scholarly journals 13 Genetic selection using pooled semen

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 6-6
Author(s):  
Ithalo Coelho de Sousa ◽  
Rohan Fernando ◽  
Jack C Dekkers ◽  
Moysés Nascimento ◽  
Richard J Leach ◽  
...  
Keyword(s):  
Standard Procedure ◽  
Genetic Selection ◽  
Equal Probability ◽  
Relationship Matrix ◽  
Response To Selection ◽  
Swine Industry ◽  
Genetic Progress ◽  
Complete Dominance ◽  
Breeding Values ◽  
Pedigree Relationship

Abstract The use of pooled semen (PS), standard procedure at the commercial level of the swine industry, limits genetic progress, since the offspring parentage is unknown. Literature suggests that some boars have a greater number of progeny than others in the same litter when PS is used. The objective of this study was to evaluate different pedigree-relationship matrices for selection purposes when PS is used. Data on a trait with heritability of 0.4 were simulated 1,000 times for 12 scenarios: combination of sires per pool (2 or 3), number of phenotyped progeny (1 or 12), and three boar dominance levels: no dominance (equal probability of parentage), medium dominance, and complete dominance (all progeny from one boar). Ten pools were created for each scenario based on 5 sires and used for 5 dams each. Breeding values (BV) of the progeny were estimated (EBV) using three relationship matrices: known parents (A), using equal probabilities of parentage (E), and probabilities based on known boar dominance (D). Results for each relationship matrix were compared using the average of the true BV (TBV) of the 10% best animals selected based on EBV. Results are presented as percentage TBV of the selected animals compared to using A (Table). In general, D resulted in better results than E as boar dominance increased. Similar results between E and D were obtained when 12 progenies were phenotyped. When one was phenotyped, D was superior than E in the presence of boar dominance. Knowing the probability of each sire contributing to the progeny increases response to selection when pooled semen is used.

THE EFFECT OF DIFFERENT NUMERATOR RELATIONSHIP MATRICES ON BREEDING VALUES ESTIMATED FROM MULTIPLE TRAIT BLUP

1987 ◽  
Vol 67 (1) ◽  
pp. 201-204
Author(s):  
R. A. KEMP ◽  
J. W. WILTON
Keyword(s):  
Relationship Matrix ◽  
Genetic Progress ◽  
Multiple Trait ◽  
Breeding Values ◽  
Reduced Animal Model ◽  
Numerator Relationship Matrix ◽  
Best Linear Unbiased ◽  
The Mean ◽  
Estimated Breeding Values ◽  
Accuracy Of Prediction

A numerator relationship matrix (Ac) due to sires and dams was compared with a numerator relationship matrix (Ai) due to sires and maternal grandsires in a multiple-trait-reduced animal model (MT-RAM). Best linear unbiased predictors of estimated breeding values (EBV) for 200-d weight (WW) and postweaning gain (PG) (gain from 200 to 365 d of age) were estimated from data simulating a beef cattle population. As expected, mean EBV and bias (EBV-BV) for both traits were not significantly affected by different relationship matrices. The mean variances of EBV with Ac were larger than those with Ai for both traits. The mean EBV variances were closer to mean BV variances with Ac compared to Ai, which is consistent with increased precision of EBV. Product-moment correlations of EBV and BV (accuracy of prediction) were not equal (P < 0.01) for Ac compared to Ai with WW or PG. The EBV using Ac were more accurate than EBV using Ai. The increased precision and accuracy of EBV from a MT-RAM with Ac would result in greater genetic progress in the population. Key words: Relationship matrices, estimated breeding values, MT-RAM

scholarly journals Comparison of models for missing pedigree in single-step genomic prediction

2021 ◽  
Vol 99 (2) ◽  
Author(s):  
Yutaka Masuda ◽  
Shogo Tsuruta ◽  
Matias Bermann ◽  
Heather L Bradford ◽  
Ignacy Misztal
Keyword(s):  
Density Function ◽  
Single Step ◽  
Joint Density ◽  
Pedigree Information ◽  
Relationship Matrix ◽  
Genomic Information ◽  
Breeding Values ◽  
Joint Density Function ◽  
Information Updates ◽  
Genetic Trends

Abstract Pedigree information is often missing for some animals in a breeding program. Unknown-parent groups (UPGs) are assigned to the missing parents to avoid biased genetic evaluations. Although the use of UPGs is well established for the pedigree model, it is unclear how UPGs are integrated into the inverse of the unified relationship matrix (H-inverse) required for single-step genomic best linear unbiased prediction. A generalization of the UPG model is the metafounder (MF) model. The objectives of this study were to derive 3 H-inverses and to compare genetic trends among models with UPG and MF H-inverses using a simulated purebred population. All inverses were derived using the joint density function of the random breeding values and genetic groups. The breeding values of genotyped animals (u2) were assumed to be adjusted for UPG effects (g) using matrix Q2 as u2∗=u2+Q2g before incorporating genomic information. The Quaas–Pollak-transformed (QP) H-inverse was derived using a joint density function of u2∗ and g updated with genomic information and assuming nonzero cov(u2∗,g′). The modified QP (altered) H-inverse also assumes that the genomic information updates u2∗ and g, but cov(u2∗,g′)=0. The UPG-encapsulated (EUPG) H-inverse assumed genomic information updates the distribution of u2∗. The EUPG H-inverse had the same structure as the MF H-inverse. Fifty percent of the genotyped females in the simulation had a missing dam, and missing parents were replaced with UPGs by generation. The simulation study indicated that u2∗ and g in models using the QP and altered H-inverses may be inseparable leading to potential biases in genetic trends. Models using the EUPG and MF H-inverses showed no genetic trend biases. These 2 H-inverses yielded the same genomic EBV (GEBV). The predictive ability and inflation of GEBVs from young genotyped animals were nearly identical among models using the QP, altered, EUPG, and MF H-inverses. Although the choice of H-inverse in real applications with enough data may not result in biased genetic trends, the EUPG and MF H-inverses are to be preferred because of theoretical justification and possibility to reduce biases.

scholarly journals The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections

2011 ◽  
Vol 93 (3) ◽  
pp. 203-219 ◽  
Author(s):  
KATHRYN E. KEMPER ◽  
DAVID L. EMERY ◽  
STEPHEN C. BISHOP ◽  
HUTTON ODDY ◽  
BENJAMIN J. HAYES ◽  
...  
Keyword(s):  
Complex Traits ◽  
Sampling Error ◽  
Snp Markers ◽  
Snp Marker ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Phenotypic Variance ◽  
Breeding Values ◽  
Genetic Merit ◽  
Independent Population

SummaryGenetic resistance to gastrointestinal worms is a complex trait of great importance in both livestock and humans. In order to gain insights into the genetic architecture of this trait, a mixed breed population of sheep was artificially infected with Trichostrongylus colubriformis (n=3326) and then Haemonchus contortus (n=2669) to measure faecal worm egg count (WEC). The population was genotyped with the Illumina OvineSNP50 BeadChip and 48 640 single nucleotide polymorphism (SNP) markers passed the quality controls. An independent population of 316 sires of mixed breeds with accurate estimated breeding values for WEC were genotyped for the same SNP to assess the results obtained from the first population. We used principal components from the genomic relationship matrix among genotyped individuals to account for population stratification, and a novel approach to directly account for the sampling error associated with each SNP marker regression. The largest marker effects were estimated to explain an average of 0·48% (T. colubriformis) or 0·08% (H. contortus) of the phenotypic variance in WEC. These effects are small but consistent with results from other complex traits. We also demonstrated that methods which use all markers simultaneously can successfully predict genetic merit for resistance to worms, despite the small effects of individual markers. Correlations of genomic predictions with breeding values of the industry sires reached a maximum of 0·32. We estimate that effective across-breed predictions of genetic merit with multi-breed populations will require an average marker spacing of approximately 10 kbp.

Multi-trait selection index and cluster analyses in Angus cattle

2021 ◽  
pp. 1-8
Author(s):  
G. M. Fernandes ◽  
R. P. Savegnago ◽  
L. A. Freitas ◽  
L. El Faro ◽  
V. M. Roso ◽  
...  
Keyword(s):  
Production System ◽  
Selection Process ◽  
Selection Index ◽  
Genetic Selection ◽  
Genetic Profile ◽  
Breeding Values ◽  
Cluster Analyses ◽  
Scrotal Circumference ◽  
Breeding Programmes ◽  
Economic Selection

Abstract In breeding programmes, the genetic selection process is based on the prediction of animal breeding values, and its results may vary according to the employed selection method. The current study developed an economic selection index for animals of the Angus breed; performed cluster analyses using the breeding values in order to evaluate the genetic profile of the animals candidates to selection, and compared the obtained results between the economic selection index and the cluster analyses. The evaluated traits included weaning weight, 18-month weight, scrotal circumference, fat thickness and ribeye area. Economic values were obtained using bioeconomic modelling, simulating a complete cycle production system of beef cattle breeds in Brazil, and the selection objective were the weaning rate and slaughter weight. The chosen selection index was composed of all of the traits used as selection criteria for the simulated production system. During the cluster analyses, the population was divided into two to four groups, in which the groupings containing potential animals were assessed. The animals of the grouping which was used for comparison with the selection index were identified, and most of the bulls that were included in the index were among the best in the analysed group. These results suggest that the cluster analyses can be used as a tool for the selection of animals to be used as parents for future generations.

scholarly journals Genomic Correlations Between the Gaits of Young Horses Measured by Accelerometry and Functional Longevity in Jumping Competition

2021 ◽  
Vol 12 ◽  
Author(s):  
Manon Dugué ◽  
Bernard Dumont Saint Priest ◽  
Harmony Crichan ◽  
Sophie Danvy ◽  
Anne Ricard
Keyword(s):  
Principal Components ◽  
Genomic Data ◽  
Principal Component ◽  
Well Being ◽  
Relationship Matrix ◽  
Significant Qtls ◽  
Breeding Values ◽  
A Genome ◽  
Young Horses ◽  
Show Jumping

Functional longevity is essential for the well-being of horses and the satisfaction of riders. Conventional selection using longevity breeding values calculated from competition results is not efficient because it takes too long to obtain reliable information. Therefore, the objective was to identify early criteria for selection. We assessed two types of early criteria: gait traits of young horses and QTLs. Thus, our aim was to estimate the genetic correlation between gait traits and longevity and to perform a genome-wide association study (GWAS) for longevity. Measurements of gaits by accelerometry were recorded on 1,477 show jumping horses that were 4 to 5 years old. Gait analysis provided 9 principal components describing trot, canter, and walk. Longevity estimated breeding values (EBVs) for stallions were calculated using a survival analysis of more than 900,000 years of performances by 179,448 show jumping horses born from 1981 onwards. Longevity was measured as the number of years spent in competition. Model included region and month of birth, age at first competition, year, and performance level. Longevity EBVs were deregressed to obtain weighted pseudo-performances for 1,968 stallions. Genomic data were available for 3,658 jumping horses. Seventy-eight percent of the horses measured for gaits and twenty-five percent of those measured for longevity were genotyped. A GWAS of longevity revealed no significant QTLs. Genetic parameters between each of the 9 principal components of the gait variables and longevity were evaluated with a bi-trait animal linear mixed model using single-step GBLUP analysis with the relationship matrix constructed from genomic data and genealogy (24,448 ancestors over four generations). The heritability of the gait traits varied from 0.11 to 0.44. The third principal component for trot (high lateral activity) and the first principal component for canter (high dorsoventral activity and low stride frequency) were moderately genetically correlated with higher longevity: rg = 0.38 (0.15) and 0.28 (0.13), respectively. Our study revealed that functional longevity is a polygenic trait with no major genes. We found new correlations between longevity and gait traits. Before using gait characteristics in a selection plan, these correlations need to be understood better at the biomechanical level.

scholarly journals Reduced Animal Models Fitting Only Equations for Phenotyped Animals

2021 ◽  
Vol 12 ◽  
Author(s):  
Mohammad Ali Nilforooshan ◽  
Dorian Garrick
Keyword(s):  
Animal Model ◽  
Animal Models ◽  
Mixed Model ◽  
Reduced Model ◽  
Relationship Matrix ◽  
Full Model ◽  
Breeding Values ◽  
Reduced Animal Model ◽  
Numerator Relationship Matrix ◽  
Model Equations

Reduced models are equivalent models to the full model that enable reduction in the computational demand for solving the problem, here, mixed model equations for estimating breeding values of selection candidates. Since phenotyped animals provide data to the model, the aim of this study was to reduce animal models to those equations corresponding to phenotyped animals. Non-phenotyped ancestral animals have normally been included in analyses as they facilitate formation of the inverse numerator relationship matrix. However, a reduced model can exclude those animals and obtain identical solutions for the breeding values of the animals of interest. Solutions corresponding to non-phenotyped animals can be back-solved from the solutions of phenotyped animals and specific blocks of the inverted relationship matrix. This idea was extended to other forms of animal model and the results from each reduced model (and back-solving) were identical to the results from the corresponding full model. Previous studies have been mainly focused on reduced animal models that absorb equations corresponding to non-parents and solve equations only for parents of phenotyped animals. These two types of reduced animal model can be combined to formulate only equations corresponding to phenotyped parents of phenotyped progeny.

scholarly journals The Alterations of Endometrial and Myometrial Receptivity in Early Pregnant Gilts in Response to Estrus Induction With PMSG/hCG

2021 ◽  
Author(s):  
Magdalena Szymanska ◽  
Agnieszka Blitek
Keyword(s):  
Mrna Expression ◽  
Standard Procedure ◽  
Oxytocin Receptor ◽  
Hormonal Control ◽  
Receptor Expression ◽  
Control Group ◽  
Peroxisome Proliferator ◽  
Uterine Receptivity ◽  
Swine Industry ◽  
Junction Protein

Abstract Background: The hormonal control of ovulation has become a standard procedure in the swine industry. However, exogenous gonadotropins can be detrimental to reproductive function, affecting follicle development, corpus luteum formation, and embryo development and survival. Much less is known about uterine receptivity in gilts with induced estrus. Therefore, our objective was to determine the effect of estrus induction with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (hCG) on the expression of steroid, prostaglandin, cytokine, and oxytocin receptors, as well as nuclear factor kappa B subunit 1 (NFKB1), peroxisome proliferator activated receptor gamma (PPARG), and gap junction protein alpha 1 (GJA1), in the endometrium and myometrium of early pregnant gilts. Twenty prepubertal gilts received 750 IU PMSG and 500 IU hCG 72 h later, while eighteen prepubertal gilts in the control group were observed daily for estrus behavior. All gilts were inseminated in their first estrus and slaughtered on days 10, 12, and 15 of pregnancy to collect uterine tissues for mRNA expression analyses using real-time PCR.Results: Estrus induction did not affect progesterone receptor expression in either uterine tissue. In the endometrium, greater mRNA expression of estrogen receptors (ESR1 and ESR2), androgen receptor (AR), prostaglandin (PG) E2 receptors (PTGER2 and PTGER4), PGF2α receptor (PTGFR), interleukin 6 receptor (IL6R), tumor necrosis factor α receptors (TNFRSF1A and TNFRSF1B), and oxytocin receptor (OXTR) was detected in the control than in the PMSG/hCG-treated gilts (P < 0.05). In the myometrium, concentrations of AR, PTGER2, PTGFR, and NFKB1 transcripts were lower, while PGI2 receptor and PPARG transcripts were elevated in gilts with gonadotropin-induced estrus as compared with naturally ovulated gilts (P < 0.05). Furthermore, the administration of PMSG/hCG resulted in the greater expression of GJA1 mRNA in both the endometrium and myometrium of day 15 pregnant gilts (P < 0.05). Conclusions: Estrus induction with PMSG/hCG in prepubertal gilts may affect steroid, prostaglandin, cytokine, and oxytocin receptor expression in the endometrium and myometrium, thereby altering uterine receptivity to local or systemic factors. This may, in turn, contribute to disorders in embryo-maternal interactions and the process of implantation.

Indices of cellular development in muscles of lambs are influenced by sire estimated breeding values and pastoral nutritional system

2006 ◽  
Vol 57 (6) ◽  
pp. 651 ◽  
Author(s):  
P. L. Greenwood ◽  
G. E. Gardner ◽  
R. S. Hegarty
Keyword(s):  
Muscle Growth ◽  
Genetic Selection ◽  
Inverse Association ◽  
Semitendinosus Muscle ◽  
Eye Muscle ◽  
Weaning Weight ◽  
Breeding Values ◽  
Sire Group ◽  
Selection For ◽  
Estimated Breeding Values

This study examined influences of sire (n = 9) estimated breeding values (EBVs), sire-group (Muscle, Growth, and Control), and nutrition (low and high quality and availability pasture) from birth to slaughter at ~8 months of age on indices of muscle cellularity and transcriptional and translational capacity in 56 castrate lambs. Effects of nutritional systems to 8 months of age were greater, overall, than those due to EBVs or sire-group. Amount of DNA increased with increasing EBV for post-weaning eye muscle depth (PEMD or Muscle EBV) in longissimus but not in semimembranosus and semitendinosus muscles, while Muscle EBV also had an inverse association with concentration of DNA. Protein to DNA and RNA to DNA were related positively to Muscle EBV, the associations being strongest for the semitendinosus muscle. Post-weaning weight (PWWT or Growth) EBV correlated positively with the RNA to DNA ratio and, among high but not low nutrition lambs, was inversely related to concentration of muscle DNA, whereas post-weaning fat depth (PFAT or Fat) EBV was correlated positively with RNA concentration. Overall, the magnitude of effects of sire-group was less than for sire EBVs, presumably due to differing selection pressures for muscling, fatness, and growth. High nutrition lambs had more protein to DNA than low nutrition lambs in the longissimus and semitendinosus muscles, but not in the semimembranosus muscle. In low compared with high nutrition lambs, concentration of DNA was greater in the longissimus and semitendinosus muscles. Total amount of DNA was reduced by more in low compared with high nutrition in the longissimus and semimembranosus than in the semitendinosus, and amount of protein was reduced by more in low compared with high nutrition in the longissimus than in the other two muscles. We conclude that genetic selection for eye muscle depth in sheep has differing effects on cellular characteristics of the longissimus, semimembranosus, and semitendinosus muscles, and has greater effects on muscle cellular characteristics than genetic selection for post-weaning weight or fat depth.

Genetic and phenotypic trends and parameters in reproduction, greasy fleece weight and liveweight in Merino lines divergently selected for multiple rearing ability

2004 ◽  
Vol 44 (8) ◽  
pp. 745 ◽  
Author(s):  
S. W. P. Cloete ◽  
A. R. Gilmour ◽  
J. J. Olivier ◽  
J. B. van Wyk
Keyword(s):  
Genetic Correlations ◽  
Annual Production ◽  
Production Traits ◽  
Genetic Progress ◽  
Additive Variance ◽  
Genetic Changes ◽  
Environmental Correlations ◽  
Breeding Values ◽  
Reproduction Traits ◽  
Fleece Weight

Genetic and phenotypic trends and parameters were estimated for reproduction, fleece weight and liveweight in a South African Merino population, divergently selected from 1986, either for (H line) or against (L line) maternal multiple rearing ability. Annual reproduction, ewe greasy fleece weight and pre-joining liveweight data were recorded on 809 Merino ewes, from 1986 to 2002. Phenotypic trends indicated divergence in reproduction traits between the H and L lines. The direct additive variance ratio (h2 ± s.e.) for day of lambing was 0.08 ± 0.02. Estimates of h2 for reproduction traits were: 0.10 ± 0.02 for number of lambs born per ewe; 0.04 ± 0.02 for number of lambs weaned per ewe; and 0.04 ± 0.02 for weight of lamb weaned per ewe, corrected for the gender of the lamb. Corresponding h2 estimates for annual production were 0.57 ± 0.06 for greasy fleece weight and 0.48 ± 0.06 for ewe liveweight at joining. Service sire only exerted a significant (P<0.05) effect on day of lambing, but it accounted for merely 2% of the overall phenotypic variation. Ewe permanent environment variance ratios (c2ewe) for the reproduction traits were: 0.07 ± 0.03 for number of lambs born per ewe; 0.11 ± 0.03 for number of lambs weaned per ewe; and 0.11 ± 0.03 for total weight of lamb weaned per ewe. Corresponding c2ewe estimates for annual production traits were 0.14 ± 0.05 for greasy fleece weight and 0.27 ± 0.06 for ewe joining weight. Genetic and ewe permanent environmental correlations between measures of reproduction exceeded 0.7. Genetic correlations of reproduction traits with greasy fleece weight were low and variable in sign. Genetic correlations of reproduction traits with ewe joining weight were positive and particularly high for weight of lamb weaned. Permanent environmental correlations of reproduction traits with greasy fleece weight and joining weight were generally low to moderate. Genetic trends for the H and L lines (derived from averaged direct breeding values within birth years) were divergent (P<0.01) for all reproduction traits. Expressed as percentage of the overall least squares means of the respective traits, breeding values in the H line increased annually, with 1.3% for lambs born per ewe, 1.5% for lambs weaned per ewe and by 1.8% for weight of lamb weaned per ewe. Corresponding trends in the L line were, respectively, –0.6%, –1.0% and –1.2% per year. Substantial genetic progress in annual lamb output was attainable, despite relatively small h2 estimates. This response was achieved without unfavourable genetic changes in wool and liveweight.

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