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Toward Understanding the Genetic Basis of Cross-Incompatibility in Sorghum: de novo genome Assembly of Johnsongrass and Resequencing of Iap and BAM1 loci
Cell and Molecular Biology
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Sorghum [Sorghum bicolor (L.) Moench] (referred to as “sorghum” hereafter) is a C4 grain crop in the grass family Poaceae. It is closely-related to other members of subfamily Panicoideae, including the staple crops maize [Zea mays L.] and rice [Oryza sativa L.], and is the 5th-most produced cereal crop in the world.31,33,72 The U.S. leads production of sorghum globally.34 Johnsongrass is the weedy species of sorghum, considered a noxious weed in 46 states in the United States and often found growing within close proximity to sorghum where it has been shown to contaminate harvest seed through gene flow. The risk of gene flow is the primary reason why GE sorghum has not been approved for commercialization by USDA-APHIS (personal communication, Dr. Subray Hegde, USDA Biotechnology Regulatory Services branch chief in the Biotechnology Risk Analysis Program). Many efforts71,73-77 have been made to determine the rate of gene flow between sorghum and Johnsongrass to empirically assess the risk of sorghum traits transferring to feral Johnsongrass populations, but these studies have used limited numbers of accessions from both species and the lack of high-throughput genotyping methods or a high-quality Johnsongrass reference genome have led to inconsistent results. Given the polyploid history of Johnsongrass (a putative allotetraploid [2n = 4x = 40] and the close relationship between ancestral genomes, this risk is not insignificant. In order to determine the frequency of sorghum alleles segregating in feral Johnsongrass populations, an assembled and annotated Johnsongrass reference genome is needed to identify species-specific alleles, and their copy number, that may differ from ii those in the existing, well-annotated sorghum reference genome. Availability of a Johnsongrass reference genome would enable researchers around the world to directly quantify stably introgressed sorghum alleles segregating in local Johnsongrass populations of interest. Local rates of gene flow are needed because different sorghum genotypes and production methods are used in different geographies, and both factors could impact rates of reproductive success, genetic drift, or the fixation of crop alleles. This thesis provides the basic genomic framework necessary to assist in NGSbased inquiries into the ancestry, speciation, and comparative genomics of Johnsongrass and sorghum. We completed the first Johnsongrass de novo genome assembly and amplified, through long-read resequencing, the putative reproductive barrier loci (Inhibition of Alien Pollen, Iap and Barely Any Meristem, BAM164) in Johnsongrass that are known to impact rates of gene flow among Sorghum species and closely-related genera (Zea and Saccharum). This new Johnsongrass reference genome and targeted competed resequencing data will greatly facilitate population genetic studies aimed to clarify empirical rates of gene flow among sorghum and Johnsongrass specifically, and within the Sorghum species complex generally. They will additionally assist with genetic and physiological investigations into the roles of key loci involved in processes of speciation and reproductive isolation.