Association analysis for feed efficiency traits in beef cattle using preserved haplotypes

Genome ◽  
2013 ◽  
Vol 56 (10) ◽  
pp. 586-591 ◽  
Author(s):  
Duc Lu ◽  
Mehdi Sargolzaei ◽  
Changxi Li ◽  
Mohammed Abo-Ismail ◽  
Gordon Vander Voort ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Current Knowledge ◽  
Average Daily Gain ◽  
Phenotypic Variance ◽  
Production Traits ◽  
Multiple Traits ◽  
Extended Haplotype ◽  
A Genome ◽  
Significance Levels ◽  
Chromosome Regions

This study reports a genome wide scan for chromosome regions and their haplotypes that significantly associated with average daily gain (ADG), dry matter intake (DMI), and residual feed intake (RFI) in beef cattle. The study used data from 597 Angus, 450 Charolais, and 616 crossbred beef cattle, and the Illumina Bovine SNP50 beadchip. Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups of animals. Such regions in the crossbreds were tested for association with ADG, DMI, and RFI. At false discovery rates of 5% and 10%, there were six and eight chromosome regions showing significant associations with the traits, respectively. At nominal significance levels (at least P < 0.05), 23 regions with a total number of 31 haplotypes were found significantly associated with at least one of the three traits. The proportion of phenotypic variance explained by these 23 regions varied depending on the trait; the highest proportion for ADG, DMI, and RFI was 13.50%, 9.92%, and 2.64%, respectively. Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple traits. Thirty-six quantitative trait loci for 16 production traits, from the current literature, covered fully or in part the 23 chromosome regions. The findings from this study might be an important contribution to the current knowledge of the beef cattle genome and to the effective identification of causative genes associated with important traits in cattle.

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.

scholarly journals Effects of SNPs CAPN316 and CAST282 on quantitative characteristics of offspring produced by dairy and beef bulls

1970 ◽  
Vol 21 ◽  
pp. 255-260
Author(s):  
S. Yu. Ruban ◽  
N. G. Lysenko ◽  
L. V. Mitioglo ◽  
I. V. Goraichuk ◽  
A. I. Kolesnyk ◽  
...  
Keyword(s):  
Pearson Correlation ◽  
Molecular Genetic ◽  
Average Daily Gain ◽  
Molecular Genetic Analysis ◽  
Production Traits ◽  
Significance Levels ◽  
Beef Bulls ◽  
Productive Traits ◽  
Dairy Bulls ◽  
Daily Gain

Aim. The aim of the study was to analyze effects of SNPs CAPN316 in CAST282 in calpain and calpastatin genes on offspring productive traits produced by dairy and beef bulls. Methods. Data on offspring productivity included milk performance traits (for dairy bulls), birth weight and average daily gain (for beef bulls). Molecular genetic analysis was performed by PCR-RFLP. χ²-, t-tests and Pearson correlation coefficient were used for statistical analysis at significance levels of 0.05. Results. In progeny of dairy bulls number of alleles C in both SNPs demonstrated negative correlation with milk yield (r=-0.577), fat yield (r=-0.794) and protein yield (r =-0.798). G allele of CAPN316 (“wild type”) was associated with increased number of beef bulls progeny. Body weight and average daily gain was better in GG-bulls offspring. Conclusions. C alleles of SNPs CAPN316 in CAST282 being associated with meat quality traits were found to be ineffective in selection for milk production traits. Keywords: calpain and calpastatin genes, SNP, CAPN316, CAST282, bull’s genotype, evaluation on progeny, offspring productivity.

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.

scholarly journals 94 Genetic basis of blood traits in beef cattle and their relationship to production traits at weaning

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 29-29
Author(s):  
Josue Chinchilla-Vargas ◽  
Luke Kramer ◽  
Toby D Lester ◽  
Toby D Lester ◽  
Elizabeth A Backes ◽  
...  
Keyword(s):  
Blood Cell ◽  
Beef Cattle ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Production Traits ◽  
Phenotypic Correlations ◽  
Cell Counts ◽  
A Genome ◽  
Complete Blood Counts

Abstract Disease represents one of the main factors that determine profitability in animal production. Previous research has observed significant correlations between blood cell counts and the animal’s health status. We hypothesize that blood cell traits may be an effective indicator of performance in beef cattle. Complete blood counts were recorded from approximately 500 crossbred animals at weaning (Angus background crossed with Hereford, Charolais, Sim-Angus, Brangus) born between 2015 and 2016 and raised on toxic or novel tall fescue on three different farms. The animals were genotyped at an approximate density of 50,000 SNPs and the genotypes were imputed to an approximate density of 200,000 SNPs. Heritability, genetic and phenotypic correlations were estimated for 15 blood and 4 production traits across and within environments. Finally, with the objective of identifying the genetic basis underlying the different blood traits, a genome wide association study (GWAS) was performed for all traits. Heritability estimates ranged from 0.11 to 0.60, and generally weak phenotypic correlations and strong genetic correlations were found, however these parameters varied across environments, pointing to GxE interactions. GWAS identified 90 1 Mb windows that explained 0.5% or more of the estimated genetic variance for at least 1 trait with 21 windows overlapping two or more traits. Further research efforts include identifying underlying candidate genes for traits and comparing toxic and novel fescue effects on blood traits. It appears that blood traits have weak phenotypic correlations but strong genetic correlations among themselves, as evidenced by important overlapping regions of genetic control for similar blood traits. However, blood traits have limited potential as indicator traits for productivity.

scholarly journals PSIII-12 Peripheral blood parameters as proxies of performance in beef cattle: Heritability and genetic correlations between peripheral blood parameters and performance phenotypes

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 163-164
Author(s):  
Josue Chinchilla-Vargas ◽  
Luke M Kramer ◽  
John D Tucker ◽  
Donald S Hubbell ◽  
Jeremy G Powell ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Peripheral Blood ◽  
High Performance ◽  
Disease Incidence ◽  
Average Daily Gain ◽  
Genetic Correlations ◽  
Blood Parameters ◽  
Production Traits ◽  
Blood Samples ◽  
Cell Parameters

Abstract Disease incidence and feed costs are two main drivers in cattle production operations. Frequently environmental stressors such as fescue toxicosis have negative effects on livestock performance and health. Low-cost methods to measure these types of health and stress response phenotypes are needed to capture their impact on production traits. Previous research has correlated white blood cell parameters to disease resistance in beef cattle. Based on this, blood parameters at weaning may be candidates that could be a proxy for selection and identification of high-performance animals in commercial settings. To identify candidate blood parameters, blood samples were collected at weaning on approximately 500 crossbred animals (Angus background crossed with Hereford, Charolais, Sim-Angus, Brangus) born between 2015 and 2016 and raised on toxic fescue. The animals were also genotyped at an approximate density of 50,000 SNPs. Complete blood counts (CBC) were obtained the blood samples and heritabilities for 15 peripheral blood parameters were estimated. For the CBC traits that were measured, heritabilities ranged from low to moderate (0.02 to 0.35). Based on current findings, a substantial genetic component for some CBC parameters exists and selection could be effective at improving these traits. Further research will estimate genetic correlations between peripheral blood parameters, weaning weight and average daily gain (ADG) with the intention of identifying correlated traits to be used in commercial selection programs.

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.

Association of Micro RNA and Postoperative Cognitive Dysfunction: A Review

2020 ◽  
Vol 20 (17) ◽  
pp. 1781-1790
Author(s):  
Noor Anisah Abu Yazit ◽  
Norsham Juliana ◽  
Srijit Das ◽  
Nur Islami Mohd Fahmi Teng ◽  
Nadia Mohd Fahmy ◽  
...  
Keyword(s):  
Cognitive Dysfunction ◽  
Chromosomal Abnormalities ◽  
Current Knowledge ◽  
System Development ◽  
Genetic Disorder ◽  
Postoperative Cognitive Dysfunction ◽  
Clinical Importance ◽  
Nervous System Development ◽  
Micro Rna ◽  
A Genome

Postoperative Cognitive Dysfunction (POCD) refers to the condition of neurocognitive decline following surgery in a cognitive and sensory manner. There are several risk factors, which may be life-threatening for this condition. Neuropsychological assessment of this condition is very important. In the present review, we discuss the association of apolipoprotein epsilon 4 (APOE ε4) and few miRNAs with POCD, and highlight the clinical importance for prognosis, diagnosis and treatment of POCD. Microarray is a genome analysis that can be used to determine DNA abnormalities. This current technique is rapid, efficient and high-throughout. Microarray techniques are widely used to diagnose diseases, particularly in genetic disorder, chromosomal abnormalities, mutations, infectious diseases and disease-relevant biomarkers. MicroRNAs (miRNAs) are a class of non-coding RNAs that are widely found distributed in eukaryotes. Few miRNAs influence the nervous system development, and nerve damage repair. Microarray approach can be utilized to understand the miRNAs involved and their pathways in POCD development, unleashing their potential to be considered as a diagnostic marker for POCD. This paper summarizes and identifies the studies that use microarray based approaches for POCD analysis. Since the application of microarray in POCD is expanding, there is a need to review the current knowledge of this approach.

An association analysis between PRL genotype and milk production traits in Italian Mediterranean river buffalo

2017 ◽  
Vol 84 (4) ◽  
pp. 430-433 ◽  
Author(s):  
Jun Li ◽  
Aixin Liang ◽  
Zipeng Li ◽  
Chao Du ◽  
Guohua Hua ◽  
...  
Keyword(s):  
Milk Production ◽  
Milk Yield ◽  
Milk Fat ◽  
Fat Content ◽  
Phenotypic Variance ◽  
River Buffalo ◽  
Production Traits ◽  
Milk Production Traits ◽  
Exon 2 ◽  
Mediterranean River

This Research Communication describes the association between genetic variation within the prolactin (PRL) gene and the milk production traits of Italian Mediterranean river buffalo (Bufala mediterranea Italiana). High resolution melting (HRM) techniques were developed for genotyping 465 buffaloes. The association of genetic polymorphism with milk production traits was performed and subsequently the effects of parity and calving season were evaluated. Single nucleotide polymorphisms (SNPs) were identified at exons 2 and 5 and at introns 1 and 2. All the SNPs were in Hardy–Weinberg equilibrium, and statistical analysis showed that the polymorphism of intron1 was significantly (P < 0·05) associated with milk yield, milk protein content and peak milk yield. The average contribution of the intron1 genotype (r2intron1) to total phenotypic variance in milk production traits was 0·09, and the TT genotype showed lower values than CC and CT genotypes. A nonsynonymous SNP was identified in exon 2, which resulted in an amino acid change from arginine to cysteine. Moreover, the polymorphism of exon 2 was associated significantly with milk fat content (P < 0·05), and the buffaloes with TT genotype showed higher total fat content than the buffaloes with CT genotype. These findings provide evidence that polymorphisms of the buffalo PRL gene are associated with milk production traits and PRL can be used as a candidate gene for marker-assisted selection in Italian Mediterranean river buffalo breeding.

scholarly journals Effect of BioPlus YC Probiotic Supplementation on Gut Microbiota, Production Performance, Carcass and Meat Quality of Pigs

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1581
Author(s):  
Artur Rybarczyk ◽  
Elżbieta Bogusławska-Wąs ◽  
Alicja Dłubała
Keyword(s):  
Bacillus Subtilis ◽  
Meat Quality ◽  
Bacillus Licheniformis ◽  
Average Daily Gain ◽  
Production Performance ◽  
Probiotic Bacteria ◽  
Control Group ◽  
Production Traits ◽  
Feed Conversion

The objective of the study was to determine the effects of probiotic bacteria Bacillus licheniformis and Bacillus subtilis on microbiological properties of feed mixtures and on the digestive tract content as applicable to production traits and carcass characteristics of fatteners. The experiment was performed on 83,838 fatteners from four successive (insertions) productions in two groups. From the seventy eighth day of age till marketing to the slaughter plant, the pigs were supplied with BioPlus YC probiotic (Chr. Hansen) in the amount of 400 g/t. The preparation contained a complex of probiotic bacteria Bacillus licheniformis DSM 5749, and Bacillus subtilis DSM 5750 spores in a 1:1 ratio. From the fourth insertion, after reaching a body weight of approximately 112 kg, 60 fatteners were selected from each group to measure carcass quality and half of them for meat quality evaluation. Moreover, microbiological analyses in feed and colon were performed. The study showed that BioPlus YC probiotics supplementation resulted in a significantly higher count of B. subtilis and B. licheniformis in the feed, a higher count of B. subtilis, B. licheniformis and LAB, as well as a lower count of Enterobacteriaceae, Enterococcus, Clostridium and Bacillus sp. in the mucosa and in the colorectal content of the test pigs. Our work has shown that supplementation with the BioPlus YC probiotic had a positive effect on the production traits of pigs mainly by reducing mortality (2.83%, p = 0.010), lowering feed conversion ratio—FCR (2.59 kg/kg, p = 0.013), better average daily gain—ADG (0.95 kg/day, p = 0.002) and shorter fattening period (77.25 days, p = 0.019) when compared to the control group (4.19%; 2.79 kg/kg; 0.89 kg/day; 92.8 days, respectively). The addition of the specific Bacillus bacteria did not influence carcass and meat characteristics of the test fatteners.

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