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

大米是世界上一半以上人口的主食，其中90%以上的大米在亚洲消费。有色米，如黑米和红米，传统上用于特殊场合的食物。随着人们对促进健康的功能性食品的兴趣日益浓厚，色素米的消费量也在迅速增长。色素米含有高水平的植物化学物质，如花青素、黄酮类化合物和维生素e。这些植物化学物质的抗氧化活性有助于清除人体细胞中的自由基（ROS），从而降低癌症、高胆固醇和心血管疾病等退行性疾病的风险。由于色素米的价格是白米的两倍以上，并且色素米在国际市场上的潜力很大，因此种植色素米作为白米的替代品或与白米一起种植将为菲律宾农民带来更高的收入。目前，菲律宾水稻研究所（PhilRice）的遗传资源部门从菲律宾不同地区收集了800多份有色水稻。这些水稻材料可能具有营养和治疗成分，可用于色素水稻新品种的选育和开发，但其潜力尚未得到开发。通过该项目，菲律宾水稻研究所（PhilRice）、国家农业植物学研究所（NIAB）和国际水稻研究所（IRRI）将合作筛选和鉴定菲律宾本土色素水稻种质，以发现可作为色素水稻育种新供体的色素水稻品种。PhilRice和NIAB将对着色水稻种质的农业形态性状、籽粒品质、营养成分、种皮颜色、抗氧化活性和植物化学性质（花青素、类黄酮）的变化进行表征。此外，IRRI将利用Illumina Infinium 6K芯片通过SNP基因分型确定色素水稻种质资源的遗传多样性。基于这些表型和基因型数据，我们将选择一个核心收集的色素水稻材料。这些核心品种将代表不同类别的形态性状、籽粒品质、营养价值、抗氧化活性、植物化学特征和遗传亚群。该核心收集将用于NIAB使用HPLC和液相色谱/质谱（LC/MS）分析对色素大米中的抗氧化成分进行深入研究。已知和潜在的新型抗氧化成分的遗传基础将通过全基因组关联筛选（GWAS）进行。根据GWAS分析的结果，我们将选择几个可以用作捐助者的水稻品种。我们将鉴定与具有高抗氧化活性的植物化学物质密切相关的单核苷酸多态性（SNP），并开发性状特异性SNP标记用于标记辅助选择。SNP标记的优势在于它们可以用于高通量系统，具有快速的周转时间，因此使育种者能够在更短的时间内选择理想的植物材料。

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.