Genome‐wide association study for fatty acid composition in <scp>J</scp>apanese <scp>B</scp>lack cattle

Ishii, Atsushi; Yamaji, Keita; Uemoto, Yoshinobu; Sasago, Nanae; Kobayashi, Eiji; Kobayashi, Naohiko; Matsuhashi, Tomohiro; Maruyama, Shin; Matsumoto, Hirokazu; Sasazaki, Shinji; Mannen, Hideyuki

doi:10.1111/asj.12063

Cited by 52 publications

(59 citation statements)

References 39 publications

(35 reference statements)

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“…Previous studies suggested that polymorphism of the SCD gene should affect the FA composition of fatty acids in beef (Matsuhashi et al 2011;Li et al 2012; M a n n e n et al 2012; Ishii et al 2013). Our results, however, did not confirm this claim.…”

Section: Discussioncontrasting

confidence: 90%

Polymorphic effects of FABP4 and SCD genes on intramuscular fatty acid profiles in longissimus muscle from two cattle breeds

et al. 2015

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The aim of this study was to evaluate the polymorphic effects of two single nucleotide polymorphisms (SNPs) of fatty acid binding protein (FABP4) and stearoyl-CoA desaturase (SCD) genes on intramuscular fatty acid profiles in the longissimus muscle in two cattle breeds. Two previously reported SNPs of bovine FABP4 (7516G>C) and SCD (878C>T) were in turn assessed for their associations with intramuscular fatty acid profiles from the upper sirloin cuts of Aberdeen Angus and Blonde d'Aquitaine cattle. In total, 33 animals were genotyped using PCR-RFLP. Intramuscular fatty acid composition was evaluated using two complementary statistical approaches: a classical univariate regression model and a multivariate approach using a combination of Principal Component Analysis and Random Forests. Significant effect of FABP4

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Section: Discussioncontrasting

confidence: 90%

Polymorphic effects of FABP4 and SCD genes on intramuscular fatty acid profiles in longissimus muscle from two cattle breeds

et al. 2015

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“…The fatty acid synthase (FASN) locus, contained in this region, was proposed as putative candidate gene affecting milk fatty acid composition. In the present research, the marker ARS-BFGL-NGS-39328 was found associated to FP, thus confirming the presence of a QTL for fat traits on BTA19 as suggest by Ishii et al (2013) (Supplementary Material S1).…”

Section: Discussionsupporting

confidence: 84%

“…Recently, in a GWAS on the Japanese Black cattle breed, Ishii et al (2013) identified a significant number of SNPs affecting milk fatty acid composition in a region between 49 and 52 Mb of the BTA19. The fatty acid synthase (FASN) locus, contained in this region, was proposed as putative candidate gene affecting milk fatty acid composition.…”

Section: Discussionmentioning

confidence: 99%

Maximum difference analysis: a new empirical method for genome-wide association studies

Cellesi

Dimauro

Sorbolini

et al. 2016

Italian Journal of Animal Science

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The availability of high-density single nucleotide polymorphism (SNPs) panels for humans and, recently, for several livestock species has given a great impulse to genome-wide association studies towards the identification of genes associated with complex traits and diseases. The frequentist and the Bayesian approach are commonly used to investigate marker associations with traits of interest. Briefly, the former is the most widely used method, being intuitive and easily to apply, whereas the latter requires deeper statistical knowledge, but has the advantage to include prior information to obtain a posterior probability of association. Both methods, however, require parameters or distributions to be set a priori by the researcher. In this work, we suggest a new empirical method for genome-wide studies (GWAS), which verifies marker-trait associations using the bootstrap resampling and Chebyshev's inequality. This method, called Maximum Difference Analysis (MDA), was tested on a real dataset of 2093 Italian Holstein bulls with the objective of finding associations between SNPs and milk, fat and protein yield and fat and protein percentage. Results of the MDA method were compared with those obtained to a genome-wide association analysis performed using the R package GenABEL. In addition, we assessed the bovine annotated genes related to the traits under study. The MDA method was able to locate known important loci for milk productive traits, such as the DGAT1, PRLR, GHR and SCD. Moreover, some new putative candidate genes were detected. The python script of MDA procedure is available at www.animalbreeding.uniss.it. ARTICLE HISTORY

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“…Polymorphisms in chka have been identified to be associated with human diabetes [41]. The tanc2 gene has been investigated as a candidate gene for the locus on BAT19 where BTB-00755526 at 48.24 Mb was associated with mirystic acid (C14:0) of intramuscular adipose tissue in Japanese Black cattle [42]. Interestingly, this gene was up-regulated in the high-fat groups compared to the low-fat groups in pig longissimus muscle at 110 kg Body Weight [43].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

Zheng

Kuang

et al. 2016

PLoS ONE

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Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.

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Genome‐wide association study for fatty acid composition in Japanese Black cattle

Cited by 52 publications

References 39 publications

Polymorphic effects of FABP4 and SCD genes on intramuscular fatty acid profiles in longissimus muscle from two cattle breeds

Polymorphic effects of FABP4 and SCD genes on intramuscular fatty acid profiles in longissimus muscle from two cattle breeds

Maximum difference analysis: a new empirical method for genome-wide association studies

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

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