Phenotypic and genomic variation in a halophytic turfgrass
The genetic basis of salt tolerance is poorly understood. Especially in highly salt tolerant (halophytic) species for which standard phenotyping methods are inadequate and genetic tools are unavailable. For my thesis work I will use the halophytic turfgrass seashore paspalum (Paspalum vaginatum) to investigate the genetic basis of salt tolerance in halophytes. In doing so I will develop a high-throughput and accurate phenotyping protocol to measure salt-tolerance in a halophyte using a combination of ionomics and image analysis. I will also sequence the whole genomes of many accessions to measure genomic variation in the species and identify the genes controlling salt-tolerance.
The genetic basis of disease resistance in rice
Rice is a staple crop for most of the world’s population. One of the largest challenges faced by the rice farming community is controlling disease. Millions of dollars are spent every year on fungicides and other treatment methods. In an effort to develop more resistant varieties of rice we are searching for fungal resistance genes found in weedy-rice populations that can be bred into cultivated varieties. We are using two weed x crop RIL populations to perform QTL mapping analysis on resistance to various rice diseases including rice blast and sheath blight.
The evolution of the CLE gene family
The CLE (CLavata3-like/Embryo surrounding region) gene family is a large group of genes unique to plants. Most are small signalling molecules involved in regulating a wide variety of developmental pathways. CLEs are notoriosly hard to group phylogenetically because they are only conserved in a small 12 amino acid region known as the “CLE domain”. I used the search tool hmmer to identify CLEs in over 40 plant genomes and used clustering software to order them into distinct groups. In doing so I found more conservation in the “neutrally evolving” regions than would be expected.