Genome-wide association analysis of grain yield and Striga hermonthica and S. asiatica resistance in tropical and sub-tropical maize populations

Genetic improvement for Striga hermonthica (Sh) and S. asiatica (Sa) resistance is the most economical and effective control method to enhance the productivity of maize and other major cereal crops. Hence, identification of quantitative trait loci (QTL) associated with Striga resistance and economic traits will guide the pace and precision of resistance breeding in maize. The objective of this study was to undertake a genome-wide association analysis of grain yield and Sh and Sa resistance among tropical and sub-tropical maize populations to identify putative genetic markers and genes for resistance breeding. 126 maize genotypes were evaluated under controlled environment conditions using artificial infestation of Sh and Sa. The test genotypes were profiled for grain yield (GY), Striga emergence counts at 8 (SEC8) and 10 (SEC10) weeks after planting, and Striga damage rate scores at 8 (SDR8) and 10 (SDR10) weeks after planting. Population structure analysis and genome-wide association mapping were undertaken based on 16,000 single nucleotide polymorphism (SNP) markers. A linkage disequilibrium (LD) analysis in 798,675 marker pairs revealed that 21.52% of pairs were in significant linkage (P < 0.001). Across the chromosomes, the LD between SNPs decayed below a critical level (r2 = 0.1) at a map distance of 0.19 Mbp. The genome-wide association study identified 50 significant loci associated with Sh resistance and 22 significant loci linked to Sa resistance, corresponding to 39 and 19 candidate genes, respectively. The study found non-significant QTL associated with dual resistance to the two examined Striga species Some of the detected genes reportedly conditioned insect and pathogen resistance, plant cell development, variable senescence, and pollen fertility. The markers detected in the present study for Sa resistance were reported for the first time. The gene Zm00001eb219710 was pleiotropic, and conditioned GY and SEC10, while Zm00001eb165170 affected SDR8 and SDR10, and Zm00001eb112030 conditioned SDR8 and SDR10 associated with Sh resistance. The candidate genes may facilitate simultaneous selection for Sh and Sa resistance and grain yield in maize after further validation and introgression in breeding pipelines. Overall, we recommend breeding maize specifically for resistance to each Striga species using germplasm adapted to the endemic region of each parasite.