PSXII-12 Partitioning direct and maternal genetic effects into additive and non-additive components for growth and maternal traits in Yorkshire pigs

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 251-252
Author(s):  
Jicai Jiang ◽  
Shauneen O’Neill ◽  
Christian Maltecca ◽  
Justin Fix ◽  
Tamar Crum ◽  
...  
Keyword(s):  
Birth Weight ◽  
Environmental Effect ◽  
Linear Mixed Model ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Effects ◽  
Average Weight ◽  
Yorkshire Pigs ◽  
Direct Dominance ◽  
Daily Gain

Abstract This study investigates how much direct and maternal non-additive genetic effects contribute to growth and maternal traits in swine. We analyzed a sample of 19,475 genotyped Yorkshire pigs from Acuity Ag Solutions, LLC (Carlyle, IL). Approximately 50K SNPs were kept after quality control, and missing genotypes were then imputed using findhap.f90. The genotypes were used to construct genomic relationship matrices (GRMs) corresponding to additive (A), dominance (D), and additive-by-additive epistasis (E) effects for both direct and maternal effects. The GRMs were subsequently employed as covariance structure matrices in a linear mixed model consisting of eight random components, namely three direct genetic effects (Ad, Dd, and Ed), three maternal genetic effects (Am, Dm, and Em), maternal environmental effect, and common litter environmental effect. We estimated these variance components (VCs) for six growth traits (birth weight, average daily gain, back fat, and loin area) and six maternal traits of a sow (total number of piglets born, number of piglets born alive, average weight of piglets at birth, average weight of piglets weaned) using REML in MMAP (https://mmap.github.io/). As shown in Table 1, we found significant (P< 0.05) direct dominance and epistasis VCs for all six growth traits. Additionally, direct epistasis effects explained a larger proportion of phenotypic variation than direct dominance for all growth traits (0.04–0.12 vs. 0.01–0.04). In contrast, direct non-additive VCs were not significant for any maternal trait except for epistasis in average weight of piglets weaned. As for maternal non-additive effects, we only discovered significant additive VC in birth weight and average daily gain and significant epistasis VC in back fat (P< 0.05). Other maternal genetic VCs were largely negligible. In summary, direct dominance and epistasis effects play a prominent role in growth traits of Yorkshire pigs.

THE EFFECT OF INBREEDING ON PREWEANING GROWTH OF YANKASA SHEEP

2021 ◽  
Vol 26 ◽  
pp. 6-10
Author(s):  
E. M. Awemu ◽  
B. Y. Abubakar ◽  
L. N. Nwakalor
Keyword(s):  
Birth Weight ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Regression Coefficients ◽  
Breeding Period ◽  
Weaning Weight ◽  
Inbreeding Coefficients ◽  
Using Data ◽  
Inbreeding Level ◽  
Daily Gain

The accumulated and annual levels of inbreeding and their effects on growth traits of lambs were investigated using data collected over 11 years at the National Animal Production Research Institute Zaria. Inbreeding level averaged 1.313% per year, cumulating to 14.45% over the years. Average individuals inbreeding coefficients of offspring from sires used for more than one breeding period was 0.103% across the inbred individuals and 0.004% over all lambs. Regression coefficients of growth traits (everage values per year) on inbreeding levels by year were – 0.185kg ± 1.820g and -0.391kg for birth weight, preweaning average daily gain and weaning weight, respectively. All regression coefficients indicated that birth weight and weaning weight declined by 0.185kg and 0.391kg, respectively while preweaning average daily gain increased by 1.820g. Conscious efforts to reduce inbreeding level and its effects on growth traits will greatly lead to improved productivity

The relationships between pre- and post-weaning growth traits in lambs of Iranian fat-tailed sheep and their crosses with Corriedale and Targhee rams

1978 ◽  
Vol 26 (2) ◽  
pp. 185-192 ◽  
Author(s):  
A. Farid ◽  
M. Makarechian
Keyword(s):  
Body Weight ◽  
Birth Weight ◽  
Growth Traits ◽  
Average Daily Gain ◽  
High Growth ◽  
Negative Association ◽  
Food Conversion ◽  
Weaning Weight ◽  
Daily Gain ◽  
Total Gain

ABSTRACTThe pre-weaning records (birth weight, weaning weight and gain from birth to weaning) of 291 male and female lambs and the post-weaning records (body weight, feedlot gain and food conversion) of 136 male lambs were used to study relationships between different traits. The lambs were derived from three fat-tailed Iranian sheep breeds (Karakul, Mehraban and Naeini) and their crosses with Corriedale and Targhee rams. All lambs were weaned at 75 + 5 days of age and the males were fed in a feedlot for 100 days after weaning. Feedlot measurements were taken at 20-day intervals.Weaning weight and pre-weaning average daily gain showed positive and significant associations with birth weight. Birth weight, weaning weight and gain from birth to weaning were positively associated with body weight at subsequent ages in feedlot as well as with final weight (P<0·01). Birth weight, weaning weight and pre-weaning average daily gain were positively and significantly associated with total feedlot gain.Of the different traits, total gain during the first 20 days in feedlot (adjust period) had the lowest and total gain during the second 20 days had the highest association with total feedlot daily gain. There was no evidence that the heavier lambs at weaning and those showing high growth rate before weaning, were more efficient in the feedlot. Gain during the second 20-day period in the feedlot had a significant negative association with the total food conversion (unit food/unit gain) and therefore was a good predictor for food conversion.When the feedlot period was divided into two 40-day periods, it was found that gain during both had a significant negative association with the corresponding food conversion. A similar association was observed between total feedlot gain and food conversion, indicating that the rate and efficiency of gain improved simultaneously.

Short communication: The genotype of growth hormone gene that affects the birth weight and average daily gain in crossbred beef cattle

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
Tety Hartatik ◽  
AHMAD FATHONI ◽  
SIGIT BINTARA ◽  
ISMAYA ◽  
PANJONO ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Birth Weight ◽  
Beef Cattle ◽  
Short Communication ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Growth Hormone Gene ◽  
Production Traits ◽  
Significant Difference ◽  
Daily Gain

Abstract. Hartatik T., Fathoni A, Bintara S., Ismaya, Panjono, Widyobroto B.P, Agus A, Budisatria I.G.S, Leroy P. 2020. Short communication: The genotype of growth hormone gene that affects the birth weight and average daily gain in crossbred beef cattle. Biodiversitas 21: 941-945. Growth Hormone gene has been proposed to direct search for quantitative trait loci, and polymorphisms at these loci have been associated with several production traits in bovine. This research aimed to investigate the association of the genotype of partial growth hormone gene with birth weight and average daily gain in crossbred beef cattle. The materials of this research consist of 47 samples from four different breeds. Birth weight was measured just after calving delivery from the mother. The average daily gain was calculated from the period since birth weight to the second weight (90 days). Genotyping of the growth hormone gene was determined by the sequencing and PCR-RFLP method with the AluI restriction enzyme. The association between genotype and growth traits data was analyzed using analysis of variance (ANOVA) by RStudio version 1.1.383. The results showed the significantly different (P<0.001) in birth weight and average daily gain according to the different breed. Friesian Holstein breed showed the highest birth weight, followed by Belgian Blue Bull cross and others. The genotype valine/valine only occurs in Belgian blue bull cross and Wagyu bull cross cattle and showed moderate birth weight. Genotype affects birth weight significantly (P<0.001). The birth weight for genotype leucine/leucine, leucine/valine, and valine/valine was 34.82±18.13, 25.31±13.10, and 29.35±13.65, respectively. There was no significant difference in average daily genes according to the different genotypes. In conclusion, the growth hormone gene was probably one of the molecular genetics markers for excellent growth traits in different crossbred beef cattle.

GENETIC EFFECTS ON POSTWEANING GROWTH OF THREE-WAY CROSS BEEF CATTLE

1988 ◽  
Vol 68 (3) ◽  
pp. 647-654 ◽  
Author(s):  
G. W. RAHNEFELD ◽  
G. M. WEISS ◽  
H. T. FREDEEN ◽  
J. A. NEWMAN ◽  
J. E. LAWSON
Keyword(s):  
Beef Cattle ◽  
Key Words ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Effects ◽  
Genetic Interactions ◽  
Cross Breeding ◽  
Terminal Sire ◽  
Daily Gain ◽  
Sire Breed

Genetic effects on postweaning growth traits were evaluated for 3592 crossbred steers and heifers fed at two locations, Brandon, Manitoba and Lacombe, Alberta during a 6-yr period (1973–1978). The calves were sired by Chianina (Chi), Charolais (C), Limousin (L) and Simmental (S) bulls mated to 10 F1 dam-crosses representing the Hereford × Angus (HA) and nine dam-cross combinations produced by mating C, S and L sires with H, A and Shorthorn (N) females. Progeny rankings by terminal sire breed for weight on-test were C = Chi = S > L. For the trait 140-d postweaning average daily gain, progeny rankings were C > Chi = S, C = Chi > L and Chi > S > L. The progeny from the majority of "exotic" cross-dams were heavier on-test, and had higher postweaning average daily gain than progeny from HA dams. Ranking of dam-crosses according to their breed of sire (DS) for the trait weight on-test were S > C > L. The DS comparisons for postweaning average daily gain were C > S > L. The ranking of dam-crosses by breed of dam's dam, for on-test weight and postweaning average daily gain were N > H = A. Genetic interactions (terminal sire by breed cross of dam) were absent. Genotype environment interactions involving breed of terminal sire with year, sex and location were found for weight on-test and postweaning average daily gain. All resulted from changes in the magnitude of breed of sire differences, not from changes in sire rankings. Key words: Cattle, breeds, cross breeding, growth

scholarly journals Korelasi Genetik Pada Sifat Pertumbuhan Sapi Aceh di Kecamatan Indrapuri Provinsi Aceh

2014 ◽  
Vol 14 (1) ◽  
pp. 37-41 ◽  
Author(s):  
Widya Pintaka Bayu Putra ◽  
Sumadi Sumadi ◽  
Tety Hartatik
Keyword(s):  
Birth Weight ◽  
Genetic Correlation ◽  
Standard Error ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Weaning Weight ◽  
Final Weight ◽  
Aceh Province ◽  
Daily Gain

(The genetic correlation of growth traits in Aceh cattle at indrapuri district Aceh Province)ABSTRACT. This research was conducted to estimate genetic correlation of growth traits on Aceh cattle including birth weight (BW), weaning weight (WW), yearling weight (YW), and Average Daily Gain (ADG). The research was done at Indrapuri Breeding and Forage Centre (IBFC) of Aceh cattle from March 2013 to April 2013. The materials of this research consist of growth records from 2010 to 2012. The genetic correlation was analyzed by variance and covariance. The results indicated that the lowest standard error (SE) value of heritability showed on birth weight 0.15+0.13. Most of genetic correlation value on growth traits was positive and high categorized ( 0.50). The lowest SE value showed on correlation between birth weight and pre-weaning ADG (0.55+0.54), birth weight and post-weaning ADG (0,63+0,62), pre-weaning ADG and post-weaning ADG (0.71+0.33), pos-weaning ADG and weight/age or W/A (0.72+0.33) then final weight and W/A (0.94+0.69). It could be concluded that most of genetic correlation value on Aceh cattle growth traits were positive and high therefore the selection based on growth traits can be done for increasing performance in Aceh cattle.

32 A Bayesian Hierarchical Model to Integrate Growth Models into Genomic Evaluation of Pigs

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 18-19
Author(s):  
Haipeng Yu ◽  
Jaap Milgen ◽  
Egbert Knol ◽  
Rohan Fernando ◽  
Jack C Dekkers
Keyword(s):  
Genomic Prediction ◽  
Genetic Improvement ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Effects ◽  
Latent Growth ◽  
Bayesian Hierarchical ◽  
Additive Genetic Effects ◽  
Daily Gain ◽  
Genomic Predictions

Abstract Genomic prediction has advanced genetic improvement by enabling more accurate estimates of breeding values at an early age. Although genomic prediction is efficient in predicting traits dominated by additive genetic effects within common settings, prediction in the presence of non-additive genetic effects and genotype by environmental interactions (GxE) remains a challenge. Previous studies have attempted to address these challenges by statistical modeling, while the augmentation of statistical models with biological information has received relatively little attention. A pig growth model assumes growth performance is a nonlinear functional interaction between the animal’s genetic potential for underlying latent growth traits and environmental factors and has the potential to capture GxE and non-additive genetic effects. The objective of this study was to integrate a nonlinear stable Gompertz function of three latent growth traits and age into genomic prediction models using Bayesian hierarchical modeling. The three latent growth traits were modeled as a linear combination of systematic environmental, marker, and residual effects. The model was applied to daily body weight data from ~83 to ~186 days of age on 4,039 purebred boars that were genotyped for 24K markers. Bias and prediction accuracy of genomic predictions of selection candidates were assessed by extending the linear regression method of predictions based on part and whole data to a non-linear setting. The accuracy (bias) of genomic predictions was 0.58 (0.82), 0.46 (0.90), 0.54 (0.78), and 0.60 (0.84) for the three latent growth traits and average daily gain derived from integrated nonlinear model, respectively, compared to 0.58 (0.87) for genomic predictions of average daily gain using standard linear models. In subsequent work, the growth model will be extended to include daily feed intake and carcass composition data. Resulting models are expected to substantially advance genetic improvement in pigs across environments. Funded by USDA-NIFA grant # 2020-67015-31031.

Genetic parameter estimates for growth traits of Gansu Alpine Finewool sheep

2012 ◽  
Vol 52 (5) ◽  
pp. 321 ◽  
Author(s):  
Wenhui Li ◽  
Ian W. Purvis
Keyword(s):  
Fixed Effects ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Genetic Effects ◽  
Western China ◽  
Parameter Estimates ◽  
Weaning Weight ◽  
Likelihood Ratio Testing ◽  
Daily Gain

Estimation of genetic parameters for growth traits of Gansu Alpine Finewool sheep that separately identify maternal effects has not been previously conducted. (Co)variance components and corresponding genetic parameters for lamb growth traits were estimated from Gansu Alpine Finewool sheep maintained at Gansu Sheep Breeding Technology Extension Station in north-western China. Records of 17 703 lambs at birth, born over 9 years (2000–2008) and sired by 315 rams, were used in the study. Birth type, sex, dam age, record age and birth year were fitted as fixed effects. Analyses were carried out using a restricted maximum likelihood procedure (ASReml). Six different animal models were fitted for all traits and the most appropriate model was selected through log-likelihood ratio testing. After identifying the appropriate model through single-trait analysis, bivariate analyses were used to obtain the phenotypic and genetic correlations among the growth traits. In addition to the direct genetic effect, and maternal genetic effects, significant negative correlations between direct genetic and maternal genetic effects were found for all the growth traits. The maternal permanent environmental effects were only significant for birthweight, weaning weight and pre-weaning growth rate. The estimates of direct heritability for birthweight, weaning weight, pre-weaning average daily gain, post-weaning average daily gain and yearling weight were 0.22, 0.16, 0.15, 0.27 and 0.19 respectively. The maternal heritability estimates were relatively high and ranged from 0.17 to 0.27. The study provides the breed and its associated finewool sheep industry with a more encompassing basis for designing more effective breeding programs for improvement of growth traits of Gansu Alpine Finewool sheep.

Genetic parameters for growth traits of a local breed of sheep in the United Arab Emirates

2001 ◽  
Vol 137 (3) ◽  
pp. 365-371 ◽  
Author(s):  
S. A. AL-SHOREPY
Keyword(s):  
Birth Weight ◽  
Maternal Effects ◽  
Environmental Effects ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Direct Effects ◽  
Weaning Weight ◽  
Local Breed ◽  
Daily Gain

Genetic parameters were estimated for purebred and crossbred lambs of a local breed using a single trait animal model. The traits recorded were: birth weight (BWT), weight at 30 days (WT30), weaning weight (WWT), average daily gain from 1 to 30 days (ADG1) and average daily gain from 30 to 90 days (ADG2). Five different animal models were fitted for each trait; all including additive direct genetic variance and various combinations of additive maternal and environmental maternal effects. The most appropriate model was chosen based on likelihood ratio tests. Additive maternal and permanent environmental effects were important (P < 0·05) for birth weight in purebred and crossbred lambs, when compared with a model containing only additive direct effects. Inclusion of maternal permanent environmental effects provided a better fit (P < 0·05) for weaning weight in purebred lambs than a model containing only additive direct effects. Estimates of heritability from the model containing additive direct, maternal effects and maternal permanent environmental effects, but not additive direct-maternal correlation, for combined purebred and crossbred lambs were 0·32 for BWT, 0·19 for WT30, 0·24 for WWT, 0·26 for ADG1 and 0·12 for ADG2. Estimates of additive maternal and maternal permanent environmental variances, respectively, as a proportion of phenotypic variance were 0·06 and 0·07 for BWT, 0·05 and 0·02 for WT30, 0·02 and 0·03 for WWT, 0·03 and 0·05 for ADG1 and 0·00 and 0·03 for ADG2. Estimates of direct-maternal correlation in subsequent analyses were significant and ranged from −0·16 to −0·95 for live weights and from −0·73 to −1·0 for daily gains. However, the very large negative correlations probably resulted from undefined non-genetic covariances as well as possible antagonistic genetic effects. These results indicate that it would be possible to improve growth traits in a local sheep breed through genetic selection.

scholarly journals A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Pingxian Wu ◽  
Kai Wang ◽  
Jie Zhou ◽  
Dejuan Chen ◽  
Anan Jiang ◽  
...  
Keyword(s):  
Feed Intake ◽  
Genetic Architecture ◽  
Average Daily Gain ◽  
Significant Snps ◽  
Genetic Effects ◽  
Single Locus ◽  
Yorkshire Pigs ◽  
Feeding Speed ◽  
Daily Gain ◽  
Gwas Approach

AbstractSocially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles ‘GGG’ for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.

scholarly journals Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pattarapol Sumreddee ◽  
El Hamidi Hay ◽  
Sajjad Toghiani ◽  
Andrew Roberts ◽  
Samuel E. Aggrey ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Recent Common Ancestor ◽  
Pedigree Information ◽  
Grid Search ◽  
Genomic Information ◽  
The Impact ◽  
Daily Gain ◽  
Harmful Effects

Abstract Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.

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