Genomics applications to the study of gene evolution and adaptation in pine trees
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Several pine trees co-exist in the Southeastern United States, where they represent the principal commercial forest species. The forest products industry, which is dominated by these pines, is responsible for 5.5% of the jobs and 7.5% of total industrial output in the region. Loblolly pine and slash pine in particular are of great commercial relevance given their abundance, rapid juvenile growth, and pulpwood and lumber value.About three-fourths of all tree seedlings planted each year in the U.S. are loblolly pine. This trees also plays a fundamental ecological role in the forest landscape from Texas to Virginia. The conservation and commercial improvement of these pine species are instrumental for the long-term management of Southeastern United States forests and to support the forest products industry. Understanding the genetic basis of trait (phenotype) variation and local adaptation of loblolly and other pine trees would greatly benefit these activities. Large-scale genetic analyses have provided important information about the genetic architecture of economically and ecologically important traits, particularly in loblolly pine. In addition, the nuclear genome of the loblolly pine has been recently sequenced, providing the scaffold for future studies aimed at characterizing genomic variants responsible for phenotypic changes and for investigations on the evolution of the very large pine tree genomes. Despite the successful sequencing and assembly of this extremely large genome, as well as two spruce genomes, conifer genomics is still in its infancy. A better characterization of conifer genomes, and the understanding of molecular processes with genome-wide impact--including how genes and chromosomes changed through time and between species, and what this means for their current ability to live in different environments--represent fundamental goals advancing our understanding of conifer biology in the coming years.This research program will blend molecular and bioinformatics techniques to investigate these major areas of conifer genetics and genomics. In particular, I will develop and implement both molecular and computational approaches tailored for the study of the large pine tree genomes, to more easily identify the DNA changes between trees that are responsible for their changes in tolerance to drought and other harsh environmental conditions. In addition, these methods will allow to better predict the productivity of pine trees long before they reach the age when they become commercially profitable, thus assisting tree breeders in their effort to grow only trees with desired characteristics. These studies will also provide a framework to understand the genetic causes of the enormous size of conifer genomes.Several students and postdoctoral fellows will be trained and instructed in this program both in the classroom and in the lab, and many of them will have the opportunity to participate to research projects. Seminars for the general public will also be held to inform about the progresses in genomics and how this discipline can be applied to forest tree improvement programs.