Comparative genomics of conifers
1) Evolution of new genes in conifers
Comparative analyses of conifer genomes have shown that a large fraction of genes in these species have no detectable homologs in angiosperms or other eukaryotes. While the origin of these conifer-specific genes is still largely unexplained, there are several known mechanisms that could have contributed to generating new genes in this group of plants. My group is developing computational tools to determine the possible role of gene duplication and other processes in the emergence of lineage-specific genes in conifers. We are also interested in determining if, similarly to the nucleotide substitution rate, conifers also experience a much lower frequency of gene duplications and gene losses compared to flowering plants.
2) Genome size evolution
With C-values between 4 and 36 Gb, conifer genomes are consistently larger than most other eukaryotic groups, including angiosperms. The confer tolerance towards transposable elements (TEs) amplification and retention appear to be the key mechanisms leading to genome gigantism in these trees. We are interested in determining the evolutionary dynamics of several TE groups to understand their contribution to genome size evolution in conifers. We are also studying how horizontal transfer of TEs from non-conifer species contributed to the genome evolution in pine trees and spruces. Finally, we are investigating the possible role of TE sequencing in gene expression regulation.
Improving genome assembly in pine trees
Improving assembling strategies for large genomes using single-chromosome capture and sequencing in loblolly pine and other conifers.
The very large and highly repetitive pine tree genomes represent a challenge to current sequencing technologies and assembly strategies. This reflects in a relatively low quality of conifer assemblies compared to most other plant genomes, and the lack of mapped reference sequencing onto chromosomes. To overcome these limitations, we are developing single-chromosome capture, sequencing and assembly strategies in collaboration with the Forest Science Laboratory here in College Station, with the support of a USDA-AgriLife joint venture agreement fund.
Genetic basis of drought tolerance in loblolly pine
In East Texas, nearly 12.1 million acres are occupied by forestland, largely represented by loblolly pine, with a major impact on the regional economy and ecology. Climate projections for the years 2021-2065 show that mean annual temperatures, warm and dry spells and the number of days/year with a minimum temperature above 20°C will increase in East Texas, whereas precipitation will decrease in this region (Sun et al., 2015). Most plants exhibit population variation in drought tolerance mainly a consequence of local adaptation to different climates. By studying loblolly pine tree clones with different tolerance to drought we aim to identify genes and genetic networks involved in drought tolerance, particularly in needle and root tissues of young seedlings grown in our Department’s green house. We are currently analyzing transcriptome (RNA-seq) data generated in collaboration with other labs in our Department.
Genotyping, adaptation and breeding programs in loblolly pine
1) Gene copy-number variants (CNVs) in loblolly pines
Many genes in a genome can be present in 0,1 or >1 copies in different individuals of a given population or species. Variations in the number of copies of these genes are called copy-number variants or CNVs. In plants, hundreds to thousands of CNVs have been discovered, with at least some of these CNVs involved in important traits such as disease resistance and adaptation to harsh environmental conditions. We are working on genomic tools that will enable us to identify CNVs in pine trees and determine possible associations between CNVs and phenotypic variation.
2) Loblolly pine genotyping and genome-wide selection
Loblolly pine (Pinus taeda L.) represents the principal commercial forest species in the Southeastern United States, due to its abundance, rapid juvenile growth, and pulpwood and lumber value. Almost three-fourths of all tree species seedlings planted each year in the U.S. are Pinus taeda, and virtually all those planted seedlings are genetically-improved developed by cooperative tree breeding programs. Because of its widespread distribution, loblolly pine also plays a fundamental ecological role in the forest landscape from Texas to Virginia. The management, conservation, and commercial improvement of this pine species are therefore key priorities for forest tree scientists. Understanding the genetic basis of phenotypic variation and local adaptation in loblolly pine would greatly benefit these activities. Large-scale genotyping efforts have provided important information about the genetic architecture of economically and ecologically important traits in Pinus taeda; our objective is to make high-throughput genotyping techniques more cost-effective and efficient through increased multiplexing and broader genome coverage while maintaining data quality and reproducibility in the large, highly repetitive loblolly pine genome.