Selection of parents and estimation of genetic parameters using BLUP and molecular methods for lentil (Lens culinaris Medik.) breeding program in Argentina

2019 ◽  
Vol 56 (1) ◽  
pp. 12-25
Author(s):  
Carolina Bermejo ◽  
Federico Cazzola ◽  
Fernando Maglia ◽  
Enrique Cointry
Keyword(s):  
Quantitative Traits ◽  
Genetic Parameters ◽  
Selection Process ◽  
Recombinant Inbred Lines ◽  
Correlation Coefficients ◽  
Cost Effective ◽  
Molecular Data ◽  
Breeding Value ◽  
Breeding Values ◽  
High Yields

AbstractThe most important objective of lentil breeding programs is to develop new genotypes that are genetically more productive. Besides, it is necessary that the varieties obtained have short flowering cycles to allow the later sowing of summer crops. Selection is based through phenotypic means; however, we argue it should be based on genetic or breeding values because quantitative traits are often influenced by environments and genotype–environment interactions. The objectives of this study were to: (i) identify genotypes with the highest merit; (ii) estimate genetic parameters to know the genetic control of morphological traits in macrosperma and microsperma lentil types using best linear unbiased prediction (BLUP). Twenty-five recombinant inbred lines (RILs) from six F4 families selected on the basis of precocity and high yields were tested in four environments for important quantitative traits. The analysis of variance showed significant differences between genotypes, environments, and genotype–environment interactions for all the traits. Seven macrosperma- and two microsperma-type RILs were selected. Based on average ranking from breeding values and molecular data obtained with sequence-related amplified polymorphism (SRAP), the same genotypes were selected. Genotypic coefficients of variation, heritability across and by environment, and genetic correlation coefficients using BLUP were obtained. According to our results BLUP could replace molecular analysis methods because the selection process was simpler, more cost-effective, and more accurate. The breeding value of parents would give a better ranking of their genetic value than would their phenotypic value; therefore, the selection efficiency would be enhanced and the genetic gain would be more predictable. The selected genotypes could become potential commercial varieties or be used as parental lines in future hybridization programs.

scholarly journals Weaning results of beef Hungarian Fleckvieh calves 2. Genetic parameters, breeding values

2010 ◽  
Vol 53 (1) ◽  
pp. 26-36 ◽  
Author(s):  
S. Bene ◽  
I. Füller ◽  
A. Fördős ◽  
F. Szabó
Keyword(s):  
Genetic Parameters ◽  
Correlation Coefficients ◽  
Breeding Value ◽  
Phenotypic Variance ◽  
Weaning Weight ◽  
Breeding Values ◽  
Estimated Breeding Values ◽  
Genetic Value ◽  
Maternal Heritability ◽  
Daily Gain

Abstract. Weaning weight, preweaning daily gain and 205-day weight of Hungarian Fleckvieh calves (n=8 929, bulls =4 539, heifers =4 390) born from 232 sires between 1980 and 2003 were examined. Variance, covariance components and heritability values and correlation coefficients were estimated. The effect of the maternal permanent environment on genetic parameters and breeding values were examined. Two animal models were used for breeding value estimation. The direct heritability (hd2) of weaning weight, preweaning daily gain and 205-day weight was between 0.37 and 0.42. The maternal heritability (hm2) of these traits was 0.06 and 0.07. The direct-maternal correlations (rdm) were medium and negative −0.52 and −0.74. Contribution of the maternal heritability and maternal permanent environment to phenotype is smaller than that of direct heritabilities (hm2+c2< hd2). The ratio of the variance of maternal permanent environment in the phenotypic variance (c2) changed from 3 to 6 %. Estimated breeding values changed whether the permanent environmental effect of dam wasn’t taken into consideration but the rank of the animals was not modified. The genetic value for weaning results of Hungarian Fleckvieh population has increased since 1997.

scholarly journals A note on genetic parameters and accuracy of estimated breeding values in honey bees

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Evert W. Brascamp ◽  
Piter Bijma
Keyword(s):  
Honey Bees ◽  
Variance Components ◽  
Genetic Parameters ◽  
Additive Genetic Variance ◽  
Breeding Value ◽  
Phenotypic Variance ◽  
Breeding Values ◽  
Estimated Breeding Values ◽  
Additive Genetic Relationship ◽  
The Relationship

Abstract Background In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) and by the breeding value for the queen effect of the queen of the colony. Because the worker group consists of multiple individuals, interpretation of the variance components and heritabilities of phenotypes observed on the colony and of the accuracy of selection is not straightforward. The additive genetic variance among worker groups depends on the additive genetic relationship between the drone-producing queens (DPQ) that produce the drones that mate with the queen. Results Here, we clarify how the relatedness between DPQ affects phenotypic variance, heritability and accuracy of the estimated breeding values of replacement queens. Second, we use simulation to investigate the effect of assumptions about the relatedness between DPQ in the base population on estimates of genetic parameters. Relatedness between DPQ in the base generation may differ considerably between populations because of their history. Conclusions Our results show that estimates of (co)variance components and derived genetic parameters were seriously biased (25% too high or too low) when assumptions on the relationship between DPQ in the statistical analysis did not agree with reality.

scholarly journals Genetic diversity among Brazilian okra landraces detected by morphoagronomic and molecular descriptors

2019 ◽  
Vol 42 ◽  
pp. e43426
Author(s):  
Luana Rainieri Massucato ◽  
Karina Kazue Nakamura ◽  
Paulo Mauricio Ruas ◽  
Douglas Mariani Zefa ◽  
Derly José Henrique da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quantitative Traits ◽  
Genetic Parameters ◽  
Molecular Descriptors ◽  
Geographical Origin ◽  
Molecular Data ◽  
Gene Bank ◽  
Aflp Markers ◽  
Distance Measures ◽  
Breeding Programmes

The conservation of okra landraces [Abelmoschus esculentus (L.) Moench] in gene banks is essential for the success of their use in breeding programmes. This study evaluated the genetic diversity among okra landraces in Brazil based on morphoagronomic descriptors and AFLP markers. We studied 30 accessions of the vegetable gene bank of the Universidade Federal de Viçosa. To this end, 17 morphoagronomic descriptors and five combinations of AFLP primers were used. Genetic parameters were estimated for the quantitative traits and the accessions were grouped by Ward’s method, using the Gower’s and Jaccard’s distance measures, respectively, for the morphoagronomic and molecular data. Polymorphisms were observed for all qualitative traits, while the quantitative traits were significant by deviance analysis. The genetic parameters confirmed the existence of variability among accessions, and high accuracy and heritability indices were found for the traits related to fruit and plant height. Ward’s grouping showed no relationship between the clusters formed with the morphoagronomic and molecular data and the geographical origin of the accessions. No association between morphoagronomic descriptors and AFLP markers was observed. The lack of correlation suggests that both approaches of characterization are important to understand and differentiate the okra accessions.

scholarly journals Quantitative traits under selection: derivations of distributions, higher moments, and the effects of recombination

2021 ◽  
Author(s):  
Reginald D Smith
Keyword(s):  
Quantitative Traits ◽  
Exact Formula ◽  
Breeding Value ◽  
Breeding Values ◽  
Mean And Variance ◽  
The Mean ◽  
The Impact ◽  
First Four Moments ◽  
First Time ◽  
Fertile Area

The mathematical theory of quantitative traits is over one hundred years old but it is still a fertile area for research and analysis. However, the effects of selection on a quantitative trait, while well understood for the effects on the mean and variance, have traditionally been difficult to attack from the perspective of analyzing the probability density of the breeding values and deriving higher (third and fourth) moments as well as analyzing the impact of recombination. In this paper, the exact formula for the breeding value distribution after selection is derived and, using new integral tables, the first four moments are given exact expressions for the first time. In addition, the effects of recombination on the full distribution of breeding values are demonstrated. Finally, the changes of GXE covariance in the selected parent population caused by factors similar to the Bulmer Effect are also investigated in detail.

scholarly journals Evaluation of Breeding Value Based on Scores Achieved in the Polish Championships for Young Horses

2015 ◽  
Vol 15 (4) ◽  
pp. 879-887
Author(s):  
Tomasz Próchniak ◽  
Iwona Rozempolska-Rucińska ◽  
Grzegorz Zięba ◽  
Marek Łukaszewicz
Keyword(s):  
Genetic Improvement ◽  
Genetic Parameters ◽  
Performance Test ◽  
Breeding Value ◽  
Genetic Trend ◽  
Breeding Values ◽  
Physical Traits ◽  
Young Horses ◽  
Show Jumping ◽  
Detailed Picture

Abstract Genetic improvement of show jumping horses is problematic, given the multitude of physical traits that determine sport usability and the specific mental predispositions required during training and competitions. The Polish Championships for Young Horses (PCYH) provide an opportunity to evaluate usability traits in Polish horses, which, however, is not a basis for evaluation of the breeding value. The aim of the study was to propose a model for evaluation of the breeding value of horses taking part in the Championships. In total, 1232 starts of 894 4-, 5-, 6-, and 7-year-old horses were analysed. Indices of BLUP breeding values were calculated based on 7 traits with known genetic parameters (ranking in the championship, style rating on days 1, 2, and 3, and penalty points on days 1, 2, and 3). A low and irregular genetic trend, significant only in the case of penalties scored on days 1 and 2 of the championships, was shown. Compatibility of the evaluation of the breeding value estimated on the basis of scores achieved in the Polish Championships for Young Horses with the scores of the performance test carried out in Training Centres was shown. It was also demonstrated that the “sum penalty” and “sum style” measured during the three days of the Championships is sufficient for evaluation of the BLUP breeding value. It was suggested that the evaluation combined with the results achieved at the PCYH (in four age categories) would provide a more detailed picture of the genetic predispositions of jumping horses.

scholarly journals Estimation of genetic parameters for growth related traits at different stages of development in Paralichthys olivaceus (Temminck & Schlegel, 1846)

2016 ◽  
Vol 63 (3) ◽  
Author(s):  
F. Liu ◽  
S. L. Chen ◽  
L. Wang ◽  
Y. P. Zhang ◽  
Y. S. Tian ◽  
...  
Keyword(s):  
Body Weight ◽  
Growth Stage ◽  
Genetic Parameters ◽  
Developmental Stages ◽  
Growth Traits ◽  
Paralichthys Olivaceus ◽  
Correlation Coefficients ◽  
Breeding Value ◽  
Estimated Breeding Value ◽  
Estimation Of Genetic Parameters

Genetic parameters of growth traits at different growing stages of Paralichthys olivaceus (Temminck and Schlegel, 1846) were estimated using 30 families. The estimates of heritability for body weight at four developmental stages viz., 210, 450, 720 and 830 days of age, varied from 0.12 to 0.37. The heritability at 720 days of age was the lowest and that of 450 days was the highest. The maternal effect was 0.08 at 210 days, 0.03 at 450 days and almost zero (8.89 E-8 and 2.40 E-7) at 720 and 830 days. Correlation coefficients of the estimated breeding value (EBV) and phenotypic value (PV) of body weight at different developmental stages were 0.470-0.803, which were highly significant (p<0.01). Correlation of estimated breeding value (EBV) and phenotypic value (PV) was the highest at 210 days of age and the lowest at 720 days. Genetic correlation among the four stages showed large variation (0.339-0.811), which were highly significant except that of 210 and 830 days. The value and accuracy of estimating genetic parameters for growth traits at different stages was different. Therefore, the growth stage should be taken into account when designing a breeding program for growth traits in P. olivaceus.

scholarly journals Estimation of inbreeding effect on conception in Czech Holstein

2019 ◽  
Vol 64 (No. 7) ◽  
pp. 309-316
Author(s):  
Michala Hofmannová ◽  
Josef Přibyl ◽  
Emil Krupa ◽  
Petr Pešek
Keyword(s):  
Genetic Parameters ◽  
Negative Impact ◽  
Additive Genetic Variance ◽  
Random Effect ◽  
Inbreeding Coefficient ◽  
Conception Rate ◽  
Breeding Value ◽  
Breeding Values ◽  
Binary Model ◽  
Animal Model Blup

The influence of calculated inbreeding coefficients on the conception of heifers and cows was analysed by a two-trait binary model for conceived/not conceived after each insemination on 677 234 Czech Holstein cows and heifers with 3 248 299 insemination records as the covariable in a statistical model. The data between 1996 and 2014 were analysed. Various effects and their statistical influence on traits were tested by a generalized linear model. Consequently, genetic parameters were estimated by the Gibbs sampling method and used in predicting breeding values using the best linear unbiased prediction by animal model (BLUP-AM). The mean for the conception rate of cows averaged over lactations was 33.7% and for heifers it reached 53.8%. Average inbreeding coefficient increased from 1% in 1996 to almost 5% by 2013 and was in the range of 0–45%. The rate of inbreeding per generation was 0.20%. Although the effect of inbreeding was statistically significant (P = 0.05) for both traits, the proportion of variability explained by the models was relatively low. Estimated genetic parameters were low for both traits. Coefficient of heritability was 2.00% and 1.30% for cows and heifers, respectively, whereas coefficients of repeatability reached 6.09% and 7.08% for cows and heifers, respectively. The random effect of the permanent environment (PE) reached higher values than the additive genetic variance (G) and explained 5.67% and 4.09% of variability for cows and heifers, respectively. A negative impact of inbreeding on heifer and cow conception was observed, whereby every 10% increase in inbreeding coefficient resulted in a conception decline by 2.23%. Calculated Spearman’s rank correlation coefficient between estimated breeding values considering and not considering the effect of inbreeding was close to one. Presented results indicate that inbreeding has a negligible influence on the breeding values of conception. The results also indicate that it is not necessary to include inbreeding coefficient in the routine breeding value evaluation of conception rate of heifers and cows. On the other hand, monitoring of inbreeding is necessary to avoid an increase of its rate.

scholarly journals Zusammenhang zwischen Parametern des Glukosetoleranztestes bei Jungbullen und deren Nachkommenzuchtwert

2000 ◽  
Vol 43 (3) ◽  
pp. 231-240 ◽  
Author(s):  
L. Panicke ◽  
R. Staufenbiel ◽  
O. Burkert ◽  
E. Fischer ◽  
F. Reinhardt
Keyword(s):  
Glucose Tolerance ◽  
Glucose Tolerance Test ◽  
Correlation Coefficients ◽  
Tolerance Test ◽  
Intravenous Glucose Tolerance Test ◽  
Breeding Value ◽  
Central Position ◽  
Intravenous Glucose ◽  
Genetic Determination ◽  
Breeding Values

Abstract. Title of the paper: Relationships between parameters of the glucose tolerance test by young sires and estimated their breeding values A high milk Performance connected to a sound health regarding metabolism and a sufficient fertility in dairy cows depends on a well balanced distribution of energy in body. The terms "type of tumover" and "type of deposition" embody two extremes of food energy preferably for milk production or for body composition. Insulin plays an outstanding role based on its central position in energetic metabolism. The function of insulin may be recorded by means of the intravenous glucose tolerance test (GTT). The reaction of insulin and glucose was investigated after infusion of 1 g Glucose/kg075 because of the probable genetic determination of the reactive ability. The coefficients of heritability range from h2 = 0.16 + 0.10 to h2 = 0.28 ± 0.16. Investigating 28 sires the correlation coefficients amount to r = 0.5 for parameters of gluccose tolerance test and estimated breeding values which is closer than those between pedigree breeding value and glucose tolerance test.This is expecting additional Information for young sires before the insert of the test.

scholarly journals Estimation of additive and dominance variance for litter size components in rabbits

2014 ◽  
Vol 59 (No. 4) ◽  
pp. 182-189 ◽  
Author(s):  
I. Nagy ◽  
J. Farkas ◽  
I. Curik ◽  
G. Gorjanc ◽  
P. Gyovai ◽  
...  
Keyword(s):  
Environmental Effects ◽  
Variance Components ◽  
Correlation Coefficients ◽  
Data File ◽  
Breeding Value ◽  
Environmental Variance ◽  
Relative Significance ◽  
Breeding Values ◽  
Dead Animal ◽  
Additive Genetic Effects

Additive, dominance, and permanent environmental variance components were estimated for the number of kits born alive, number of kits born dead, and total number of kits born of a synthetic rabbit line (called Pannon Ka). The data file consisted of 11 582 kindling records of 2620 does collected between the years 1996&ndash;2013. The total number of animals in the pedigree files was 4012. The examined traits were evaluated using single-trait and two-trait (number of kits born alive-dead) animal models containing all or part of the following effects: additive genetic effects, permanent environmental effects, dominance effects. Heritability estimates calculated using the basic single-trait and two-trait models were 0.094 &plusmn; 0.018 and 0.090 &plusmn; 0.016 for number of kits born alive, 0.037 &plusmn; 0.010 and 0.041 &plusmn; 0.012 for number of kits born dead, and 0.117 &plusmn; 0.018 for total number of kits born, respectively. The relative significance of permanent environmental effects was 0.069&nbsp;&plusmn; 0.014 and 0.069 &plusmn; 0.012 for number of kits born alive, 0.025 &plusmn; 0.011 and 0.023 &plusmn; 0.010 for number of kits born dead, and 0.060 &plusmn; 0.013 for total number of kits born, respectively. Using the extended single-trait and two-trait models, the ratios of the dominance components compared to the phenotypic variances were 0.048 &plusmn; 0.008 and 0.046&nbsp;&plusmn; 0.007 for number of kits born alive, 0.068 &plusmn; 0.006 and 0.065 &plusmn; 0.006 for number of kits born dead, and 0.005&nbsp;&plusmn; 0.0073 for total number of kits born, respectively. Genetic correlation coefficients between number of kits born alive and number of kits born dead were 0.401 &plusmn; 0.171 and 0.521 &plusmn; 0.182, respectively. Spearman&rsquo;s rank correlations between the breeding values of the different single-trait models were close to unity in all traits (0.992&ndash;0.990). Much lower breeding value stability was found for two-trait models (0.384&ndash;0.898), especially for number of kits born dead. Results showed that the dominance components for number of kits born alive and number of kits born dead were not zero and affected the ranking of the animals (based on the breeding values). &nbsp;

scholarly journals Stability of estimated breeding values for average daily gain in Pannon White rabbits

2011 ◽  
Vol 56 (No. 8) ◽  
pp. 365-369 ◽  
Author(s):  
I. Nagy ◽  
J. Farkas ◽  
P. Gyovai ◽  
I. Radnai ◽  
Z. Szendrő
Keyword(s):  
Average Daily Gain ◽  
Rank Correlation ◽  
Correlation Coefficients ◽  
The Other ◽  
Breeding Value ◽  
Breeding Values ◽  
Spearman’S Rank Correlation ◽  
The Common ◽  
Estimated Breeding Values ◽  
Daily Gain

Stability of estimated breeding values for average daily gain (ADG) between 5 and 10 weeks of age was analysed for 47 242 Pannon White rabbits, reared in 7470 litters and born between 2000 and 2008. The dataset was divided into 5 successive 5-year periods: (1) 2000&ndash;2004, (2) 2001&ndash;2005, (3) 2002&ndash;2006, (4) 2003&ndash;2007, and (5) 2004&ndash;2008. Then, after selecting the appropriate part of the pedigree for these sub-datasets, genetic parameters and breeding values were estimated for ADG using REML and BLUP methods. In the applied models sex, year-month, animal and random litter effects were considered. Estimated heritabilities for all 5 periods from 1 to 5 were moderate and stable (0.28 &plusmn; 0.01, 0.28 &plusmn; 0.02, 0.29 &plusmn; 0.02, 0.27 &plusmn; 0.02, and 0.28 &plusmn; 0.02). Magnitudes of random litter effects were low and stable (0.14 &plusmn; 0.01, 0.15 &plusmn; 0.01, 0.15 &plusmn; 0.01, 0.16 &plusmn; 0.01, and 0.16 &plusmn; 0.01). After breeding value estimation the dataset of period 5 was merged pair-wise with the other periods 4, 3, 2 and 1 using an inner join. Thus only the common records of the datasets representing the periods 5-4, 5-3, 5-2, and 5-1 were included in the merged datasets. In these merged datasets each rabbit had two breeding values for ADG based on two different periods. Spearman's rank correlation coefficients were calculated between the breeding values based on the dataset of period 5 and the other periods. With the successive years the rank correlation coefficients decreased (0.989, 0.979, 0.965 and 0.924). The correlation coefficients between ranks remained moderately high, even when the proportion of the common rabbits in the merged datasets was low. However, a reasonable re-ranking occurred among the top animals. Rank correlations for the top 100 and 1000 animals varied from 0.41 to 0.55 and from 0.37 to 0.54, respectively, which could influence selection efficiency if the rolling base were used for genetic evaluation.

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