A Genome-wide Association Study of the Quantitative Resistance to Striga hermonthica and Plant Architecture of Sorghum bicolor in Northwestern Ethiopia

Abstract

Sorghum (Sorghum bicolor) is a well-known\nagronomic crop of global importance. The demand for sorghum as a food crop\nmakes it the fifth most important cereal in the world. The grain of sorghum is\nutilized for food and feed, whereas the sorghum biomass may have many other\nuses such as for fodder, bioenergy or even for construction. Globally, sorghum\nis consumed as a food crop and used for home construction primarily in the\ndeveloping world. The grain and biomass\nyield of sorghum is drastically reduced by the parasitic plant Striga hermonthica which is endemic to\nSub-Saharan Africa. To date, only one sorghum gene, LGS1, has been characterized as a genetic mechanism that reduces S. hermonthica parasitism by altering\nthe strigolactone composition of the host root exudates which results in a\nreduction of the parasites ability to germinate. To establish more durable\nresistance additional genetic variation needs to be identified that reduces the\nS. hermonthica parasitism in sorghum,\nbut also reduces the parasitic weed seed bank by promoting suicidal\ngermination. To that end, the PP37 multi-parent advanced generation inter-cross\n(MAGIC) population was developed, originally as a recurrent selection\npopulation that was developed to recombine sorghum accessions with different\nputative resistance mechanisms to S.\nhermonthica. Whole genome sequences were developed for approximately 1,006\nindividuals of the PP37 MAGIC population. The population was phenotyped for S. hermonthica resistance during the\n2016 and 2017 growing season in Northwestern Ethiopia. There was significant\nspatial variation in the S. hermonthica natural\ninfestations that were partially attenuated for with artificial inoculation.\nThe data was used to conduct a genome-wide association study that detected\nseveral subthreshold peaks, including the previously mapped LGS1. The highly quantitative nature of S. hermonthica resistance confounded\nwith the complex spatial variation in the parasite infestations across a given\nlocation make it difficult to detect highly heritable variation across years\nand environments. In\naddition to S. hermonthica resistance,\nthe plant architecture of the PP37 MAGIC was also assessed at a location in\nNorthwestern Ethiopia that is free of the parasite, as it significantly reduces\nplant height. To asses plant architecture the total plant height, the height of\nthe panicle base, flag leaf height, and pre-flag leaf height were collected\nusing a relatively high-throughput barcoded measurement system. Sorghum head\nexertion and panicle length were derived from this data. The actual measures of\nplant architecture and the derived traits were used to conduct a genome-wide\nassociation study. The high heritability of this trait demonstrated the\nstatistical power of the PP37 mapping population. Highly significant peaks were\ndetected that resolved the dwarf3\nlocus and an uncharacterized qHT7.1 that had only been previously resolved\nusing a recombinant inbred line population. Furthermore, a novel significant\nlocus was associated with exertion on chromosome 1. The random mating that was\nutilized to develop the PP37 MAGIC has broken the population structure that\nwhen present can hinder our ability associate regions of the genome to a given\nphenotype. As a result, novel candidate gene lists have been developed as an\noutcome of this research that refined the potential genes that need to be\nexplored to validate qHT7.1 and the novel association on chromosome 1. \n\nThis research\ndemonstrated the power of MAGIC populations in determining the genomic regions\nthat influence complex phenotypes, that facilitates future work in sorghum\ngenetic improvement through plant breeding. \nThis research however also demonstrates a large international research\neffort. The nuisances and lessons learned while conducting this international research\nproject are also discussed to help facilitate and guide similar research\nprojects in the future. The broader impacts of this research on the society at\nlarge are also discussed, to highlight the unique potential broader impacts of\ninternational research in the plant sciences. The broader impacts of this\nresearch include germplasm development and extensive human capacity building in\nplant breeding genetics for developing country students and aspiring\nscientists. Overall this research attempts to serve as a model for highlighting\nthe interdisciplinary nature and complexity of conducting international plant\nscience research, while also making significant strides in improving our understanding\nthe genetic architecture of quantitative traits of agronomic importance in\nsorghum.