Maximum Likelihood Program Research Articles

Genetic assessment of productive and reproductive traits in Friesian, native, and crossbred cattle in Egypt

This study utilized a dataset comprising 3023 lactation records for Friesian cows, 596 records for Native cows (Baladi), and 1189 records for Crossbred cows spanning from 1994 to 2015. The objective was to estimate and assess genetic and phenotypic parameters and breeding values for 305-day milk yield (305-DMY), lactation period (LP), calving interval (CI), and days open (DO) within the Egyptian dairy context. The motivation for this research stemmed from the need to understand the genetic potential of different cattle genotypes in Egypt and identify opportunities for enhancing dairy production. Data were analyzed using the linear mixed model least squares and maximum likelihood (LSMLMW) and multiple-trait derivative-free restricted maximum likelihood (MTDFREML) programs. The analytical model included fixed effects such as season and year of calving, parity, and genotype groups, while random effects included animal and error. Unadjusted means for 305-DMY, LP, CI, and DO were calculated for each genotype group. Genotype groups significantly impacted all studied traits. Heritability estimates varied across genotype groups, with higher estimates observed in Crossbred (0.32, 0.26, 0.25, 0.23) and Native cows (0.26, 0.28, 0.28) compared to Friesian cows (0.24, 0.22, 0.16, 0.17) for productive and reproductive traits, respectively. Genetic correlations among traits ranged from 0.10 to 0.86 for the three genotype groups, while corresponding phenotypic correlations were generally small to moderate and positive. Regarding breeding values, the accuracy estimates suggested that both sires and cows could contribute to genetic improvement. This indicates the potential for enhancing dairy production through selective breeding strategies.

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics.

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6/15 phylogenomic datasets. Finally, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

Performance Evaluation of Khari and Boer Crossbred Goats in Mid Hills Under Optimum Management Regime.

Goats are recognized as a vital and versatile livestock commodity with significant importance in rural farmers’ communities of developing countries, including Nepal. Growth, reproductive and litter performances are considered as the major economic traits of goats. This study was designed to compare the growth, reproduction and litter traits of goat kids and does at mid hill region for different non-genetic factors such as genetic groups (Khari, Boer 75% and 50%), parity (early, mid and late), season of conception and kidding (summer, autumn, winter, spring), sex (male and female) and type of birth (single, twins and triplet) under optimum management regime. Data for the four-year study period (2017 to 2021) on production performance were entered into MS-Excel sheet from the data record book of the National Goat Research Program, Bandipur and analyzed by using Mixed Model Least-square and Maximum Likelihood Computer Program PC-2 statistical package. The means were compared using Duncans' Multiple Range Test (DMRT). Results revealed that the effect of genetic group, parity, type of birth and sex were significant (p<0.05) with respect to growth at different stages along with genetic group and parity that were significant with major non-genetic factors affecting reproduction and litter traits. Better reproduction parameters were recorded for the Khari goat breed than Boer crossbred. Similarly, litter traits at both birth and weaning were found better in later parities with better performance in Khari. Males were born heavier and consistent throughout the study period up to eighteen months. Hence, based on the findings of this study, it can be concluded that Khari goat breed has high potential for its reproduction and litter traits with a massive scope of improvement through selection within the population. Likewise, it is also important to consider the growth of inferior Khari goats can also be genetically improved through upgrading up to 75% blood level using an appropriate breed, such as Boer.

An open-access T-BAS phylogeny for emerging Phytophthora species.

Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1876, it has expanded to comprise over 190 formally described species. There is a need for an open access phylogenetic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood program. A search engine was also developed to identify microsatellite genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, the tree can be updated in real-time as new species are described. The tool contains metadata including clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for other Oomycete, bacterial or fungal pathogens.

Evaluation of reproductive performance and litter traits of Khari, Jamunapari and Sirohi crossbred goats in Surkhet district of Karnali province, Nepal

Goat produces 20.36% of meat, ranking in second position after buffalo meat production in Nepal and contributes 4% in agriculture GDP. Making out the influence of non-genetic factors on the phenotypic expression of reproductive and litter traits of goat is important to develop selection/evaluation criteria with healthier precision. Khari, Jamunapari and Sirohi crosses were considered for the comparative study of their reproductive and litter traits. Data obtained from the study of different reproductive and litter traits were firstly entered into the computer via excel package programs. The data were analyzed by Mixed Model Least-square and Maximum Likelihood Computer Program PC-2statistical package developed by Walter R. Harvey and the means were compared by Duncan’s Multiple Range Test (DMRT). Results revealed that the pooled means for AFC, AFK, PPE, GL, and KI were 344.31, 493.69, 173.42, 148.93, 319.58 days respectively. Similarly, pooled means for LSB, LWB, LSW, and LWW were 1.43, 5.16 kg, 1.37 and 28 kg respectively. Production system and breed were important nongenetic factor affecting reproductive traits significantly whereas parity is the most important non genetic factor affecting litter traits of goat. Almost all of the reproductive traits (except PPE) were observed better under the grazing system in Khari breed. Winter kidding goat had better PPE. Likewise, all the litter traits were significantly better in later parities with almost similar performance in all the breeds. To summarize, Khari was explored as a high potential goat regarding its reproductive traits with a massive scope of improvement in its litter weight trait through effective selection measures within the population.

Genetic Analysis of Fitness Traits of Kashmir Merino Sheep at Organized Farms of Kashmir

Background: Fitness traits include measures of reproductive efficiency of sheep. The improvement in reproductive efficiency has significant impact on overall economy of sheep. Methods: Data spanning over 21 years (1997-2017) were collected from two sheep breeding farm and analyzed with mixed model least-squares maximum likelihood (LSMLMW) computer (PC-2) programme designed by Harvey (1990) to estimate number of lambs born per ewe (NLBE), number of lambs weaned per ewe (NLWE), litter size (LS) and sex ratio (SR) of Kashmir Merino sheep. Result: Overall estimates of 3.56±0.11, 3.20±0.10, 48.32±0.04 and 1.06±0.01 for number of lambs born per ewe (NLBE), number of lambs weaned per ewe (NLWE), litter size (LS) and sex ratio (SR), respectively were observed in the present study. The period of birth had significant (p less than 0.05) effect on NLBE and NLEE. The effect of sire was highly significant on all the traits under study whereas effect of all the non-genetic factors considered had non-significant effect on LS and SR.

Factors affecting greasy fleece yield in Rambouillet sheep

Greasy wool yield in sheep is an important trait governed by genetic and environmental factors during pre- and postnatal life. A study was therefore, undertaken to study the wool yield and some environmental factors affecting it in Rambouillet sheep. The data spread over three years (2018 to 2020) pertaining to Rambouillet sheep maintained at Government Sheep Breeding Farm Balnoi was analyzed by least squares and maximum likelihood computer program, PC-2 version (Harvey, 1990). The least square mean of 1.77±0.01 kg for greasy fleece yield (GFY) in Rambouillet sheep was observed. All the factors non-genetic (age, sex and year) included in the model influenced GFY significantly (P

Effect of non-genetic factors on prolificacy and pre-weaning kid mortality of Khari goats in Nawalpur, Nepal

Present study was carried out mainly aiming at studying the effect of non-genetic factors on prolificacy and pre-weaning kid mortality of Khari goats in Nawalpur, Nepal. The traits were recorded for 1005 does were measured and analyzed using fixed effect Least Square Mixed Model and Maximum Likelihood Computer Program (LSMMML PC-2). Results revealed that overall mean prolificacy and pre-weaning kid mortality in this study were 145 and 6.2%, respectively. According to the results, non-genetic factors such as altitude, coat color and dam’s parity were the important sources of variation with respect to pre-weaning kid mortality and prolificacy of Khari goats in this study. Thus, the results of present study suggested the scope of improvement in prolificacy and pre-weaning kid mortality through selective breeding.

Determinants of Major Body Morphometric Traits of Khari Goat Kids (Capra hircus L.) in Nawalpur District, Nepal

This study was carried out aiming at studying the non-genetic determinants affecting three major body morphological traits of Khari goats in Nawalparasi, Nepal. Body length, wither height and heart girth at the age of birth, weaning, nine months and fifteen months of 1260 kids born from 1005 does were measured and analyzed using fixed effect Least Square Mixed Model and Maximum Likelihood Computer Program (LSMMML PC-2). Significantly different means of body length, wither height and heart girth were between different sub-classes of non-genetic factors compared using Duncan’s Multiple Range Test (DMRT) computer software. Findings revealed that overall mean wither height of kids ranged from 28.84±0.59 cm at birth to 61.95±1.03 cm at fifteen months, respectively. Similarly, overall mean hearth girth of kids varied from 29.62±0.58 cm at to 65.04±1.17 cm at fifteen months’ age, respectively. Overall mean body length of Khari goat kids was at birth, weaning, nine months and fifteen months’ age was determined 28.09±0.67 cm at birth and reached to 59.96±0.98 cm at fifteen months’ age. Altitude, coat color, kidding season, dam’s parity, dam’s size, sex and birth type of kids were the important sources of variation (p<0.05 to <0.001) with respect to wither height, hearth girth and body length of kids at most of the stages of growth in case Nepalese hill goats. Thus, the results of present study help describe indigenous Khari goat breed using the phenotypic values of morphometric traits such as body length, heart girth and wither height which may be useful to estimate the phenological variations within breed.

Variation in growth performance of pure and crossed meat type chickens

Genetic variation from a combination of four breeds of chickens (Anak Titan, Alpha, Giriraja and Normal indigenous chickens) were examined for importance of sire, dam, season and sex on growth traits using a Mixed-model Least-Squares and Maximum LIkelihood computer program. The results show that sire and dam genotypes significantly (P<0.05) affected growth. Anak Titan cocks and hens performed best in body weight (BW) with values ranging from 38.45±0.74g and 40.21±0.66g at day old to 1135.93 35.67g and 953.38 35.38g at week 12 respectively. Normal indigenous and Alpha improved indigenous performed better in linear body parameters. Genetic correlation coefficients among parameters for all the breeds were generally high. Positive estimates ranged from 0.15 for breast girth (BG) and keel length (KL) at week four to 0.99 for BG-KL at week tweve while negative values ranged from -0.783 for body weight (BW) and wing length (WL) at week four to -0.99 for BW-BG at week twelve. Heritability estimates for body weight ranged from 0.14 at week one to 0.63 at week four. It can be concluded that appreciable variation exists for growth traits among the strains of chickens. Such variations can be utilized for improvement in the present emvironment.

Genetic response to short-term index selection in females and mass selection in males of the Nigerian heavy local chicken ecotype

The study aimed to determine genetic gain in growth and egg production in the Nigerian indigenous chicken (NIC) subjected to multiple trait index selection for females and mass selection for males. The experimental birds (G generation) were generated from a reference 0 population of NIC and reared according to sire families from hatch. At point of lay, females were housed individually in laying cages for egg production. Hens were selected based on index scores calculated using an index of weighted breeding values constructed from own performance in body weight at first egg (BWFE), egg weight (EW) and egg production (EN), trait heritabilities and relative economic weights while cocks were selected based on own performance in body weight at 39 weeks of age (BW ). Selected parents were mated to 39 generate the G generation which in turn yielded the parents of the G generation. A control 1 2 population was used to measure environmental effects. Data were analyzed using the Restricted Maximum Likelihood (REML) computer programme. For hens, expected average direct genetic gain per generation was 12.58, 2.98g and 25.04g for EN, EW and BWFE, respectively while realized genetic gain was 2.19 and 1.59 for EN, 1.65 and 0.26g for EW, and -25.60 and 123.64g for BWFE for G and G generations, respectively. The corresponding 0 1 values for ratio of realized to expected genetic gains were 2.27 and 1.22, 3.15 and 0.24, and 0.95 and 2.21, respectively. Heritability (h2) ranged from 0.12 to 0.24 for EN, 0.34 to 0.43 for EW and 0.57 to 0.69 for BWFE, across the three generations. Similar improvements in BW 39 were observed in males with an average expected gain of 508.50g per generation. In conclusion, growth and egg production in the NIC can be improved using mass selection for cocks and index of weighted breeding values for hens.

Lifetime productivity and repeatability estimation of selected traits of crossbred cows in Savar Dairy Farm

The study was conducted on 244 crossbred cows of (Central Cattle Breeding and Diry Farm), Savar, Dhaka to evaluate the effect of different productive groups on their lifetime performance of various productive traits using twenty years data. Data were accumulated from a prescribed data sheet maintained by Central Cattle Breeding Station, Savar, Dhaka. Genetic groups for this experiment were Local Friesian (LF), Local Jersey (LJ), Local Hariana X Friesian (LH x F), Local Friesian X Local Friesian (LF x LF) and Local Jersey X Local Jersey (LJ x LJ). The studied parameters were age at puberty, lactation length, lactation yield, total milking days, and total milk yield in lifetime. The data were analyzed using Least-Squares Mixed Model and Maximum Likelihood Computer Program (Harvey, 1990). Analysis showed that genetic groups had a significant effect on age at puberty, lactation length and lactation yield (P<0.01), total milking days and milk yield in lifetime (P<0.001). From the result it was found that earliest age at puberty were in L x F (749.27±99.01). Lactation length and standardized lactation yield were also higher in L x F (258.69±20.04 days and 1408.80±83.60 kg respectively). Total milking days and milk yield were observed higher in (LH x F) with mean of 1468.30±198.58 days and 7340.32±1813.28 kg, respectively. The repeatability estimates of lactation length for genetic groups LF, LJ, LH x F, LF x LF and LJ x LJ were 0.24±0.09, 0.04(-ve), 0.10±0.05, 0.07±0.05 and 0.49±0.22, respectively. The same for lactation yield was 0.17±0.08, 0.27± 0.02, 0.07±0.04, 0.17±0.08 and 0.03±0.05 respectively. From analysis it was revealed that in respect of productive performances the L x F genetic group was found superior compared to other groups but interns of total lifetime productivity, LH x F ranked the highest in the given environment. It is concluded that lifetime productivity needs to be considered as an appropriate guideline for selecting genetic groups for future productivity.Progressive Agriculture 29 (2): 168-177, 2018

The relationship between healthy life expectancy and smoking, hypertension and body mass index in a Japanese population: A multistate life table method using Nippon Data90

Introduction Healthy life expectancy (HLE) is an important measure for describing population health. Human factors such as smoking, hypertension, and obesity can reduce overall HLE in a population. Little is known about the relationship between HLE and cardiovascular risk factors in Asian populations. Our study aimed to estimate HLE in various combinations of cardiovascular risk factors in a Japanese population using a multistate life table approach. Methods Data were obtained from NIPPON DATA90, which is a nationwide cohort study of nine thousand Japanese people that was established in 1990. From among the NIPPON DATA90 participants, our analysis focused on people who were aged 60 years or older at the baseline survey and had received activities of daily living (ADL) assessment. Participants underwent a two-wave interview survey process using the Katz ADL index in 1995 and 2000. The participants were queried on five items of the Katz ADL index, and any participant who answered that they were “not independent” for at least one item was designated “disabled” in the multistate life table. Smoking status was categorized into non-smokers (never-/ex-smokers) and current smokers. Blood pressure (BP) was categorized into four groups (optimal, normal, stage 1 hypertension, and stage 2 hypertension). Obesity was defined using body mass index (BMI), which was categorized into three groups (thin: 18.5; normal: 18.5–24.9; and overweight/obese: ≥ 25). All HLE calculations were performed using iMaCh version 0.98r7 (A Maximum Likelihood Computer Program using Interpolation of Markov Chains). Results The study sample comprised 6676 participants (2840 men and 3836 women). Among all the BMI and BP groups, HLE at age 60 in current smokers was shorter than that of non-smokers. Among obese men with optimal BP, HLE in current smokers was 20.0 years, whereas that of non-smokers was 17.7 years. Among obese current smokers, HLE at age 60 decreased linearly as BP increased in men (optimal BP: 19.8 years, normal BP: 19.3 years, stage 1 hypertension: 18.1 years, stage 2 hypertension: 17.7 years) and women (optimal BP: 23.1 years, normal BP: 22.6 years, stage 1 hypertension: 21.4 years, stage 2 hypertension: 21.0 years). Among thin current smokers, HLE at age 60 also decreased linearly as BP increased in men (optimal BP: 18.3 years, normal BP: 17.8 years, stage 1 hypertension: 16.6 years, stage 2 hypertension: 16.3 years) and women (optimal BP: 21.8 years, normal BP: 21.2 years, stage 1 hypertension: 19.9 years, stage 2 hypertension: 19.6 years). The distribution of HLE at age 60 showed a slight inverted U-shape as BMI increased in both sexes. Conclusions We examined the relationship between HLE at age 60 and combinations of BMI, BP, and smoking status using a nationwide cohort study of the Japanese population. HLE at age 60 was clearly shorter in smokers and individuals with higher BP. Furthermore, both thin and obesity has a slight impact on HLE at age 60.

Continued propagation of the CRF19_cpx variant among HIV-positive MSM patients in Spain.

The HIV-1 CRF19_cpx genetic form has been recently associated with greater pathogenicity. We used CoRIS, a national cohort of 31 reference hospitals in Spain, to investigate the current epidemiological situation of this variant in Spain. We analysed 4734 naive HIV-1-positive patients diagnosed during the 2007-15 period with an available pol gene sequence in the CoRIS resistance database. HIV-1 CRF19_cpx was ascribed through REGA3.0 and confirmed by a phylogenetic analysis. We analysed the presence of the transmission clusters of HIV-1 CRF19_cpx by maximum likelihood [with the randomized accelerated maximum likelihood (RAxML) program] and the time to the most recent common ancestor using Bayesian inference (BEAST, v. 1.7.5). Nineteen patients were infected with CRF19_cpx: all were male, they had a mean age of 42.9 years (95% CI: 36.4-52.5 years), the majority were MSM [n = 18 (95%)] and of Spanish nationality [n = 16 (84.2%)] and they had high CD4+ T cell counts (∼415 cells/mm3). Fifteen patients were grouped into four different transmission clusters: two clusters (two patients each) grouped the patients from Valencia and another cluster grouped one patient from Madrid and another from Seville. We found a larger cluster that grouped nine patients from southern Spain (Malaga and Seville), of which six presented mutation G190A. We estimated the origin of all the transmission clusters to take place between 2009 and 2010. We demonstrate that this variant has spread in Spain in recent years among young HIV-positive MSM and we note a recent expansion in southern Spain in patients who carry mutation G190A. We alert healthcare managers to enhance preventive measures to prevent the continuous spread of HIV-1 CRF19_cpx.

Genetic analysis of first lactation production traits in Kankrej cattle.

Aim:The aim was to estimate genetic factors affecting the first lactation milk production traits in Kankrej cattle of North Gujarat.Materials and Methods:The 475 first lactation records of Kankrej cows that were maintained at the Livestock Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, over a period of 35 years from 1980 to 2014 were studied. The least squares maximum likelihood program was used to estimate genetic parameters of first lactation traits. Heritability was estimated through paternal half-sib analysis in adjusted data.Results:The heritability estimate for production traits was 0.40±0.17, 0.45±0.17, 0.35±0.18, and 0.20±0.14 for standard 300 days milk yield (F300Y), total lactation milk yield (FLY), wet average (FWA), and lactation length (FLL), respectively, in the first parity. All the genetic and phenotypic correlations among different production efficiency traits were high and positive. Genetic correlations between F300Y and FLY, FLL, and FWA were 0.80±0.20, 0.59±0.16, and 0.81±0.32, where as the phenotypic correlations were 0.969, 0.688, and 0.868, respectively. Genetic correlations of FLY with FLL and FWA were 0.60±0.13 and 0.79±0.20, whereas the phenotypic correlations were 0.777 and 0.817, respectively. Genetic and phenotypic correlation between FLL and FWA was 0.63±0.28 and 0.31, respectively.Conclusion:The heritability estimate of all first parity lactation traits waslow to medium (0.20-0.45) indicated the scope for further improvement in this trait through selection as well as managemental practice. Higher genetic and phenotypic correlation between thefirst lactation milk production traits gives theidea that genetic gain due to selection for one trait also givesmorecorrelated response of selection for other traits which is economically advantageous.

Gaussian and robust Kronecker product covariance estimation: Existence and uniqueness

We study the Gaussian and robust covariance estimation, assuming the true covariance matrix to be a Kronecker product of two lower dimensional square matrices. In both settings we define the estimators as solutions to the constrained maximum likelihood programs. In the robust case, we consider Tyler’s estimator defined as the maximum likelihood estimator of a certain distribution on a sphere. We develop tight sufficient conditions for the existence and uniqueness of the estimates and show that in the Gaussian scenario with the unknown mean, p/q+q/p+2 samples are almost surely enough to guarantee the existence and uniqueness, where p and q are the dimensions of the Kronecker product factors. In the robust case with the known mean, the corresponding sufficient number of samples is max[p/q,q/p]+1.

Estimates of genetic parameters for fat yield in Murrah buffaloes.

Aim:The present study was performed to investigate the effect of genetic and non-genetic factors affecting milk fat yield and to estimate genetic parameters of monthly test day fat yields (MTDFY) and lactation 305-day fat yield (L305FY) in Murrah buffaloes.Materials and Methods:The data on total of 10381 MTDFY records comprising the first four lactations of 470 Murrah buffaloes calved from 1993 to 2014 were assessed. These buffaloes were sired by 75 bulls maintained in an organized farm at ICAR-National Dairy Research Institute, Karnal. Least squares maximum likelihood program was used to estimate genetic and non-genetic parameters. Heritability estimates were obtained using paternal half-sib correlation method. Genetic and phenotypic correlations among MTDFY, and 305-day fat yield were calculated from the analysis of variance and covariance matrix among sire groups.Results:The overall least squares mean of L305FY was found to be 175.74±4.12 kg. The least squares mean of overall MTDFY ranged from 3.33±0.14 kg (TD-11) to 7.06±0.17 kg (TD-3). The h2 estimate of L305FY was found to be 0.33±0.16 in this study. The estimates of phenotypic and genetic correlations between 305-day fat yield and different MTDFY ranged from 0.32 to 0.48 and 0.51 to 0.99, respectively.Conclusions:In this study, all the genetic and non-genetic factors except age at the first calving group, significantly affected the traits under study. The estimates of phenotypic and genetic correlations of MTDFY with 305-day fat yield was generally higher in the MTDFY-5 of lactation suggesting that this TD yields could be used as the selection criteria for early evaluation and selection of Murrah buffaloes.

Genetic and non-genetic factors affecting morphometry of Sirohi goats.

Aim:The aim was to estimate genetic and non-genetic factors affecting morphometric traits of Sirohi goats under field condition.Materials and Methods:The detailed information of all animals on body measurements at birth, 3, 6, 9, and 12 months of age was collected from farmer’s flock under field condition born during 2007-2013 to analyze the effect of genetic and non-genetic factors. The least squares maximum likelihood program was used to estimate genetic and non-genetic parameters affecting morphometric traits.Results and Discussion:Effect of sire, cluster, year of birth, and sex was found to be highly significant (p<0.01) on all three morphometric traits, parity was highly significant (p<0.01) for body height (BH) and body girth (BG) at birth. The h2 estimates for morphometric traits ranged among 0.528±0.163 to 0.709±0.144 for BH, 0.408±0.159 to 0.605±0.192 for body length (BL), and 0.503±0.197 to 0.695±0.161 for BG.Conclusion:The effect of sire was highly significant (p<0.01) and also h² estimate of all morphometric traits were medium to high; therefore, it could be concluded on the basis of present findings that animals with higher body measurements at initial phases of growth will perform better with respect to even body weight traits at later stages of growth.

GENETIC AND PHENOLYTIC PARAMETERS FOR EARLY GROWTH TRAITS ON EGYPTION BALADI CALVES

Data on the pre-weaning growth traits of 815 Egyptian native baladi calves borned from the period 1993 to 2014 were used to study the non-genetic, and genetic phenotypic factors of pre-weaning growth traits. The data were collected from Animal Production Research Station at El-Serw, Ministry of Agriculture. Covariance component for birth weight (W0), weaning weight (WW) and average daily gain from birth to weaning (ADG) were estimated by using least squares and maximum likelihood (LSMLMW) computer program of Harvey (1990). Model included sirs and dams within sires as random effects, year and season of birth, sex of calf and parity of cow as fixed effects. In addition, cow weight at calving and suckling days were used as covariate. The means and standard deviations of body weight at birth, weaning, and average daily gain were 23.47±4.29 kg, 80.59±6.36 kg and 0.477±0.06 g/d, respectively. Statistically season and year of calving and parity of cow did not showed significant effects, but sire and sex of calf had significant effects on studied traits. The values of heritability were 0.15, 0.33 and 0.38 for body weights at birth, weaning and average daily gain from birth to weaning, respectively. The results showed that most estimates of genetic and phenotypic correlations among body weights and daily gain traits were positive.

Approximate Bayesian Logistic Regression via Penalized Likelihood by Data Augmentation

We present a command, penlogit, for approximate Bayesian logistic regression using penalized likelihood estimation via data augmentation. This command automatically adds specific prior-data records to a dataset. These records are computed so that they generate a penalty function for the log likelihood of a logistic model, which equals (up to an additive constant) a set of independent log prior distributions on the model parameters. This command overcomes the necessity of relying on specialized software and statistical tools (such as Markov chain Monte Carlo) for fitting Bayesian models, and allows one to assess the information content of a prior in terms of the data that would be required to generate the prior as a likelihood function. The command produces data equivalent to normal and generalized log- F priors for the model parameters, providing flexible translation of background information into prior data, which allows calculation of approximate posterior medians and intervals from ordinary maximum likelihood programs. We illustrate the command through an example using data from an observational study of neonatal mortality.