Genetic Studies of Pearl Millet (Pennisetum Glaucum (L.) R. Brown) Downy Mildew Resistance in Senegal

Abstract

Pearl millet is an important cereal crop for food security in Senegal. However, the production of this crop has stagnated due to several factors, among them, downy mildew. A participatory rural appraisal and a survey conducted in the groundnut basin of Senegal involving 150 farmers revealed the occurrence of the disease across the main pearl millet growing areas. Almost all the farmers interviewed (99%) were able to recognize the disease and 94% of them observed it in their fields during the just ended season of 2014. However, they neglected the damages caused by the disease and did not rank it as the main constraint to pearl millet production. They rather ranked Striga and low soil fertility as the main pearl millet production constraints. They unanimously considered grain yield as the most important trait to be incorporated in a new pearl millet variety. The spatiotemporal pathogenic variation of the downy mildew disease was also studied using pearl millet downy mildew resistance differential lines. Significant differences were observed among the genotypes, location, year and their interactions for downy mildew incidence providing evidence of spatio-temporal pathogenic variation. Except for ICMR356, the downy mildew resistant differential lines differed in their resistance to the pathogen from the four agro-ecological zones across the years. The highest average downy mildew incidence over the two years was recorded in Nioro (18.7%), Kolda (17.6%) and Bambey (12.1%) research stations while the mean downy mildew incidence was the lowest in Sinthiou (6.9%). Therefore, Kolda, Nioro and Bambey research stations should be used for screening pearl millet materials. Thus, a set of 99 inbred lines, derived from landraces collected in several West and Central African countries, were evaluated under field conditions in Bambey and Nioro research stations during the rainy season of 2016. A highly significant differences were observed among lines for the downy mildew disease parameters and other agronomic traits. The lines were classified into 3 clusters with disease parameters and plant height as the most discriminant factors. One of the groups contained 38 lines that were characterized as resistant, early flowering, and the tallest plants with longest panicles. Out of these 38 lines, 17 were crossed with SOSAT C88 and Souna3 following a line x tester mating design in order to study their combining ability. General combining ability (GCA) and specific combining ability (SCA) means squares were significant for most of the traits indicating that both additive and non-additive gene effects were involved in the control of the inheritance of these traits. However, the contribution of GCA to the total mean squares was higher than that of SCA for all the traits, meaning that additive gene action was more important in the inheritance of these traits. Lines IBL003-B-1, IBL091-1-1, IBL095-4-1, IBL110-B-1 and IBL206-1-1 had positive GCA effects for grain yield and negative GCA effects for downy mildew, flowering time and plant height. These lines can be used as parents to create synthetic varieties or F1 hybrids adapted to the groundnut basin agro-ecological zone. Positive mid-parent, best parent and standard heterosis were observed for hybrids IBL206-1-1 x Souna3; IBL091-1-1 x Sosat C88; IBL206-1-1 x Sosat C88; IBL001-4-1 x Souna3 and IBL003-B-1 x Sosat C88. An association analysis was conducted with 77 genotypes to identify single nucleotide polymorphisms (SNPs) markers associated with downy mildew resistance. Three sub-groups based on panicle length were identified and a rapid linkage disequilibrium decay was noted. Sixteen significant markers, located on four linkage groups (LG) were identified across locations. Among these SNPs, the ones located on LG6 explained 15 to 20% of the downy mildew phenotypic variation and were consistent across the two locations. These SNPs were located on the same LG that a Quantitative Trait Loci detected in a previous study against population of pathogens that originated from Senegal while the ones located on LG1, LG3 and LG4 were discovered for the first time under Senegalese environments and therefore could be considered as new markers. With the pearl millet genome sequenced, candidate genes surrounding these identified genomic regions can be identified and validated.