The Genomic Basis of Heterosis in High-Yielding Triploid Hybrids of Willow (Salix spp.) Bioenergy Crops
Investigators: Lawrence Smart and Christopher Town
Institutions: Cornell University, J. Craig Venter Institute
Non-Technical Summary: Yield improvement in many crops has been based on capturing hybrid vigor (aka heterosis), but even in well-studied species the complex genetic basis for hybrid vigor is poorly understood. Breeding for yield improvement in willow bioenergy crops has relied primarily on capturing hybrid vigor through interspecific hybridization, yet we know little about the genomic basis for heterosis in these hybrids, the best of which are triploids resulting from crosses of tetraploids with diploids. We will take advantage of the genome sequence of Salix purpurea being completed in our collaboration with JGI as a reference genome in asking how the gene expression patterns in willow hybrids are related to their yield potential and other traits important for biofuels production. In particular, we will learn if there is a bias in the expression of key genes from one parent versus the other in species hybrids, and whether there is a gene dosage effect skewing gene expression patterns in triploid progeny compared with their diploid and tetraploid parents.
Objectives: (1) Quantify hybrid vigor for yield and biomass traits across eight families representing intraspecific diploids and interspecific diploid and triploid progeny. (2) Determine which parental genome is responsible for the patterns of gene expression related to biomass production in intraspecific diploid and interspecific diploid and triploid hybrids. (3) Validate specific instances of biased patterns of gene expression in hybrids and triploids by methologically distinct, gene-specific methods. This project will leverage previous investments by DOE and other public funding in Salix genomic resources to gain a better understanding of the molecular basis for heterosis in outcrossing and polyploid species that can be applied broadly to the breeding of perennial bioenergy crops.
Approach: We will develop eight families with 100 progeny each through controlled pollination and establish replicated field trials to determine the extent of heterosis by hybrid type through rigorous phenotyping for yield and biomass composition. We will utilize next-generation transcriptomics (RNA-seq) to study relative levels of gene expression and allele-specific expression. We will correlate these expression data with phenotypic characterization of heterosis for yield and biomass composition determined in replicated field trials with these eight families. We will look for networks of coordinated gene regulation controlling yield and lignocellulosic deposition. For approximately 350–400 genes identified as displaying non-additive or allele biased expression in RNA-seq data, we will validate the allele-specific patterns of expression in gene-specific, quantitative Sequenom assays. We will analyze allele-specific expression in the three highest and three lowest yielding progeny relative to the parents of each family to determine if there is a correlation between leaf and stem gene expression patterns and heterosis for yield traits.
Name: Larry Smart