High-throughput next-generation DNA sequencing technologies (NGS) are causing a major revolution in life sciences research by allowing rapid and cost-effective sampling of genomes and transcriptomes (expressed genomic sequences). Assembly of genomes and transcriptomes from billions of such randomly sampled sequences is an important problem in computational biology. While significant strides have been made, much work remains in addressing the diverse and rapidly emerging platforms, improving assembly quality, and scaling to both large-scale data sizes and large genomes.
NRT- DESE: Predictive Phenomics of Plants (P3)
This proposal focuses on the development of hierarchical models and parallelized Bayesian inference for the analysis of RNA sequencing (RNAseq) data. Special emphasis is placed on gene expression profiling of parental inbred lines and their hybrid offspring for the discovery of key genes underlying heterosis, the genetic phenomenon otherwise known as hybrid vigor.
The shoot apical meristem (SAM) is responsible for development of all above ground organs in the plant. SAM structure and function correlates with agronomically-important adult traits in the maize plant, and is also affected by planting density and shade stresses induced by agricultural environments. The ultimate goal of this project is to increase understanding of the regulatory networks controlling SAM structure and function and the responses of these networks to environmental stresses.
Our civilization depends on continuously increasing levels of agricultural productivity, which itself depends on (among other things) the interplay of crop varieties and the environments in which these varieties are grown. Hence, to increase agricultural productivity and yield stability, it is necessary to develop improved crop varieties that deliver ever more yield, even under the variable weather conditions induced by global climate change, all the while minimizing the use of inputs such as fertilizers that are limiting, expensive or have undesirable ecological impacts.
The overall goal of the proposed project is to increase the efficiency of crop breeding programs by developing and deploying improved genomic selection strategies that rely on improvements in the selection and mating steps.As a consequence of growing populations, changing diets, and the challenges of climate change, agricultural systems must produce more with less. More means greater demand for agricultural products such as food, feed, energy and fiber.