In this study, we analyzed the Rc and Rd genes that are responsible for the coloration of rice pericarps from six upland rice varieties. We also examined the association of pericarp coloration to the single nucleotide polymorphism in 9-cisepoxycarotenoid dioxygenase 2 (NCED2), a key gene involved in abscisic acid (ABA) biosynthesis. Our findings demonstrated that all the upland rice varieties analyzed have a Rd gene which encodes a complete dihydroflavonol-4-reductase without early translational termination codon irrespective of their pericarp colors. However, the upland rice varieties with white pericarps were found to have a defective Rc gene with a 14-base deletion at exon 7 which could disrupt the function of a positive regulator of proanthocyanidin biosynthesis. In addition, the NCED2 genes from the upland rice varieties with white pericarps in this study have a C-allele while the NCED2 genes from Pandasan Red, Tomou and Taragang varieties that bear red pericarps were found to have a T-allele which was reported to be associated with a higher ABA level in upland rice. A better understanding of the gene sequences of upland rice varieties with red pericarp may provide important information for rice breeding programs.

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Analyses of morphological and agronomic traits not only provide important information in the selection of rice varieties for breeding, these data are also important in deciding plant materials for molecular characterization and analysis of phenotypic traits of interest. The aim of the present study was to collect, analyze and compare the agro-morphological data of 6 upland rice and 17 lowland rice varieties (Oryza sativa L.) from the Malaysian rice germplasms grown under the same greenhouse condition. The common factors that contributed to yield per plant in both upland and lowland rice varieties are plant height and percentage of filled grains. Panicle length was positively correlated to grain yield in upland rice varieties while many other agronomic traits could affect the yield per plant in lowland rice varieties such as total number of tillers, total number of panicles per plant, flag leaf width and days-to-flowering. The upland rice varieties have a slightly higher average total grain number per panicle in compensation of a low number of panicles. The compensation in total grain numbers per panicle was not sufficiently significant to affect the total yield per plant most probably due to a low total number of grains per plant. Despite a high 100-grain weight in general, some of these upland rice varieties have more than 50% percentage of unfilled grains. Data on these rice germplasms may offer information on a valuable gene pool which can be utilized in different varietal improvement/development program in future.