scholarly journals Estimated breeding values and genetic trend for milk yield in Nili Ravi buffaloes

2007 ◽  
Vol 6 (sup2) ◽  
pp. 393-396
Author(s):  
M. Ahmad
Keyword(s):  
Milk Yield ◽  
Genetic Trend ◽  
Breeding Values ◽  
Estimated Breeding Values

scholarly journals Comparison of BLUP and Bayesian methods for different sizes of training population in genomic selection

2020 ◽  
Vol 44 (5) ◽  
pp. 994-1002
Author(s):  
Samet Hasan ABACI ◽  
Hasan ÖNDER
Keyword(s):  
Genomic Selection ◽  
Milk Yield ◽  
Predictive Ability ◽  
Breeding Value ◽  
Training Population ◽  
Breeding Values ◽  
Value Prediction ◽  
The Usa ◽  
Population Sizes ◽  
Estimated Breeding Values

This study aims to compare the accuracy of pedigree-based and genomic-based breeding value prediction for different training population sizes. In this study, Bayes (A, B, C, Cpi) and GBLUP methods for genomic selection and BLUP method for pedigree-based selection were used. Genomic and pedigree-based breeding values were estimated for partial milk yield (158 days) of Holstein cows (400 individuals) from a private enterprise in the USA. For this aim, populations were created for indirect breeding value estimates as training (322–360) and test (78–40) populations. In animals genotyped with a 54k SNP, the marker file was encoded as –10, 0, and 10 for AA, AB, and BB marker genotypes, respectively. Bayes and GBLUP methods were performed using GenSel 4.55 software. A total of 50,000 iterations were used, with the first 5000 excluded as the burn-in. Pedigree-based breeding values were estimated by REML using MTDFREML software employing an animal model. Correlations between partial milk yield and estimated breeding values were used to assess the predictive ability for methods. Bayes B method gave the highest accuracy for the indirect estimate of breeding value.

scholarly journals AlphaPart—R implementation of the method for partitioning genetic trends

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Jana Obšteter ◽  
Justin Holl ◽  
John M. Hickey ◽  
Gregor Gorjanc
Keyword(s):  
Genetic Gain ◽  
R Package ◽  
Breeding Programme ◽  
Genetic Trend ◽  
Breeding Values ◽  
Poultry Breeding ◽  
Breeding Programmes ◽  
Estimated Breeding Values ◽  
The Relationship ◽  
Genetic Trends

Abstract Background In this paper, we present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from estimated breeding values averaged by year of birth. While sources of the overall genetic gain are generally known, their realised contributions are hard to quantify in complex breeding programmes. The aim of this paper is to present the AlphaPart R package and demonstrate it with a simulated stylized multi-tier breeding programme mimicking a pig or poultry breeding programme. Results The package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by pre-defined selection paths, and a set of functions for handling data and results. The package is freely available from the CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by partitioning the nucleus and multiplier genetic gain of the stylized breeding programme by tier-gender paths. For traits measured and selected in the multiplier, the multiplier selection generated additional genetic gain. By using AlphaPart, we show that the additional genetic gain depends on accuracy and intensity of selection in the multiplier and the extent of gene flow from the nucleus. We have proven that AlphaPart is a valuable tool for understanding the sources of genetic gain in the nucleus and especially the multiplier, and the relationship between the sources and parameters that affect them. Conclusions AlphaPart implements the method for partitioning breeding values and genetic trends and provides a useful tool for quantifying the sources of genetic gain in breeding programmes. The use of AlphaPart will help breeders to improve genetic gain through a better understanding of the key selection points that are driving gains in each trait.

Effect of controlling future rate of inbreeding on expected genetic gain and genetic variability in small livestock populations

2020 ◽  
Vol 60 (14) ◽  
pp. 1681
Author(s):  
S. I. Mwangi ◽  
T. K. Muasya ◽  
E. D. Ilatsia ◽  
A. K. Kahi
Keyword(s):  
Genetic Variability ◽  
Milk Yield ◽  
Genetic Gain ◽  
Genetic Relationships ◽  
Breeding Population ◽  
Breeding Values ◽  
Sahiwal Cows ◽  
Improvement Programs ◽  
Small Livestock ◽  
Estimated Breeding Values

Context In the present study we assessed the use of average relationship as a means to control future rates of inbreeding in small cattle closed nucleus and its effect on genetic gain for milk yield as a means of managing genetic variability in livestock improvement programs. Aim The aim was to strike an ideal balance between genetic gain and loss of genetic variability for Sahiwal population. Methods A total of 8452 milk yield records of Sahiwal cows from National Sahiwal Stud, Kenya, were used to estimate breeding values and 19315 records used to estimate average relatedness of all individuals. The estimated breeding values and genetic relationships were then used to optimise individual genetic contributions between the best two males and the top 210 females in 2000–2008-year group, as well as between the best four, six and eight males and top, 420, 630 and 840 females based on estimated breeding values for lactation milk yield. Weights on genetic merit and average relationship considered in this study were (1, 0), (1, −300), (1, −500), (1, −1000) and (0, −1). Key results When the best sires were selected and used for mating disregarding average relationship with their mates i.e. (0, –1), genetic gain of up to 213 kg was realised accompanied by a rate of inbreeding per generation of 4%. Restricting average relationship alone i.e. (0, –1), resulted in a future rate of inbreeding of 1.6% and average merit of 154 when top two sires were used for breeding. At the same restriction level but using eight top sires, the rate of inbreeding per generation was 0.9% accompanied by an average merit of 128.2 kg. Controlling average relationship between mates resulted in increased genetic variability i.e. lower rate of inbreeding though average merit declined. Conclusion A rate of inbreeding per generation of <1% is required for a population to maintain its long-term viability. For this level to be attained, the size of the breeding population should be increased from the current two sires vs 210 dams to eight sires vs 840 dams. Implications Practical implications for closed nucleus programs such as the Sahiwal program in Kenya should include expanding the nucleus to comprise other institutional and privately-owned herds.

scholarly journals AlphaPart - R implementation of the method for partitioning genetic trends

2020 ◽  
Author(s):  
Jana Obšteter ◽  
Justin Holl ◽  
John M. Hickey ◽  
Gregor Gorjanc
Keyword(s):  
Gene Flow ◽  
Open Source ◽  
Open Source Software ◽  
Genetic Gain ◽  
R Package ◽  
Genetic Trend ◽  
Breeding Values ◽  
Breeding Programmes ◽  
Estimated Breeding Values ◽  
Genetic Trends

AbstractBackgroundIn this paper we present the AlphaPart R package, an open-source software that implements a method for partitioning breeding values and genetic trends to identify sources of genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from averaged year of birth estimated breeding values of selection candidates. While sources of the overall genetic gain are generally known, their realised contributions are hard to quantify in complex breeding programmes. The aim of this paper is to present the AlphaPart R package and demonstrate it with a simulated pig breeding example.ResultsThe package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by analyst defined paths, and a set of functions for handling data and results. The package is freely available from CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by examining the genetic gain in a pig breeding example, in which the multiplier achieved higher breeding values than the nucleus for traits measured and selected in the multiplier. The partitioning analysis revealed that these higher values depended on the accuracy and intensity of selection in the multiplier and the extent of gene flow from the nucleus. For traits measured only in the nucleus, the multiplier achieved comparable or smaller genetic gain than the nucleus depending on the amount of gene flow.ConclusionsAlphaPart implements a method for partitioning breeding values and genetic trends and provides a useful tool for quantifying the sources of genetic gain in breeding programmes. The use of AlphaPart will help breeders to better understand or improve their breeding programmes.

scholarly journals Genetic and permanent environmental variations in daily milk yield and milk flow rates in Hungarian Holstein Friesian

2007 ◽  
Vol 50 (6) ◽  
pp. 535-548
Author(s):  
A. A. Amin
Keyword(s):  
Milk Yield ◽  
Genetic Correlations ◽  
Random Regression ◽  
Lactation Performance ◽  
Flow Rates ◽  
Breeding Values ◽  
Milk Flow ◽  
Holstein Friesian ◽  
Estimated Breeding Values ◽  
Daily Milk Yield

Abstract. Random regression animal model was applied for analyzing the relationships between test-day milk yields (DY), and milk flow rate (FR). The current study involved 169,491 sample test-day records of Hungarian Holstein- Friesian cows. A quadratic random regression was applied for declaring additive genetic variances in all studied traits during biweekly observations across the first three parities. Estimates of heritability for test-day milk yield and udder milk flow rates ranged from 0.09 to 0.58 and from 0.02 to 0.50, respectively through 42 milk-weeks (Wk). The highest heritability estimates occurred during the end of trajectory for both traits. In general DY tended to be more heritable than FR across lactation except during the first few weeks of lactation. Performance of DY was less affected by environmental variation than FR, while both values were moderate to high (0.63 to 0.75). Correlations among measurements showed that additive correlations (Ra) of 4WkFR with the reminder part of lactation were high during early and late lactation. Also 24WkFR was more genetically correlated with next measures and reached Ra = 0.94. Whereas 42WkFR was high additively correlated with other biweekly measurements and ranged from 0.53 to 0.99. Performance of early and late DY was negative additively correlated and ranged from −0.03 to −0.53. Heritability of DY within levels of FR ranged from 0.09 to 0.33 within very slow and medium milk flow, respectively. Correlations among both traits increased linearly toward lactation end. DY during 24Week and 42Week of lactation accounted the highest additive correlations with FR across lactation. Estimated breeding values for DY and FR increased in different rates with progressing lactation. These results may indicate that individual selection results would be favorably achieved during the late part of lactation. More details about estimates of breeding values, estimates of permanent environmental and additive genetic correlations for all traits were tabulated.

Genetic perspective of milk yield persistency in the first three lactations of Iranian buffaloes (Bubalus bubalis)

2017 ◽  
Vol 84 (4) ◽  
pp. 434-439 ◽  
Author(s):  
Navid Ghavi Hossein-Zadeh ◽  
Mohammad Ali Nazari ◽  
Abdol Ahad Shadparvar
Keyword(s):  
Milk Yield ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Bubalus Bubalis ◽  
Random Regression ◽  
Genetic Trend ◽  
Breeding Center ◽  
Regression Test ◽  
The Difference ◽  
Estimated Breeding Values

The objectives of this study were to estimate the genetic parameters and genetic trends for different measures of persistency (PM) for milk yield in Iranian buffaloes using a random regression test day model. Test day records of the first three lactations of buffaloes within 715 herds comprising 43 014, 38 941 and 33 937 records, respectively, were obtained from the Animal Breeding Center of Iran during 1992 to 2012. Legendre polynomial functions were chosen to fit the lactation curves in the framework of a random regression test day model for estimating (co)variance components. Three measures of persistency were modified based on the lactation curve conditions of buffaloes: (1) The average of estimated breeding values (EBVs) for test day milk yields from day 226 to day 270 as a deviation from the average of EBVs from day 44 to day 62 (PM1), (2) A summation of contribution for each day from day 53 to day 247 as a deviation from day 248 (PM2), (3) The difference between EBVs for day 257 and day 80 (PM3). The highest heritability estimates were observed for PM2over the first three lactations (0·29, 0·80 and 0·42, respectively). Estimates of genetic correlations between persistency measures and milk yield varied from −0·48 to 0·29 (first lactation), from −0·12 to 0·48 (second lactation), and from −0·62 to 0·63 (third lactation). Estimate of genetic trend for first lactation PM2was negative (−0·0088 ± 0·0043;P< 0·05). It is essential to include milk yield persistency in the breeding goal of Iranian buffaloes along with other important traits such as milk yield or reproductive traits.

scholarly journals Implementation of an Economic Lifetime Net Merit for the Dual-Purpose German Black Pied Cattle Breed

Agriculture ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 41
Author(s):  
Saskia Meier ◽  
Danny Arends ◽  
Paula Korkuć ◽  
Sandra Kipp ◽  
Dierck Segelke ◽  
...  
Keyword(s):  
Standard Deviation ◽  
Dairy Cattle ◽  
Milk Yield ◽  
Cattle Breed ◽  
Breeding Value ◽  
Dual Purpose ◽  
Breeding Values ◽  
Fitness Traits ◽  
Milk Performance ◽  
Estimated Breeding Values

Recently, a Total Merit Index (RZ€) has been developed for German Holstein dairy cattle on the basis of margin in Euro. Our aim was to adjust this lifetime net merit for the dual-purpose German Black Pied cattle breed (DSN) accounting for beef production in addition to milk performance and fitness traits. We used the estimated breeding values of DSN sires and developed a breeding value for carcass weight and quality. Furthermore, we adjusted the German Holstein marginal profits per standard deviation, which are used to calculate the estimated breeding values, to DSN-specific values. The DSN Net Merit is the sum of the three sub-indices DSN Net Milk, DSN Net Fitness, and DSN Net Beef, which contribute to the DSN Net Merit with 52.84%, 43.43%, and 3.73%, respectively. The DSN Net Merit that was calculated for 33 DSN sires ranged between EUR −1114 and +709. The DSN Net Merit strongly correlates with the Total Merit Index. The implementation of the DSN Net Merit is useful for selection and mating decisions. Especially, the sub-index DSN Net Beef, which does not correlate with existing breeding values, can be used to maintain the dual-purpose character of DSN while modestly improving milk yield. The approach can be easily adapted to other dual-purpose breeds.

scholarly journals Genetic trend of functional productive life in the population of black and white cattle in Serbia

Genetika ◽  
2018 ◽  
Vol 50 (3) ◽  
pp. 855-862 ◽  
Author(s):  
Dragan Stanojevic ◽  
Radica Djedovic ◽  
Vladan Bogdanovic ◽  
Nikola Raguz ◽  
Denis Kucevic ◽  
...  
Keyword(s):  
Average Length ◽  
Breeding Value ◽  
Genetic Trend ◽  
Breeding Values ◽  
Productive Life ◽  
Black And White ◽  
Time Period ◽  
Average Share ◽  
White Cattle ◽  
Estimated Breeding Values

This research was conducted with the aim ?f estimating genetic trend for a functional length of productive life (FLPL) in the population of Black and White cattle in Serbia. Research and bulls genetic evaluation for functional longevity were performed on a set of data provided by Agricultural Corporation Belgrade AD (PKB) which contained data on longevity and origin of 22109 cows out of which 26% records were right-censored. Functional length of productive life (FPLP) represents a time period from the first calving to culling or censoring corrected for milk production. Breeding values were estimated using Weibull method of proportional risks within survival analysis a genetic trend for FLPL was calculated using of a regression analysis. The cows included in the analysis were on average first calved in the age of 809 days and had an average share of 81.9% genes of Holstein Friesian breed. An average length of productive life was 1267 days (41.6 months). Distribution of bull standardised breeding values did not statistically significantly differ from normal distribution. An average standardised breeding value was 99. A slightly positive genetic trend was determined, that is, the length of functional productive life was by selection increased by 0.021 day at an annual level while a reliability of estimated breeding values showed a negative trend.

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