A study of the diversity of Burkina Faso rice landraces and identification of source of resistance to rice yellow mottle virus (RYMV)

Abstract

The main goals of this study were to ascertain farmers' preferred traits in rice landraces and their perception of Rice yellow mottle virus, to collect rice landraces across Burkina Faso, investigate their genetic diversity, and to exploit this diversity in a search for varieties resistant and tolerant to RYMV, for their utilisation in rice breeding. Farmers' preferred traits, approaches to crop management, and disease perceptions were assessed using a Participatory Research Appraisal (PRA) approach. In the main rice growing regions of Burkina Faso, 330 rice landraces were collected. The agro-morphological diversity of the germplasms was evaluated in the field with 20 quantitative and 30 qualitative agro-morphological parameters. Thereafter, 22 Simple Sequence Repeat molecular markers were used to assess the genetic diversity and the population structure of the collection. Finally, the rice landraces were screened against four RYMV isolates to assess the susceptibility, tolerance and resistance of the landraces in the collection using visual assessment and Enzyme Linked Immunosorbent Assay. The PRA identified sweet taste, grain expansion when cooking, easy cooking and yield as paramount selection criteria in rural rice farming communities in Burkina Faso. Drought and disease resistance are characters that farmers wish to have in their varieties. The PRA also highlighted that farmers are conscious of RYMV disease in their fields. However, they are unaware about the epidemiology of the disease. An agro-morphological study of the phenotypic diversity of the collection confirmed the presence of the two cultivated rice species: O. glaberrima and O. sativa. There were more O. sativa accessions than O. glaberrima landraces. There were 48 O. glaberrima and 282 O. sativa accessions in the collection. Both species were divided into four clusters, reflecting the richness of the collection. The underlying genetic diversity of the collection was confirmed by the use of 22 Simple Sequence Repeat molecular markers. The neutral markers confirmed the existence of two substructures, namely O. glaberrima and O. sativa, and the presence of admixture varieties. However, a core collection of 52 individuals was developed. This included 13 O. glaberrima and 39 O. sativa accessions. It reflects the genetic diversity of the sub-clusters present in each species. This core collection contains 89% of the allelic richness of the collection. Its small size will facilitate the maintenance and active use of diversity of germplasm in the core collection. The entire collection was utilised to search for varieties resistant and tolerant to RYMV disease. The screening of the collection with different RYMV isolates exposed the susceptibility of most of the accessions in the collection. Most of the O. sativa indica accessions were highly susceptible. However, ten O. glaberrima accessions displayed a delay of symptom expression, and moderate resistance. However, their resistance was overcome later by a particularly virulent RYMV isolate BF1. Remarkably, a single moderately resistant cultivar, BM24, showed that partial resistance and tolerance to RYMV can be found in an O. sativa variety. Serological evaluation of this local variety in comparison with the partially resistant variety, Azucena, showed that BM24 and Azucena expressed similar resistance patterns. A genetic profile of both varieties showed that both had an identical allele status at RM101, which is a marker bracketed in the same zone as the QTL12.