35 Detecting Effective Starting Point of Genomic Selection by Divergent Trends from BLUP and ssGBLUP

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 19-19
Author(s):  
Rostam Abdollahi-Arpanahi ◽  
Daniela Lourenco ◽  
Ignacy Misztal
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Single Step ◽  
Weaning Weight ◽  
Start Date ◽  
Angus Cattle ◽  
Starting Point ◽  
Essential Question ◽  
Genetic Trends

Abstract Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree BLUP became biased because this method does not consider selection using genomic information. Hence, the point of divergence of genetic trends obtained with BLUP and Single-step genomic BLUP (ssGBLUP) may indicate the start date of genomic selection. This study aimed to find the start date of genomic selection for a set of economically important traits in pigs and Angus cattle by comparing genetic and Realized Mendelian sampling (RMS) trends obtained using BLUP and ssGBLUP. In pigs, the genetic trends from ssGBLUP and BLUP diverged for all traits with different intensity. In beef cattle, the trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with little divergence for birth weight. In pigs, the RMS trends from ssGBLUP and BLUP diverged strongly for one trait and weakly for another trait. In beef cattle, the RMS trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with little trend for birth weight. Divergence of the genetic trends from ssGBLUP and BLUP indicate onset of the genomic selection. Presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agree with industry practices across the two species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.

scholarly journals Detecting effective starting point of genomic selection by divergent trends from BLUP and ssGBLUP in pigs, beef cattle, and broilers

2021 ◽  
Author(s):  
Rostam Abdollahi Arpanahi ◽  
Daniela Lourenco ◽  
Ignacy Misztal
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Broiler Chickens ◽  
Average Daily Gain ◽  
Breeding Cycle ◽  
Production Traits ◽  
Weaning Weight ◽  
Daily Gain ◽  
Genetic Trends

Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree BLUP became biased because this method does not consider selection using genomic information. Hence, the effective start point of genomic selection can be detected in two possible ways including the divergence of genetic trends and Realized Mendelian sampling (RMS) trends obtained with BLUP and Single-step genomic BLUP (ssGBLUP). This study aimed to find the start date of genomic selection for a set of economically important traits in three livestock species by comparing trends obtained using BLUP and ssGBLUP. For this purpose, three datasets comprised a pig dataset with 117k genotypes and 1.3M animals in pedigree, Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and a purebred broiler chicken dataset included ~154k genotypes and 1.3M birds in pedigree were used. The genetic trends for pigs diverged for the genotyped animals born in 2014 for average daily gain and backfat. In beef cattle, the trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with little diverging for birth weight. In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for average daily gain than for backfat. In beef cattle, the RMS trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with a trivial trend for birth weight. In broiler chickens, the RMS trends from ssGBLUP and BLUP diverged strongly for two production traits at breeding cycle 6, with a slight divergence for another trait. Divergence of the genetic trends from ssGBLUP and BLUP indicates onset of the genomic selection. Presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agree with industry practices across the 3 species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.

scholarly journals Detecting effective starting point of genomic selection by divergent trends from BLUP and ssGBLUP in pigs, beef cattle, and broilers

2021 ◽  
Author(s):  
Rostam Abdollahi-Arpanahi ◽  
Daniela Lourenco ◽  
Ignacy Misztal
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Broiler Chickens ◽  
Average Daily Gain ◽  
Breeding Cycle ◽  
Production Traits ◽  
Starting Point ◽  
Daily Gain ◽  
Genetic Trends

Abstract Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree BLUP became biased because this method does not consider selection using genomic information. Hence, the effective starting point of genomic selection can be detected in two possible ways including the divergence of genetic trends and Realized Mendelian sampling (RMS) trends obtained with BLUP and Single-step genomic BLUP (ssGBLUP). This study aimed to find the start date of genomic selection for a set of economically important traits in three livestock species by comparing trends obtained using BLUP and ssGBLUP. Three datasets were used for this purpose: a pig dataset with 117k genotypes and 1.3M animals in pedigree, an Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and a purebred broiler chicken dataset included ~154k genotypes and 1.3M birds in pedigree were used. The genetic trends for pigs diverged for the genotyped animals born in 2014 for average daily gain and backfat. In beef cattle, the trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with little divergence for birth weight. In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for average daily gain than for backfat. In beef cattle, the RMS trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with a trivial trend for birth weight. In broiler chickens, the RMS trends from ssGBLUP and BLUP diverged strongly for two production traits at breeding cycle 6, with a slight divergence for another trait. Divergence of the genetic trends from ssGBLUP and BLUP indicates onset of the genomic selection. The presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agree with industry practices across the three species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals Factors affecting growth traits of beef cattle breeds raised inSlovakia

2011 ◽  
Vol 50 (No. 1) ◽  
pp. 14-21 ◽  
Author(s):  
E. Krupa ◽  
M. Oravcová ◽  
P. Polák ◽  
J. Huba ◽  
Z. Krupová
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Least Squares ◽  
Linear Model ◽  
Growth Traits ◽  
General Linear Model ◽  
Weaning Weight ◽  
Factors Affecting ◽  
Sex Effect ◽  
Beef Cattle Breeds

Growth traits of purebred calves of six beef breeds (Aberdeen Angus – AA, Blonde d’Aquitaine – BA, Charolais – CH,Hereford – HE, Limousine – LI and Beef Simmental – BS) born from 1998 to 2002 were analysed. Traits under study were birth weight (BW), weight at 120 days (W120), weight at 210 days – weaning weight (WW), weight at 365 days – yearling weight (YW) and average daily gains from birth to 120 days (ADG1), from birth to 210 days (ADG2), from birth to 365 days (ADG3), from 120 to 210 days (ADG4). General linear model with class effects of breed, dam’s age at calving, sex, herd-year-season (HYS) and covariation of age at weighing was used for analyses. All effects significantly affected both weight and gain traits except for dam’s age that was significant for BW, W120, YW and ADG3, and age at weighing that was significant for W120, WW, YW, ADG2, ADG3, ADG4. Estimated least squares means of growth traits were compared using Scheffe’s multiple-range tests. Highest BW (40.57 kg) and W120 (172.43 kg) were found for BA calves. BS calves had highest WW (260.30 kg), YW (424.07 kg), ADG1 (1 154 g), ADG2 (1 053 g), ADG3 (1 054 g) and ADG4 (1 098 g). Highest BW, YW, ADG3 and ADG4 were found for males-singles. Males-twins had highest W120, WW, ADG1 and ADG2. Calves descending from 5–7 years old dams had highest BW, W120, WW, ADG1, ADG2 and ADG4. The proportion of variability of growth traits explained by HYS effect (42.96–71.69%) was high, whereas proportions of variability explained by SEX effect (2.03–5.77%), age of dam (1.02–2.24%) and breed (1.05–2.21%) were low. Residuals accounted for 23.71 up to 53.79% of total variance.  

scholarly journals Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Harly J. Durbin ◽  
Duc Lu ◽  
Helen Yampara-Iquise ◽  
Stephen P. Miller ◽  
Jared E. Decker
Keyword(s):  
Heat Stress ◽  
Beef Cattle ◽  
Tall Fescue ◽  
The United States ◽  
Genetic Evaluation ◽  
Functional Enrichment ◽  
Fescue Toxicosis ◽  
Weaning Weight ◽  
Angus Cattle ◽  
Genetic Evaluations

Abstract Background Heat stress and fescue toxicosis caused by ingesting tall fescue infected with the endophytic fungus Epichloë coenophiala represent two of the most prevalent stressors to beef cattle in the United States and cost the beef industry millions of dollars each year. The rate at which a beef cow sheds her winter coat early in the summer is an indicator of adaptation to heat and an economically relevant trait in temperate or subtropical parts of the world. Furthermore, research suggests that early-summer hair shedding may reflect tolerance to fescue toxicosis, since vasoconstriction induced by fescue toxicosis limits the ability of an animal to shed its winter coat. Both heat stress and fescue toxicosis reduce profitability partly via indirect maternal effects on calf weaning weight. Here, we developed parameters for routine genetic evaluation of hair shedding score in American Angus cattle, and identified genomic loci associated with variation in hair shedding score via genome-wide association analysis (GWAA). Results Hair shedding score was moderately heritable (h2 = 0.34 to 0.40), with different repeatability estimates between cattle grazing versus not grazing endophyte-infected tall fescue. Our results suggest modestly negative genetic and phenotypic correlations between a dam’s hair shedding score (lower score is earlier shedding) and the weaning weight of her calf, which is one metric of performance. Together, these results indicate that economic gains can be made by using hair shedding score breeding values to select for heat-tolerant cattle. GWAA identified 176 variants significant at FDR < 0.05. Functional enrichment analyses using genes that were located within 50 kb of these variants identified pathways involved in keratin formation, prolactin signalling, host-virus interaction, and other biological processes. Conclusions This work contributes to a continuing trend in the development of genetic evaluations for environmental adaptation. Our results will aid beef cattle producers in selecting more sustainable and climate-adapted cattle, as well as enable the development of similar routine genetic evaluations in other breeds.

Bayesian analysis of selection for greater weaning weight while maintaining birth weight in beef cattle

2009 ◽  
Vol 87 (10) ◽  
pp. 3089-3096 ◽  
Author(s):  
L. M. Melucci ◽  
A. N. Birchmeier ◽  
E. P. Cappa ◽  
R. J. C. Cantet
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Bayesian Analysis ◽  
Weaning Weight ◽  
Selection For

EFFECTS OF YEARLING WEIGHT SELECTION IN SHORTHORN BEEF CATTLE ON AGE-OF-DAM ADJUSTMENT FACTORS

1990 ◽  
Vol 70 (3) ◽  
pp. 963-965
Author(s):  
J. C. OLTHOFF ◽  
G. H. CROW ◽  
G. W. RAHNEFELD
Keyword(s):  
Birth Weight ◽  
Beef Cattle ◽  
Key Words ◽  
Selection Line ◽  
Weaning Weight ◽  
Performance Change ◽  
Adjustment Factors ◽  
Over Time

Lines within a breed which differ in their level of performance may require different age-of-dam adjustment factors in the same way that different breeds do. Age-of-dam adjustments calculated from a control and a yearling weight selection line indicated lower values in the selected line for calf birth weight, weaning weight and yearling weight for 2- and 4-yr-old dams. Trends for adjustment factors in each line over time were generally not significant but tended to diverge. Age-of-dam adjustment factors within a breed may need to be reevaluated at intervals as levels of performance change. Key words: Beef cattle, age of dam adjustment, selection, yearling weight

Results of multivariate individual animal model genetic evaluations of british pedigree beef cattle

1997 ◽  
Vol 65 (2) ◽  
pp. 199-207 ◽  
Author(s):  
R. E. Crumps ◽  
G. Simm ◽  
D. Nicholson ◽  
R. H. Findlay ◽  
J. G. E. Bryan ◽  
...  
Keyword(s):  
Animal Model ◽  
Birth Weight ◽  
Beef Cattle ◽  
Fixed Effects ◽  
Breeding Value ◽  
Individual Animal ◽  
Group Sex ◽  
The Uk ◽  
Genetic Evaluations ◽  
Genetic Trends

AbstractThis paper reports the procedures put into place in the UK for the genetic evaluation of pedigree beef cattle and estimation of genetic trends using a comprehensive model to allow critical analysis of progress made under previous data recording schemes. Live weights of Simmental, Limousin, Charolais, South Devon and Aberdeen Angus beef cattle, recorded by the Meat and Livestock Commission (MLC) from 1970 to 1992 were analysed, as part of a project to introduce best linear unbiased predictions (BLUP) of breeding value in the British beef industry. Birth weights were available from MLC or the relevant breed society, (4000 to 84000 records, depending on the breed) and 200- and 400-day weights were estimated by within-animal linear regression on all available weights (resulting in 8000 to 48000 records per breed). Animals were retrospectively assigned to contemporary groups within herds, separately for each trait, taking account of observed calving patterns. Records were adjusted to correct for heterogeneity of variance between herds. BLUP evaluations were then performed within breed, fitting a multivariate individual animal model. In addition to additive direct genetic effects, additive maternal genetic and dam permanent environmental effects were included for birth weight and 200-day weight. Unknown parents were assigned to genetic groups, based on estimated date of birth. The model included fixed effects for contemporary group, sex, month of birth, birth type (single or multiple), embryo transfer births, fostered calves, breed of dam, proportion purebred and age of dam. Genetic trends were estimated by regressing estimated breeding values for animals on their year of birth. Trends in birth weight, 200-day weight and 400-day weight between 1970 and 1992 were approximately 0·09, 0·73 and 1·38 kg per annum respectively for the Charolais breed; 0·08, 0·76 and 1·33 kg per annum for the Simmental; 0·06, 0·53 and 0·89 kg per annum for the Limousin; 0·12, 1·02 and 1·86 kg per annum for the Aberdeen Angus; and 0·03, 0·38 and 0·82 kg per annum for the South Devon breed.

Genetic trends for weaning weight during development of a multibreed population of beef cattle in two contrasting environments

2000 ◽  
Vol 80 (1) ◽  
pp. 191-193
Author(s):  
J. J. Tosh ◽  
R. A. Kemp
Keyword(s):  
Natural Selection ◽  
Beef Cattle ◽  
Key Words ◽  
Genetic Component ◽  
Weaning Weight ◽  
Common Base ◽  
The Difference ◽  
Selection Differentials ◽  
Genetic Trends

Genetic trends for weaning weight were determined in two herds of multibreed beef cattle that originated from a common base and were subject to mutual breeding policies in separate environments. The herds diverged for the direct though not the maternal genetic component of weaning weight within the 13-yr period examined; in the final year, the difference (P < 0.001) between the herds was almost 3 kg. This could have been partly due to unequal selection differentials and generation intervals. Results suggested the extent of natural selection also differed between the two environments. Key words: Beef cattle, crossbreeding, genetic trends, selection, weaning weight

Sign in / Sign up

Export Citation Format

Share Document