Emily G. Postal¹, Matt C. Estep¹, Christoffel den Biggelaar^2,, Florien Zafiroa³

While the rich, endemic biodiversity of Madagascar is well studied, far less attention has been devoted to understanding the introduced crop diversity. Oryza sativa L. is the most widely consumed grain worldwide and constitutes 55% of the caloric diet of Malagasy peoples. A 2019 survey of rice varieties grown by 73 households around the Betampona Integral Nature Reserve in East Madagascar identified 81 locally named varieties (den Biggelaar et al., 2024). Rice varieties are named by farmers based on phenotypic and morphological characteristics (primarily of the seed and reproductive structures) and method of production (swamp/irrigated or upland/rainfed). Previous studies of Malagasy rice varieties using DNA analysis found a large number of synonyms and homonyms among studied individuals. This paper reports on the results of a microsatellite fingerprinting analysis used to determine the relatedness of named varieties in the villages around Betampona INR as well as three fokontany at different distances from the INR. Eighty-six fresh tissue samples were collected along with varietal names and specific collection coordinates. These samples were subjected to a modified CTAB extraction before conducting PCR using thirteen primers established by previous studies. Microsatellite bands were scored using a 50bp ladder on 3% agarose gels run for three hours at 50V. Results of our analysis show that within each fokontany, varieties are genetically distinct. Across the samples from the seven fokontany, we identified ten homonyms (35 samples) and sixteen synonyms. Using variety names only is, therefore, insufficient to study agrobiodiversity at larger scales, especially for a mostly self-pollinating crop such as rice, with farmers saving a portion of their crop as seed for the following crop season.

rice varieties, genetic diversity, DNA microsatellite analysis, Madagascar