Genome-Wide Association Study for Squalene Contents and Functional Haplotype Analysis in Rice

Abstract

Squalene is an isoprenoid compound that acts as the intermediate metabolite in cholesterol synthesis. Squalene is not very susceptible to peroxidation, and it quenches singlet oxygen in the skin, which is caused by UV exposure and other ionizing radiation sources. Squalene is a precursor to phytosterol synthesis, and it has been widely studied for its ability to reduce oxidation, cancer activity, and cholesterol levels. We performed a genome-wide association study for squalene in rice using 1.6 million high-quality SNPs extracted from 295 accessions’ resequencing data. The candidate gene locus Os09g0319800—an orthologue of terpene synthase in Arabidopsis—showed up as the most likely candidate gene amongst the identified loci. Nucleotide variations in the promoter were associated with squalene content variations within the japonica group. The results of this study can provide clues for understanding the mechanisms of squalene biosynthesis in rice.

Development of SNP Markers from GWAS for Selecting Seed Coat and Aleurone Layers in Brown Rice (Oryza sativa L.)

“…A total of 294 rice genome resequencing groups were finally constructed by secondarily selecting additional varieties that can be headed in the domestic climate and have a high utility value in Korea. Of the total 294 rice genome resequencing groups, the 225 domestic breeding lines consisted of 38 Indica, 178 Japonica, and 9 Tropical Japonica [ 26 ].…”

“…Genome re-sequencing was performed on an Illumina HiSeq 2500 platform (Illumina, Inc., San Diego, CA, USA), according to its standard sequencing protocol. Data analysis was compared with IRSGP1.0 downloaded from NCBI ( accessed on 30 July 2019), which is a standard genome sequence of rice [ 26 ]. Raw data files from short pair-end sequencing reads were first filtered using the software Cutadapt and Sickle, respectively [ 31 , 32 ], and then mapped to the reference genome using BWA software [ 33 ].…”