Identification of Loci Influencing Striga Germination Stimulant Activity By Genome Wide Association Studies of the Sorghum Panel

Sorghum is one of the most important cereals, providing food for millions of people in the developing world. The parasitic weed Striga (S. hermonthica and S. asiatica) is the major biological constraint to sorghum production in sub-Saharan Africa and in some semi-arid tropical regions of Asia.  The best described and most used Striga resistance mechanism in sorghum is low germination stimulant activity. Root exudates of 283 lines from the sorghum association panel, an assembly of over 400 diverse lines, were tested for their ability to cause germination of conditioned S. hermonthica seed. The germination rate of Striga seed embedded in agar varied from 0 to 100% germination, corrected against the standard germination stimulant GR24, among tested accessions of the panel. Nearly a quarter of the tested lines showed low Striga germination stimulant activity (caused germination of <30% of the germinable weed seed). Publicly available single nucleotide polymorphic (SNP) calls from the association panel were used for genome wide association studies (GWAS). To detect marker-trait associations, a mixed linear model that accounts for population structure and kinship was used for analysis. Suggestive significant marker trait associations were found on chromosomes three, five, seven and nine. The association of SNP marker S3_62628011 on chromosome three is statistically significant with its p-value well below the Bonferroni correction factor. One of the candidate genes in that area, Sobic.003G293600, is homologous to rice CCD8 that codes for a key enzyme in the strigolactone biosynthesis pathway. This gene is 16kb away from the significant SNP but well below the reported linkage disequilibrium (LD) in sorghum. Previously published data indicated Sobic.003G293600 expression was upregulated under nitrogen starvation. The product of Sobic.003G293700, another candidate only 2kb away from the S3_62628011 marker, is homologous to proteins with glucoronosyl and glucosyl transferase activity. Sobic.003G293700 is expressed in roots and leafs and upregulated with pathogen infection and nitrogen stress. Variation in alleles at these loci appear to influence Striga germination stimulant activity and therefore certain mutations here may be useful for Striga resistance breeding in sorghum.