Full Length Research Paper

Molecular profiling of interspecific lowland rice populations derived from IR64 (Oryza sativa) and Tog5681 (Oryza glaberrima)

Marie Noelle Ndjiondjop¹*, Kassa Semagn², Moussa Sie¹, Mamadou Cissoko¹, Blandine Fatondji¹ and Monty Jones³

¹Africa Rice Center (WARDA), 01 BP 2031, Cotonou, Benin.

²International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Nairobi, Kenya.

³Forum for Agricultural Research in Africa, PMB CT 173 Cantonments, Accra, Ghana.

*Corresponding author. E-mail: m.ndjiondjop@cgiar.org.

Accepted 24 October, 2008

Several lowland NERICAs (New Rice for Africa) were derived from crosses between IR64 (an Oryza sativa subsp. indica variety) and Tog5681 (an Oryza glaberrima variety) that possess useful traits adapted to lowland conditions in West Africa. The proportion of parental genomic contribution and extent of genetic differences among these sister lines is unknown at the molecular level. The objectives in this study were therefore to determine, with 60 SSR markers that cover 1162 cM of the rice genome, the frequency and magnitude of deviations from the expected parental contributions among 21 BC₂F₁₀, 17 BC₃ F₈ and 10 BC₄F₈ lines and determine patterns of their genetic relationships. The estimated average O. glaberrima genome coverage was 7.2% (83.5 cM) at BC₂F₁₀, 8.5% (99.3 cM) at BC₃F₈ and 8.1% (93.8 cM) at BC₄F₈ lines. The O. sativa parent accounted for 73.2% (851.3 cM) at BC₂F₁₀, 82.6% (959.5 cM) at BC₃F₈ and 78.2% (908.6 cM) at BC₃F₈. Non-parental alleles were detected at all 3 backcross generations but the frequency of such alleles at BC₂ (8.8%) was twice that of BC₃F₈ (3.4%) and nine times that of BC₄F₈ (0.9%). Both cluster and principal component analyses revealed two major groups irrespective of the level of backcross generations and the proportion of parental genome contribution. 

Key words: African rice, introgression, microsatellite, NERICA, Oryza glaberrima, rice.