Abstract

Rice (Oryza sativa) is a crucial staple food globally, and understanding the genetic diversity of both lowland and upland local rice varieties is essential for their effective management, conservation, and efficient utilization in varietal improvement programs. In the present study, a total of 58 rice varieties, comprising 9 uplands and 49 lowlands, were sourced from the Lowland Rice Breeding Program of the Regional Center for Agronomic Research of Sikasso at the Institute of Rural Economy. These genotypes were characterized using polymerase chain reaction-simple sequence repeat (PCR-SSR) with 101 microsatellite markers. A total of 428 alleles were recorded and the number of alleles per locus varied from 2 (RM5, RM212, RM243, RM302, RM1387, RM240, RM250, RM517, RM249, RM3330, RM3826, RM339, RM205, RM257, RM5786 and RM235) to 10 (RM009 and RM481) with an average of 4.24 alleles per locus. The Polymorphism Information Content (PIC) value was ranged from 0.120 (RM145) to 0.832 (RM5780) with an average of 0.459. Forty percent (40%) of the markers were highly informative, 44% reasonably informative and 16% slightly informative. The value of genetic diversity revealed by the markers was ranked from 0.128 to 0.848 with an average of 0.497 for the same markers as the PIC. Similarity analysis based on genetic distance allowed classifying the 58 genotypes into three groups (I, II and III). Groups I and III were formed only by traditional lowland varieties collected from rice farmers. Groups I and III exclusively comprised traditional lowland varieties obtained from rice farmers, while Group II included upland rainfed interspecific varieties like O. sativa, Oryza glaberrima, Oryza longistaminata, alongside some traditional lowland varieties such as Diema2, Sikasso56, Sikasso-1-14, Diama20, Diola, and Yorosso200. These findings offer valuable insights for breeders in managing rice genebanks, identifying lowland varieties with unknown genetic origins, and selecting lines with desirable agronomic traits for rice improvement programs.

Key words: Genetic diversity, rice varieties, lowland, upland, polymerase chain reaction-simple sequence repeat (PCR-SSR).