<![CDATA[BOL: Bioinformatics approach to Boar Taint]]> https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint? https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint Wed, 17 Jul 2013 15:50:37 -0500 https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint <![CDATA[Bioinformatics approach to Boar Taint]]> Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skatole in the fat primarily cause boar taint. Metabolism of androstenone and sex steroids share a common pathway which makes removal of boar taint a very challenging task. Castration is a traditional solution to remove boar taint but it also results in bad quality of meat due to low level of steroids which is objectionable to many consumers. Detected functional variant(s) underlying boar taint compounds can be used as genetic markers in selection of male pigs with reduced boar taint levels. Resequencing of a total of 47 samples belong to Norwegian Landrace (NL) and Duroc (D) pigs with varied boar taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previousy identified QTL regions on SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of SNPs was prepared after filtering SNPs on the basis of SNP quality, coverage of SNP allele, functional and structural annotation, and repeats, etc. Selected SNPs will be genotyped in sample population for validation and then used for constructing SNPs haplotypes in close linkage disequilibrium with QTLs and fine mapping of QTLs through association mapping of genotyped SNPs. 

 

]]> Rahul Agarwal https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint#item-annotation-3123 Sat, 14 Oct 2017 18:07:02 -0500 https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint#item-annotation-3123 <![CDATA[Comment by Rahul Agarwal]]> Fine mapping of a QTL affecting levels of skatole on pig chromosome 7

https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0549-8

]]> Rahul Agarwal https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint#item-annotation-388 Tue, 13 Aug 2013 17:57:47 -0500 https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint#item-annotation-388 <![CDATA[Comment by Rahul Agarwal]]> ISMB/ECCB 2011

Application of whole genome resequencing to detect sequence polymorphisms underlying boar taint

http://www.iscb.org/archive/conferences/iscb/cms_addon/conferences/ismbeccb2011/posterlistd227.html?cat=U

PAG 2013
Application of Whole Genome Resequencing to Detect SNPs for Selection Against Boar Taint in Norwegian Male Pig Breeds

https://pag.confex.com/pag/xxi/webprogram/Paper6007.html

]]> Rahul Agarwal https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint#item-annotation-385 Tue, 13 Aug 2013 17:53:49 -0500 https://bioinformaticsonline.com/file/view/989/bioinformatics-approach-to-boar-taint#item-annotation-385 <![CDATA[Comment by Rahul Agarwal]]> Application of whole genome resequencing in the dissection of QTLs affecting boar taint

EMBnet.journal 19.A

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CEQQFjAC&url=http%3A%2F%2Fjournal.embnet.org%2Findex.php%2Fembnetjournal%2Farticle%2Fdownload%2F637%2F888&ei=YrYKUr_eLpS5hAez7IDICQ&usg=AFQjCNE0WmvyFV0DMnGJG4OvgZt0EOJzJg&sig2=CsayOlShlN9BqH3kszF3xw&bvm=bv.50500085,d.ZG4

 

]]> Rahul Agarwal