A Primer-Extension Assay for simultaneous use in cattle Genotype Assisted Selection, parentage and traceability analysis

Sevane, Natalia; Crespo, Inmaculada; Cañón, Javier; Dunner, S.

doi:10.1016/j.livsci.2010.10.011

Cited by 7 publications

(6 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…AP-1 is also one of the transcription factors binding in the promoter of FABP4 with CEBPα ( Shin et al, 2009 ). Recently, the mutation of cholinergic receptor, nicotinic, epsilon (CHREN) is significantly associated with muscle growth in beef cattle from primer-extension assay ( Sevane et al, 2011 ). These results indicate that the genes in the red module may function in regulating muscle growth or fat-related mechanisms and co-expressed genes with similar functions in the module.…”

Section: Resultsmentioning

confidence: 99%

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle

Lim

Lee

Kim³

et al. 2013

Asian Australas. J. Anim. Sci

View full text Add to dashboard Cite

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

show abstract

Section: Resultsmentioning

confidence: 99%

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle

Lim

Lee

Kim³

et al. 2013

Asian Australas. J. Anim. Sci

View full text Add to dashboard Cite

show abstract

“…SNP 1, SNP 4, SNP 7, and SNP 10 were chosen according to Orru et al (). SNP 5 and SNP 6 were selected from Sevane, Crespo, Cañón, and Dunner (). The selection of SNP 8 and SNP 9 was based on Werner et al ().…”

Section: Methodsmentioning

confidence: 99%

Combined SNPs and miRNAs technologies for beef traceability

Wu¹,

Zhou²,

Yang³

et al. 2017

Journal of Food Safety

View full text Add to dashboard Cite

The independent and highly heterozygous single nucleotide polymorphisms (SNPs) have been shown suitable for meat traceability. The microRNAs (miRNAs) that were differently expressed among regions could be used for meat origin traceability. In the present study, ten SNPs from 148 Chinese beef cattle were screened by HRM. The results showed that these SNPs were all suitable for beef traceability with the probability error rate of .308‰. These cattle could not be clustered into different regions based on the SNP genotyping, which indicated that the SNPs assay was suitable for individual traceability. High throughput sequencing revealed that 16 miRNAs were up‐regulated expression and 18 miRNAs were down‐regulated expression in JL group (eastern part) compared to XJ group (western part). RT‐PCR confirmed that bta‐miR‐2284ab and bta‐miR‐486 were differently expressed in Jilin and Xinjiang samples. Thus, the two miRNAs could be used as biomarkers for origin traceability. Practical applications To solve meat safety problems, meat traceability is extremely important. SNPs‐based technology can trace animal individuals and miRNAs‐based technology can do origin traceability. Once suitable primers could be designed for a sufficient number of SNP loci, these primers could be loaded on an array, and then traceability could be realized by HRM. We identified the miRNAs that were differently expressed among regions and beef origin traceability could be realized by analyzing them using RT‐PCR. All the detection methods are rapidly and cost‐effectively. A combination of SNPs‐ and miRNAs‐based technologies can implement traceability management of beef cattle.

show abstract

“…The analysis of genetic diversity and relationships among breeds used the information provided by 435 SNP found in 192 candidate genes, some of which have been shown to be associated with muscle, lipid and energy metabolism. The whole dataset included: 389 SNP previously described by Williams et al (2009) and genotyped by Kbioscience using the proprietary Kaspar methodology; 46 SNP previously described by Sevane et al (2011) and genotyped by SNP multiplex and Primer Extension amplification. All SNP had a minor allele frequency above 5% in the breeds investigated.…”

Section: Selection Of Snpmentioning

confidence: 99%

“…Decker et al 2009;Gautier et al 2010;Lin et al 2010); however, these studies have invariably used random SNP, without differentiating between those linked to functional variation and those in neutral regions of chromosomes. In the present study, a set of 435 SNP markers was selected to be within functional candidate genes involved in muscle, lipid and energy metabolism (Williams et al 2009;Sevane et al 2011). This was used to examine the genetic diversity within, and the genetic relationships among, 15 European beef and dairy cattle from Spain, the United Kingdom, France, Denmark, and Italy, and to explore ancestry and the influence of selection on diversity at these loci for identifying the presence of diversity hotspots.…”

Section: Introductionmentioning

confidence: 99%

SNP included in candidate genes involved in muscle, lipid and energy metabolism behave like neutral markers

et al. 2015

View full text Add to dashboard Cite

Studies of population structure and diversity in cattle have provided insights into the origins of breeds, their history and evolution, and allow the identification of global livestock diversity hotspots, which is important for conservation of diversity. Genetic diversity, genetic relationship, population structure, and the presence of hotspots of genetic diversity among 15 European bovine breeds from five countries were assessed using 435 single nucleotide polymorphisms (SNP) markers identified in candidate genes for muscle, lipid and energy metabolism, thus providing the opportunity to compare the breed relationships obtained using putatively functional markers with previous data using neutral loci. Individuals belonging to 11 breeds tended to be clearly assigned to a single cluster when the number of pre-defined populations reached a maximum in the likelihood of the data at K = 12, whereas Asturiana de los Valles, Danish Red, Simmental, and Avileña-Negra Ibérica displayed a greater degree of admixture, which may be explained by their diverse ancestry. Although overall results were in agreement with those reported by studies based on neutral genetic variations, some additional breed relationship information emerged using markers in candidate functional loci, including the relationship between the Asturiana de los Valles and Piedmontese, and Danish Red and Charolais breeds. This study indicates that the analysed loci have not been main targets for selection or for adaptation processes, but also that SNP within candidate genes related with beef characteristics and performance may provide a slightly new perspective on past breeding and may also help in the development of strategies for the rational conservation of livestock diversity.

show abstract

A Primer-Extension Assay for simultaneous use in cattle Genotype Assisted Selection, parentage and traceability analysis

Cited by 7 publications

References 47 publications

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle

Combined SNPs and miRNAs technologies for beef traceability

SNP included in candidate genes involved in muscle, lipid and energy metabolism behave like neutral markers

Contact Info

Product

Resources

About