عنوان	Candidate genes for anthocyanin pigmentation in rice stem revealed by genome-wide association study (GWAS) and whole genome resequencing (WGR)
نوع پژوهش	مقاله چاپ‌شده در مجلات علمی
کلیدواژه‌ها	Anthocyanin biosynthesis, Genomic alignment, Metabolite, NGS, SNP.
چکیده	Anthocyanin pigment as a phenolic secondary metabolite is accumulated in areal organs of some rice varieties and is under genetic control. In spite of several research attempts the majority of genomic regions and candidate genes for purple-colored stem (Ps) due to anthocyanin pigmentation of rice leaf sheath have not been identified. In this research genome-wide association study (GWAS) coupled with whole genome resequencing (WGR) analysis was applied for genetic dissection of anthocyanin pigmentation of rice stem. Using GWAS on 282 rice accessions, the genomic regions (on chromosomes 2, 4 and 6) tagged to eight SNPs were identified to be significantly associated with purple stem, and in the vicinity of GWAS signals 19 genes were highlighted as putative candidate genes. To narrow down the genomic regions more highly associated to the trait, a WGR study on RIL sister lines with opposite phenotypes (green-colored and purple-colored stems) was conducted. After variant calling and defining the DNA variation between reference genome, maternal parent and the two sister lines, a narrow genomic region on short arm of chromosome 6 was identified to be highly associated with anthocyanin pigmentation of rice stem. In the interval of 4.7-6.2 Mbp of chromosome 6 a few candidate genes with probable role in anthocyanin biosynthesis/accumulation were identified which included five structural genes involved in the known pathways (one chalcone isomerase, two glycosyl transferases and two UDP-flavonoid-3-O-glucosyl transferases) and two transcription factors (one bHLH and one MYB coding genes). The identified candidate genes can be used in breeding programmes of rice or other gramineae species for anthocyanin accumulation in areal organs.
پژوهشگران	رضا‍ حقی دره ده (نفر اول)، آرش فاضلی (نفر دوم)، اسدالله احمدی خواه (نفر سوم)، Vahid Shariatiat (نفر چهارم)