Microsatellite marker diversity and sequence polymorphism in the red gene locus of indigenous rice populations of Bangladesh

Abstract

Bangladesh is home to diverse rice germplasm, including red rice, many of which are preferred for cultivation by farmers over high-yielding rice varieties due to their special characteristics, color, taste, and nutritional value. Red color of seed pericarp is unusual among modern cultivated varieties, though it is a common characteristic in wild relatives of rice, making the trait an important parameter when studying the domestication and evolution of crop plants. Diversity analysis using microsatellite markers and sequence variation of the red rice loci of the indigenous rice population in Bangladesh was therefore performed. Microsatellite fingerprinting could successfully cluster cultivars according to their specific phenotypic characteristics such as stickiness or aroma, irrespective of their pericarp color, and locate a set of unique identifiers. Sequence analysis of a portion of the bHLH transcription factor gene Rc, which controls the red pigment, confirmed the occurrence of the 14-bp deletion in white rice accessions which has been reported previously. The analysis included a group of rice cultivars which are known by the same name but produce two different colored seeds and are indistinguishable morphologically unless dehusked. Statistical and internal transcribed spacer region sequence diversity analyses established that such cultivars, although genetically different, had very low diversity, suggesting a close evolutionary relationship between them. Red and white seeds from cultivars with the same name were planted individually over two generations and dehusked to check for loss/gain of pigmentation. Red-seeded plants produced some dirty-white seeds in addition to red ones in the first generation, the proportion of which increased when planted in the successive generation. This loss in pigment was probably due to faulty transcription, since no deletion in the respective region of the genome of the dirty-white seeds was noted.