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 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.

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.

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.

COMPARISONS OF CROSSBRED CALVES BY SOUTH DEVON, MAINE- ANJOU AND SIMMENTAL SIRES FOR SOME BEEF PRODUCTION TRAITS

1974 ◽  
Vol 54 (2) ◽  
pp. 197-203 ◽  
Author(s):  
J. A. NEWMAN ◽  
G. M. WEISS ◽  
B. SCHRADER
Keyword(s):  
Birth Weight ◽  
Significant Interaction ◽  
Statistical Significance ◽  
Average Daily Gain ◽  
Carcass Weight ◽  
Production Traits ◽  
Marbling Score ◽  
Weaning Weight ◽  
Slaughter Age ◽  
Daily Gain

Breed of sire comparisons are made amongst calves born to commercial Hereford cows and sired by bulls of the South Devon (SD, 10 bulls used), Maine-Anjou (MA, two bulls used) and Simmental (SIM, eight bulls used) breeds. Numbers of observations ranged from 239 bulls and 224 heifers for "ease of birth" to 98 bulls for carcass traits. The feedlot test period was 91 days and three feedlot treatments were imposed. Slaughter criteria were subjective and "breed-of-sire" differences in slaughter age and carcass weight were not statistically significant (P > 0.05). Differences amongst breed-of-sire means attained statistical significance for "birth weight" (MA > SIM > SD; P < 0.001), weaning weight of males (MA > SIM > SD; P < 0.001), "on-test" weight (MA > SIM > SD; P < 0.001), average daily gain on test (MA > SIM > SD; P < 0.001) average fat depth/100 kg carcass weight (SD > MA = SIM, P < 0.05), trimmed, de-boned, defatted primal cuts per day of age (MA > SIM > SD; P < 0.01), meat marbling score (SD more marbled than SIM more marbled than MA; P <.05). A significant interaction existed between breed of sire and feeding group for average daily gain on test (P < 0.01) and cutability (P < 0.025). Breed-of-sire differences did not attain statistical significance for weaning weight of female calves, loin area/100 kg carcass weight, cut-ability, or meat color score.

The effect of breed of terminal sire on production of beef steers

1992 ◽  
Vol 72 (4) ◽  
pp. 953-957 ◽  
Author(s):  
B. D. King ◽  
R. A. Petracek ◽  
R. D. H. Cohen ◽  
C. L. Guenther
Keyword(s):  
Birth Weight ◽  
Key Words ◽  
Average Daily Gain ◽  
Carcass Weight ◽  
Beef Steers ◽  
Production Traits ◽  
Brown Swiss ◽  
Calving Ease ◽  
Terminal Sire ◽  
Daily Gain

Charolais (C), Maine-Anjou (MA), Simmental (S) and Brown Swiss (SB) bulls were evaluated using production traits of their steer calves from birth to slaughter. Traits measured were calving ease, birth weight, preweaning average daily gain (ADG), adjusted weaning weight, ADG to slaughter; liveweight at slaughter, days on feed, carcass weight, grade fat, loin-eye area, cutability and dressing percent. For most traits the ranking was MA ≥ C ≥ S ≥ SB. Key words: Beef sire, calving ease, growth, carcass

scholarly journals PSIII-5 Effects of ingredient composition of oral drenches in small piglets post-farrowing on average daily gain and pre-wean mortality

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 238-238
Author(s):  
Olivia Harrison ◽  
Samantha Tauer ◽  
Brent Frederick
Keyword(s):  
Birth Weight ◽  
Average Daily Gain ◽  
High Energy ◽  
Experimental Unit ◽  
Swine Industry ◽  
Bioactive Proteins ◽  
Randomized Design ◽  
Significant Difference ◽  
Key Factor ◽  
Daily Gain

Abstract Number of pigs born alive has been a key factor of the increasing efficiency of the U.S. swine industry. However, with increased pigs in the uterus, birth weight has been negatively impacted, with more small or at-risk pigs being born per litter. In order to overcome these changes, a study testing three commercial oral drenches against a control to determine which would increase average daily gain and decrease preweaning mortality. In a completely randomized design, 877 one-day-old suckling pigs from a high-health farm were selected for the experiment if they appeared to be in the bottom 20% of bodyweight compared to their contemporaries. Selected pigs were given one of four drenching treatments: 1) none (control), 2) bioactive proteins (BP), 3) high energy sugars (HES), and 4) immunoglobulins (IgY). Pigs were weighed on d 1 and d 19 of age (weaning), with mortality tracked during the suckling period. Data were analyzed using SAS v 9.4 (Cary, NC), with pig as the experimental unit and an accepted alpha of 0.05. Treatment had no detected effect on birth weight, weaning weight, ADG, or mortality (P = 0.79, 0.96, 0.86, 0.38 respectively). Likewise, statistical contrasts were used to determine there was no detected impact (P &gt; 0.10) of drench, regardless of type, compared to the control in any measured response criteria. Interesting, pigs drenched with BP or IgY had numerically lower preweaning mortality (11.2 and 11.5% respectively), than those administered the control or HES (15.4 and 15.2%, respectively). In conclusion, this experiment showed no significant difference in the performance between piglets given no product vs. those drenched with bioactive proteins, high energy sugars, or immunoglobulins. However, additional research is warranted with greater replication or disease stressors to better understand if oral drenches may improve preweaning performance or mortality in different situations.

scholarly journals Genome-wide association for heifer reproduction and calf performance traits in beef cattle

Genome ◽  
2015 ◽  
Vol 58 (12) ◽  
pp. 549-557 ◽  
Author(s):  
Everestus C. Akanno ◽  
Graham Plastow ◽  
Carolyn Fitzsimmons ◽  
Stephen P. Miller ◽  
Vern Baron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Research Centre ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
And Performance

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5–7, 9, 13–16, 19–21, 24, 25, and 27–29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

Corn or soybean hull incorporation into haylage-based backgrounding beef cattle diets: Effect on growth and efficiency during the backgrounding and finishing periods

2007 ◽  
Vol 87 (4) ◽  
pp. 615-621 ◽  
Author(s):  
K. C. Swanson ◽  
M. Ko ◽  
C. J. Mader
Keyword(s):  
Body Weight ◽  
Beef Cattle ◽  
Dry Matter ◽  
Average Daily Gain ◽  
Soybean Hulls ◽  
Feedlot Performance ◽  
Final Body Weight ◽  
Plasma Urea ◽  
Soybean Hull ◽  
Daily Gain

This experiment was conducted to evaluate the effects of corn or soybean hull incorporation into haylage-based diets on backgrounding calf performance and subsequent feedlot performance. Crossbred steers [n = 48, initial body weight (BW) = 303 ± 3.4 kg] were individually fed dietary treatments consisting of: (1) haylage [17.5% crude protein, dry matter (DM) basis; control], (2) haylage + 20% (DM basis) cracked corn, and (3) haylage + 20% (DM basis) soybean hulls during a 112-d backgrounding period. After the backgrounding period, all steers were adapted to a common high moisture corn-based finishing diet and fed until an ultrasound estimated backfat thickness of 7 mm was obtained. During the backgrounding period, steers fed cracked corn or soybean hulls had greater (P < 0.01) average daily gain, dry matter intake and gain:feed and lower (P = 0.05) plasma urea N as compared with controls. However, when finished on a common high-concentrate diet, steers previously fed cracked corn had greater (P < 0.08) average daily gain, final body weight, and longissimus muscle area than those fed soybean hulls, suggesting that source of supplemental energy during the backgrounding period may influence subsequent feedlot performance. Key words: Beef cattle, backgrounding, energy supplementation

scholarly journals PSVII-9 Evaluating Performance Trends of the Four Most Represented Breeds of Bulls in the Utah Beef Improvement Performance Test

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 304-304
Author(s):  
Matthew D Garcia ◽  
Madelyn Kunzler ◽  
Kim Chapman
Keyword(s):  
Birth Weight ◽  
Average Daily Gain ◽  
Rate Of Change ◽  
Test Weight ◽  
Initial Test ◽  
Final Test ◽  
Weaning Weight ◽  
Increasing Trend ◽  
Red Angus ◽  
Daily Gain

Abstract This study evaluated changes in performance of bulls enrolled in the Utah Beef Improvement Association’s (UBIA) annual performance tests conducted in accordance with central bull test standards established by the Beef Improvement Federation. Breeds with over 500 bulls enrolled over the period of 2004 to 2018 were included in the evaluation. The breeds with greater than 500 animals evaluated included the Angus, Red Angus, Hereford and Simmental Breeds. Traits evaluated included birth weight, initial weight, a 205-day adjusted weaning weight, final test weight, average daily gain, adjusted yearling weight, and weight per day of age. The mixed model procedure of SAS and interval regression analyses were utilized to evaluate the yearly rate of change for each breed and to determine if that rate of change was significantly different (P &lt; 0.05) between the evaluated breeds. When evaluating all breeds represented across years, significant differences (P &lt; 0.05) were observed for rate of change when evaluating birth weight and 205-day adjusted weaning weight. However, no differences were observed between breeds with more than 500 animals represented. Significant differences (P &lt; 0.05) for rate of change were observed when comparing the top four represented breeds, for average daily gain, initial test weight, final test weight, adjusted yearling weight and weight per day of age. Specifically, a declining trend was noted for all breeds when evaluation all significant traits. When evaluating the previously described traits, the Angus breed was significantly different in its rate of decline when compared to the Red Angus and Hereford breeds. The lone increasing trend was observed in the Hereford breed which had a positive increasing trend for initial test weight which was significantly different (P &lt; 0.05) from both the Angus and Red Angus breeds but not significantly different from the Simmental breed.

scholarly journals Effects of xylo-oligosaccharide and flavomycin on the immune function of broiler chickens

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4435 ◽  
Author(s):  
Lin Yuan ◽  
Wanli Li ◽  
Qianqian Huo ◽  
Chenhong Du ◽  
Zhixiang Wang ◽  
...  
Keyword(s):  
Immune Function ◽  
Growth Performance ◽  
Mrna Expression ◽  
Broiler Chickens ◽  
Average Daily Gain ◽  
Interleukin 2 ◽  
Test Group ◽  
Basal Diet ◽  
Toll Like Receptor 5 ◽  
Daily Gain

This study investigated the effects of xylo-oligosaccharide (XOS) and flavomycin (FLA) on the performance and immune function of broiler chickens. A total of 150 ArborAcres broilers were randomly divided into three groups and fed for six weeks from one day of age in cascade cages. The diets of each test group were (1) a basal diet, (2) the basal diet supplemented with 2 mg/kg FLA, and (3) the basal diet supplemented with 2 mg/kg XOS. At 21 and 42 days, the growth performance index values and short-chain fatty acid (SCFA) concentrations in the cecum were quantified. Furthermore, immunoglobulin G (IgG) and plasma interleukin 2 (IL-2) as well as mRNA expression of LPS-Induced TNF-alpha Factor (LITAF), Toll-like receptor-5 (TLR5) and interferon gamma (IFNγ) in the jejunum were quantified. The results showed that administration of XOS or FLA to chickens significantly improved the average daily gain. Supplementation with XOS increased acetate and butyrate in the cecum, while FLA supplementation increased propionate in the cecum. An increase in plasma IgG was observed in XOS-fed 21-day-old broilers, but FLA supplementation decreased IgG in the plasma of 42-day-old broilers and increased plasma IL-2. Furthermore, FLA or XOS supplementation downregulated mRNA expression of IFNγ, LITAF and TLR5. The above data suggest that addition of XOS and FLA to the diet could improve the growth performance of broilers and reduce the expression of cytokine genes by stimulating SCFA.

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