Isolation and nucleotide variation of COBRA gene in a tropical timber tree Neolamarckia cadamba

COBRA gene is involved in the regulation of cellulose deposition and orientation of cell expansion. Any single nucleotide differences may influence the functions of this gene. Hence, this study was carried out to isolate the partial COBRA genomic sequence and subsequently, to determine the nucleotide variation of COBRA gene in Neolamarckia cadamba. N. cadamba, also locally known as kelampayan is one of the fastgrowing deciduous and indigenous tree species with great commercial values in Malaysia. The targeted DNA sequence of COBRA gene was amplified with the designed primer pair by using Polymerase Chain Reaction (PCR) technique. The partial COBRA genomic sequence (517 bp) was subjected to BLASTn analysis to search for homology sequence and validate the identity of the sequence through NCBI. Multiple alignment was carried out by ClustalW for manual detection of single nucleotide polymorphisms (SNPs). Five SNPs were detected in the exon region and two SNPs in the intron region of COBRA partial genomic sequences. Of these five detected SNPs, four non-synonymous mutations and one synonymous mutation were discovered in the COBRA amino acid sequences. Based on the in silico restriction analysis, one possible restriction enzyme, HpyCH4III was detected to restrict at a SNP site (384 bp) which could be useful for genetic marker development, such as CAPS marker development in the efforts of genotyping project

Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets