Adjunct Professor Shahryar Kianian

This group is currently involved in three large genomics project that use MSI resources:

• A High-resolution map of recombination in maize: The goal of this project is to generate the first comprehensive high-density map of recombination in a higher eukaryote (maize). The researchers will identify sites where recombination is initiated by formation of meiotic double-strand-breaks (DSBs) in chromosomal DNA as well as sites where recombination events are resolved into crossovers. This map will elucidate how the distribution of recombination events is related to local genome and chromatin features and, eventually, allow identifying factors that control the location and frequency of recombination events in maize. It will also further understanding of how recombination affects the structure of large and complex plant genomes. The main component of this work is to generate high-resolution maps of cross over (CO) locations on maize chromosomes and relate these to double-stranded break locations. The researchers will sequence close to 330 individuals from two different mapping populations, assemble the genomes using the reference assembly, and determine the CO location. The locations of CO hotspots will be compared with DSB hotspot locations in the same genetic backgrounds. The group has already sequenced ~100 lines.
• Developing stress-tolerant plants through cytoplasmic modification: Coordination of gene expression between the genomes present in the cytoplasm (mitochondria and chloroplast) and nucleus is of crucial importance to cells of all eukaryotes. Hundreds of genetic diseases in humans and thousands of phenotypic variations in plants and other organisms are known to be the result of alterations affecting this critical communication. Wheat has the largest array of alloplasmic lines (lines with alien cytoplasm), larger than any other mammalian, insect, or plant system, which has been established by the backcross substitution method. This makes wheat an ideal model species to study NC interaction. Preliminary analysis by this group indicates a number of alloplasmic lines exhibit drastically increased disease resistance and vigor. Additional sequencing data from these lines indicate that not only the mitochondrial genome can be changed by replacement of nuclear genome but those changes result in alteration of mitochondrial gene expression patterns. The results of this initial study are exciting but have generated questions with regard to the cytoplasmic genome (chloroplast vs. mitochondria) that influences plant response to biotic stress; the molecular mechanism of this response; whether this process be engineered/modified to address important biotic or abiotic stress problems; and many more. This project intends to identify the cytoplasmic genome that is responsible for observed stress tolerance; determine if the impact extends to abiotic stress factors; and begin to understand the molecular mechanism behind the response.
• Whole-genome haplotype sequencing of Puccinia coronata f. sp. avenae, causal agent of oat crown rust disease: Oat crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is one of the most destructive pathogens affecting grain production. Pca shows very high genetic variability and resistance genes deployed in the field are often overcome in just a few years, which is of particular importance given that current domestic oat production cannot keep pace with U.S. demand. The genomic resources necessary for a greater understanding of molecular mechanisms of virulence and more targeted resistance deployment strategies of Pca are underdeveloped. Thus, these researchers have generated de novo genome assemblies of two Pca isolates with contrasting virulence phenotypes (races LBBB and STTG). Genomic analyses of rust fungi are complicated by both the dikaryotic nature in the most readily accessible life stages and also the high percentage of repetitive elements present in the genome. To overcome these obstacles, the researchers implemented emerging technologies to assemble haplotigs of urediniospores to produce a high quality reference genome. Long-read single molecule PacBio and short-read Illumina sequences are being analyzed in parallel to accurately phase the genome using recently released algorithms. The high quality genome references are annotated utilizing expression data from a variety of tissue types and life stages, including haustoria isolated from infected tissues, and a catalog of predicted effectors was generated. Moreover, the researchers are comparing sequence variation and repetitive element repertoires to assess the variability between nuclei and inter-isolate comparisons used to characterize the genomic landscape of this fungal species. They are also embarking on a resequencing project of 60 isolates to describe the pan-genome of Pca and variability among isolates. Ultimately, this project will provide tools to uncover pathogenicity mechanisms in Pca and allow comparisons to other cereal rust fungi to be readily made.

This research was featured on the MSI website in September 2018: Genomic Studies of Oat Crown Rust.