Molecular Characterization and Genetic Analysis of Nutritional Components of Philippine Indigenous Pigmented Rice Germplasm

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Rice is a staple food for more than half of the world's population, with more than 90% of rice being consumed in Asia. Pigmented rice, such as black and red rice is traditionally used for food for special occasion. The consumption of pigmented rice is rapidly growing along with the increasing interest in health-promoting functional food. Pigmented rice contains high level of phytochemicals such as anthocyanin, flavonoids and vitamin E. Antioxidant activity of these phytochemicals helps to scavenge radical oxygen species (ROS) in human cell, thus decrease the risk of degenerative diseases such as cancer, high cholesterol and cardiovascular disease. Since the price of pigmented rice is more than twice that of white rice and the potential of pigmented rice in international market is large, growing pigmented rice as an alternative to or together with white rice will give higher income for Philippines farmers. Currently, the Genetic Resources Division of the Philippine Rice Research Institute (PhilRice) has more than 800 accessions of pigmented rice collected from various regions of the Philippines. These rice accessions may have nutritional and therapeutic components that can be utilized in the breeding and development of new varieties of pigmented rice, but their potentials has not yet been explored. Through this project the Philippine Rice Research Institute (PhilRice), the National Institute of Agricultural Botany (NIAB) and the International Rice research Institute (IRRI) will collaborate to screen and characterize Philippine indigenous pigmented rice germplasm to discover those pigmented rice accessions that can be utilized as new donors for pigmented rice breeding. PhilRice and NIAB will characterize the variation in agro-morphological traits, grain quality, nutritional composition, seed coat colour, antioxidant activity and phytochemical properties (anthocyanins, flavonoids) in the pigmented rice germplasm. In addition, IRRI will determine the genetic diversity of pigmented rice germplasm through SNP genotyping using Illumina Infinium 6K chip. Based on this phenotype and genotype data we will select a Core collection of pigmented rice accessions. This Core collection will represent different classes of morphological traits, grain quality, nutritional value, antioxidant activity, phytochemical profiles and genetic subgroup. This Core collection will be used for a thorough study of the antioxidant components within pigmented rice using HPLC and Liquid Chromatography/Mass Spectrometry (LC/MS) analysis at NIAB. The genetic basis of the known and potentially novel antioxidant components will be undertaken through a genome-wide association screen (GWAS). Based on the results from the GWAS analysis we will choose several rice accessions that can be utilized as donors. We will identify single nucleotide polymorphisms (SNPs) that are closely associated with the phytochemical having high antioxidant activity and develop trait specific SNP markers for marker-assisted selection. SNP markers have the advantage in that they can be used in high-throughput systems, having fast turnaround times and therefore enable breeders to select desirable plant materials in a shorter time.