred Landrace and Yorkshire pigs.

Comparison of the multi-trait animal model and the traditional repeatability model was carried out using data obtained from 6,424 Landrace and 20,835 Yorkshire sows farrowed from January 2000 to April 2018 in order to estimate genetic parameters for litter traits at different parities. Specifically, records of the total number born (TNB), number born alive (NBA), total number of mortality (MORT), number of stillborn (NSB) and number of mummified pigs (MUM) were used. Although results showed the heterogeneity of heritability for litter traits at different parities, the mean heritability estimates from the multi-trait model were found to be higher than those of the repeatability model for all traits in both pig breeds. In terms of genetic correlation between parities, a slight difference in genetic control in the first parity was noted for TNB and NBA in Landrace and Yorkshire pigs. The correlation between the first parity and later parities ranged from 0.48 to 0.74 for TNB and NBA in both breeds. Moreover, genetic correlation between parities for MORT and NSB was observed to be high for parities higher than 2 in Yorkshire pigs. For MUM, genetic correlation between the first and other parities was generally low in both breeds, indicating that culling pigs on the basis of MUM at the first parity could probably be unreasonable. Overall, the results of this study suggest that the multi-trait approach for litter size traits is useful for the accurate estimation of genetic parameters.

Estimation of Genetic Parameters for Reproductive Traits in Hanwoo (Korean Cattle).

Simple SummaryDue to the extensive marbling of its beef, Hanwoo (Korean native cattle) has continuously gained popularity and has become a mainstay in South Korea’s animal industry. In any beef cattle production system, reproductive performance is one of the main economic aspects taken into consideration. Therefore, genetic parameter estimates are necessary to obtain indices in order to maximize the response to selection, which in turn could lead to higher profitability. To date, knowledge on the genetic parameters for reproductive traits in Hanwoo cattle is still limited. Therefore, this study estimated the variance components, heritability, phenotypic, and genetic correlations of age at first calving (AFC), calving interval (CI), days open (DO), and gestation length (GL) of Hanwoo cattle. This was done using single-trait and multi-trait animal models. Results revealed the low heritability estimates for AFC, CI, DO, and GL in both single-trait and multi-trait models, which indicated the probable slow response of these traits due to direct selection. Moreover, phenotypic and genetic correlations varied from low to high among the reproductive traits of interest. Nevertheless, heritability estimates and genetic correlations shown in this study will prove to be vital as initial estimates are considered in the genetic improvement program of Hanwoo cattle.Genetic parameters for the reproductive traits of Hanwoo cattle were estimated using data obtained from 15,355 cows in 92 herds across South Korea, which were inseminated from May 1997 to July 2016. An “average information” restricted maximum likelihood (REML) procedure that fit in single-trait and multi-trait animal models was used to estimate the variance components of age at first calving (AFC), calving interval (CI), days open (DO), and gestation length (GL). Results showed the low estimates of heritability for all reproductive traits from both single-trait and multi-trait models. Estimates of heritability for AFC were 0.08 and 0.10 with single-trait and multi-trait models, respectively, while the estimates of heritability using the same animal models ranged from 0.01 to 0.07, 0.01 to 0.09, and 0.10 to 0.16 for CI, DO, and GL, accordingly. While AFC showed positive genetic correlations of 0.52 and 0.46 with CI and DO, respectively, the estimates of genetic and phenotypic correlations of GL with AFC were close to zero. Moreover, phenotypic correlations of GL with CI and DO were also close to zero; however, the corresponding genetic correlations were 0.13 and –0.38 for CI and DO, respectively. These estimated variance components and genetic correlations for reproductive traits can be utilized for genetic improvement programs of Hanwoo cattle.

Genetic and environmental analysis of diseases with major economic impact in Israeli Holsteins

Incidences of ketosis, metritis, mastitis, and retained placenta were studied in Israeli Holstein cows calving between 2008 and 2017. These diseases were selected based on their economic impact. Ketosis, metritis, and retained placenta were scored dichotomously. Mastitis was scored as absent, a single occurrence during the lactation, or more than 1 occurrence. Ketosis and metritis were recorded during the first 21 d after calving, retained placenta during the first 5 d after calving, and mastitis up to 305 d in milk. The effects of herd-year-season, calving age, month of calving, gestation length, and occurrence of dystocia were included in the first-parity analysis models. All effects were significant for metritis and retained placenta. For ketosis, all effects were significant, except for gestation length. For mastitis, only the effects of herd-year-season and calving age were significant. Variance components were computed by the multitrait animal model. The 4 diseases were analyzed jointly based on first-parity records, and each disease was analyzed separately for parities 1 to 3 with the different parities considered separate traits. The 4 disease traits in first parity were also analyzed jointly with the 6 major traits included in the Israeli breeding index: milk, fat, and protein production; somatic cell score; female fertility; and longevity. Heritability was highest for metritis and lowest for mastitis, but all heritabilities were <0.07, similar to previous studies. For all 4 diseases, genetic correlations among the first 3 parities were >0.65, and all residual correlations were <0.07. Selection of herd-years assumed to have more accurate recording of mastitis did not result in higher heritability estimates. Genetic correlations between the disease traits and milk, fat, and protein production were economically unfavorable, while correlations between the disease traits and somatic cell score, female fertility, and longevity were economically favorable. Expected genetic changes in the disease traits after 10 yr of selection with the current Israeli breeding index were all <1%, except for ketosis, which was predicted to increase by 1.5%. Inclusion of these traits in a proposed index with the disease traits constituting 7% of the index would result in only marginal improvements for the disease traits and adversely affect genetic gain for fat and protein production. Thus, inclusion of these traits in the breeding index cannot be justified economically.

Genetic parameters for tonic immobility, body weight, and morphological traits of the red-winged tinamou (Rhynchotus rufescens).

This study was carried out to estimate genetic parameters for morphology, body weight, and tonic immobility traits in the red-winged tinamou (Rhynchotus rufescens). Information on 690 birds was used and genetic parameters were estimated using Bayesian methods under a multi-trait animal model. The following traits were considered in this study: tarsal length (TL), bill length (BL), wing length (WL), head width (HW), bill width (BW), mature weight (MW), weight at 90days (W90), and tonic immobility (TI). The heritability showed estimates between 0.15 for wing length and 0.56 for bill length. Positive and negative genetic correlations were estimated, ranging from - 0.33 to 0.81. All the morphological, production, and behavioral traits studied will have moderate to high response to selection. The body weight at 90days is a better alternative for use in breeding programs and its selection would not lead to an increase in the time of tonic immobility. Both the selection for weight gain and for reduction of tonic immobility time would lead to an increase in the size of the legs of the red-winged tinamou, which could be advantageous for thermal control of these birds in tropical systems.

Genetic parameters of pre-weaning weights in crossbred piglets using multi-trait animal model.

Variances and genetic parameters (heritability and correlation) were estimated for pre-weaning weights from birth to 6weeks of age at weekly intervals in crossbred (Landrace X Desi) pigs. Data were analysed using multi-trait animal model incorporating dam's age (covariable), parity of sow, sex of piglet, season of birth and year of birth as fixed effects and direct additive genetic, maternal genetic and permanent litter as random effects. The estimates of direct additive genetic and maternal genetic heritability were 0.18 ± 0.04 and 0.14 ± 0.04; 0.73 ± 0.06 and 0.62 ± 0.06; 0.64 ± 0.06 and 0.37 ± 0.05; 0.42 ± 0.05 and 0.30 ± 0.05; 0.37 ± 0.04 and 0.33 ± 0.05; 0.43 ± 0.04 and 0.34 ± 0.06 and 0.47 ± 0.04 and 0.36 ± 0.05 for birth weight and subsequent weights at weekly intervals up to 6weeks, respectively. The permanent litter effect ranged from 0.02 ± 0.01 (birth weight) to 0.11 ± 0.04 (weight at first week). The estimates of correlation between direct additive genetic component and maternal genetic component (i.e. ram) were moderate to high but all negative. ram ranged from - 0.79 ± 0.15 (weight at first week) to - 0.49 ± 0.26 (birth weight). The direct additive genetic and maternal genetic correlations between birth weight and weaning weight were 0.59 ± 0.04 and 0.62 ± 0.13, respectively, which revealed sufficient scope for selection based on birth weight itself. Early weights were found to be highly heritable with due influence of maternal and permanent litter effects, and thus, appropriate selection interventions may be aimed at this stage for favourable changes at subsequent ages.