scholarly journals Candidate genes for production traits in Nelore beef cattle

2012 ◽  
Vol 11 (4) ◽  
pp. 4138-4144 ◽  
Author(s):  
P.C. Tizioto ◽  
S.L. Meirelles ◽  
R.R. Tulio ◽  
A.N. Rosa ◽  
M.M. Alencar ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Production Traits

scholarly journals Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guoyao Zhao ◽  
Yuqiang Liu ◽  
Qunhao Niu ◽  
Xu Zheng ◽  
Tianliu Zhang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Average Length ◽  
Snp Array ◽  
Reproductive Traits ◽  
Farm Animals ◽  
Production Traits ◽  
Runs Of Homozygosity ◽  
Exact Test ◽  
Genomic Regions

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lili Du ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Mang Liang ◽  
Xinghai Duan ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Meat Quality ◽  
Relevant Literature ◽  
Transcriptome Profiling ◽  
Water Holding Capacity ◽  
Potential Candidate ◽  
Protein Protein Interaction ◽  
Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

scholarly journals Investigation of the association of two candidate genes (H-FABP and PSMC1) with growth and carcass traits in Qinchuan beef cattle from China

2014 ◽  
Vol 13 (1) ◽  
pp. 1876-1884 ◽  
Author(s):  
W. Liang ◽  
H.L. Zhang ◽  
Y. Liu ◽  
B.C. Lu ◽  
X. Liu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Carcass Traits

scholarly journals Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205295 ◽  
Author(s):  
Pablo Augusto de Souza Fonseca ◽  
Samir Id-Lahoucine ◽  
Antonio Reverter ◽  
Juan F. Medrano ◽  
Marina S. Fortes ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Pleiotropic Effect ◽  
Production Traits ◽  
Regulator Genes

Genetic changes in ruminants: Historic trends and future prospects

2000 ◽  
Vol 27 ◽  
pp. 29-38
Author(s):  
Brian McGuirk
Keyword(s):  
Beef Cattle ◽  
Disease Incidence ◽  
Dairy Industry ◽  
Progeny Testing ◽  
Production Traits ◽  
Genetic Progress ◽  
Genetic Changes ◽  
Frozen Semen ◽  
Type Traits ◽  
Cattle And Sheep

AbstractThe major ruminant species, dairy and beef cattle and sheep, represent a rather heterogeneous group as regards genetic improvement, which to a large extent reflects their respective breeding structures. In the UK, the beef cattle and sheep industries still span many different breeds, have small herds/flocks, and have been relatively unaffected by agribusiness investment, and are assumed to have a traditional pyramid breeding structure, in which progress is determined by a small number of breeders. Recording of production information, which to date has focussed on terminal sire characteristics, is relatively recent, and until the use of across herd evaluations, genetic progress was probably limited. However in recent years there have been gains in both growth and muscling. There is little evidence or concern for undesired consequences in commercial flocks, partly because of the extensive use of crossbreeding in these industries, which exploits both breed complementarity and heterosis.By contrast, the dairy industry is now dominated by purebred Holsteins. Increasingly breeding activities are both global in scope and dominated by a small number of large breeding companies. Because most traits of interest are only expressed in the female, improvement programmes have continued to focus on progeny testing, with test daughters in many herds. Most recording schemes and promotional activities emphasise production and type traits. The dairy industry is also notable for the publication of bull progeny test results, so that top bulls can then be used as sires of the next generation of by all companies. These bull evaluations now extend to international rankings.Data from the US indicates continuing genetic progress for production traits in the Holstein, particularly since the 1960s, by when progeny testing had been established, frozen semen widely used, and adequate statistical procedures in place for evaluating bulls. Genetic progress is also evident for type traits. There is now growing concern and evidence of undesirable genetic changes in fertility, disease incidence and overall stress, despite improved nutrition and general management. Altering this situation will require both the recording of such traits and the use of that information by breeding companies, especially in sire selection.

scholarly journals Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Thierry Tribout ◽  
Pascal Croiseau ◽  
Rachel Lefebvre ◽  
Anne Barbat ◽  
Mekki Boussaha ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Candidate Genes ◽  
Milk Production ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Udder Health ◽  
Gwas Approach

Abstract Background Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important traits. However, in general this approach does not allow to validate the effects of candidate mutations or determine if they are truly causative for the trait(s) in question. To address these questions, we applied a two-step, within-breed GWAS approach on 15 traits (5 linked with milk production, 2 with udder health, and 8 with udder morphology) in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cattle. We detected the most-promising candidate variants (CV) using imputed WGS of 2515 MON, 2203 NOR, and 6321 HOL bulls, and validated their effects in three younger populations of 23,926 MON, 9400 NOR, and 51,977 HOL cows. Results Bull sequence-based GWAS detected 84 QTL: 13, 10, and 30 for milk production traits; 3, 0, and 2 for somatic cell score (SCS); and 8, 2 and 16 for udder morphology traits, in MON, NOR, and HOL respectively. Five genomic regions with effects on milk production traits were shared among the three breeds whereas six (2 for production and 4 for udder morphology and health traits) had effects in two breeds. In 80 of these QTL, 855 CV were highlighted based on the significance of their effects and functional annotation. The subsequent GWAS on MON, NOR, and HOL cows validated 8, 9, and 23 QTL for production traits; 0, 0, and 1 for SCS; and 4, 1, and 8 for udder morphology traits, respectively. In 47 of the 54 confirmed QTL, the CV identified in bulls had more significant effects than single nucleotide polymorphisms (SNPs) from the standard 50K chip. The best CV for each validated QTL was located in a gene that was functionally related to production (36 QTL) or udder (9 QTL) traits. Conclusions Using this two-step GWAS approach, we identified and validated 54 QTL that included CV mostly located within functional candidate genes and explained up to 6.3% (udder traits) and 37% (production traits) of the genetic variance of economically important dairy traits. These CV are now included in the chip used to evaluate French dairy cattle and can be integrated into routine genomic evaluation.

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