Year 2019, Volume 3 , Issue 4, Pages 233 - 239 2019-12-24

Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment

Esin ÇALIK [1] , Volkan BALTACI [2] , Prof. Dr. Kezban CANDOĞAN [3]


Evaluation of some meat quality attributes using genetic analysis is steadily increasing. PCR based targeted variation analysis is one of the most commonly preferred techniques for this purpose. Recently, Next Generation Sequencing (NGS) method has drawn considerable attention because of its’ high analysis capacity. The purpose of the current study was to determine variations in CAST gene from Brangus and Simmental cattle by performing whole gene sequencing using NGS, and to investigate the potential of NGS method in evaluating meat tenderness based on the high genomic data it provides. Whole gene sequence analysis was performed on Calpastatin (CAST) gene of samples acquired from 52 Brangus and 52 Simmental beef cattle breeds using NGS method, and the variations detected were evaluated in terms of their potential in measuring meat tenderness and quality. NGS outputs were analyzed in Ensemble “cow” database platform and 13 variations were detected. One of these variations (EXON 8 c.439C>G/ p.L147V ) was evaluated as undeclared before. In 20 Brangus cattle and in 9 Simmental cattle, no variations were detected whereas 6 variations (V1, V2, V5, V8, V10 and V13) were found significantly different (p<0.05) based on their distribution in breeds. 


Beef tenderness, Polymorphisms, Calpastatin (CAST) gene
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Primary Language en
Subjects Food Science and Technology
Published Date December 2019
Journal Section Research Articles
Authors

Orcid: 0000-0002-5840-9170
Author: Esin ÇALIK
Institution: Ankara University, Faculty of Engineering, Department of Food Engineering, Ankara
Country: Turkey


Orcid: 0000-0002-6626-8208
Author: Volkan BALTACI
Institution: Yüksek İhtisas University School of Medicine Department of Medical Genetics, Ankara
Country: Turkey


Orcid: 0000-0002-6721-8835
Author: Prof. Dr. Kezban CANDOĞAN (Primary Author)
Institution: Ankara University, Faculty of Engineering, Department of Food Engineering, Ankara
Country: Turkey


Dates

Application Date : September 13, 2019
Acceptance Date : December 4, 2019
Publication Date : December 24, 2019

Bibtex @research article { jaefs646593, journal = {International Journal of Agriculture Environment and Food Sciences}, issn = {}, eissn = {2618-5946}, address = {Dicle University Faculty of Agriculture Department of Horticulture, 21280 Diyarbakir / Turkey}, publisher = {Gültekin ÖZDEMİR}, year = {2019}, volume = {3}, pages = {233 - 239}, doi = {10.31015/jaefs.2019.4.6}, title = {Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment}, key = {cite}, author = {ÇALIK, Esin and BALTACI, Volkan and CANDOĞAN, Prof. Dr. Kezban} }
APA ÇALIK, E , BALTACI, V , CANDOĞAN, P . (2019). Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment. International Journal of Agriculture Environment and Food Sciences , 3 (4) , 233-239 . DOI: 10.31015/jaefs.2019.4.6
MLA ÇALIK, E , BALTACI, V , CANDOĞAN, P . "Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment". International Journal of Agriculture Environment and Food Sciences 3 (2019 ): 233-239 <https://dergipark.org.tr/en/pub/jaefs/issue/50908/646593>
Chicago ÇALIK, E , BALTACI, V , CANDOĞAN, P . "Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment". International Journal of Agriculture Environment and Food Sciences 3 (2019 ): 233-239
RIS TY - JOUR T1 - Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment AU - Esin ÇALIK , Volkan BALTACI , Prof. Dr. Kezban CANDOĞAN Y1 - 2019 PY - 2019 N1 - doi: 10.31015/jaefs.2019.4.6 DO - 10.31015/jaefs.2019.4.6 T2 - International Journal of Agriculture Environment and Food Sciences JF - Journal JO - JOR SP - 233 EP - 239 VL - 3 IS - 4 SN - -2618-5946 M3 - doi: 10.31015/jaefs.2019.4.6 UR - https://doi.org/10.31015/jaefs.2019.4.6 Y2 - 2019 ER -
EndNote %0 International Journal of Agriculture Environment and Food Sciences Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment %A Esin ÇALIK , Volkan BALTACI , Prof. Dr. Kezban CANDOĞAN %T Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment %D 2019 %J International Journal of Agriculture Environment and Food Sciences %P -2618-5946 %V 3 %N 4 %R doi: 10.31015/jaefs.2019.4.6 %U 10.31015/jaefs.2019.4.6
ISNAD ÇALIK, Esin , BALTACI, Volkan , CANDOĞAN, Prof. Dr. Kezban . "Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment". International Journal of Agriculture Environment and Food Sciences 3 / 4 (December 2019): 233-239 . https://doi.org/10.31015/jaefs.2019.4.6
AMA ÇALIK E , BALTACI V , CANDOĞAN P . Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment. int. j. agric. environ. food sci.. 2019; 3(4): 233-239.
Vancouver ÇALIK E , BALTACI V , CANDOĞAN P . Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment. International Journal of Agriculture Environment and Food Sciences. 2019; 3(4): 239-233.