2013 Annual Report
1a.Objectives (from AD-416):
1)identify, genotype, and impute genetic markers in diverse Brassica napus accessions with non-reference and reference genome approaches;.
2)construct a sequence variant map for diverse Brassica napus;.
3)genotype and construct genetic linkage maps for recombinant inbred line populations; and.
4)conduct genome-wide association studies and linkage analysis of agronomic and biofuel traits in Brassica napus.
1b.Approach (from AD-416):
Genotyping-by-sequencing data collected on more than 1800 Brassica napus accessions and recombinant inbred lines from the USDA-ARS GRIN collection and ongoing ARS and academic breeding programs will be analyzed with computational biology approaches to simultaneously discover and genotype highly-dense genetic markers at genome-wide coverage, followed by the construction of sequence variant and genetic linkage maps. Statistical genetics approaches will be used to identify marker-trait associations for direct application in the development of breeding lines with improved oil production and quality for the hydrotreated renewable jet (HRJ) fuel industry.
Brassica napus is one of the most productive oilseed species, existing as either a winter or spring annual crop, with diverse oil compositions. To increase the economic return on investment in use of these crops as a source of biofuel, genetic improvement for oil yield and quality across diverse environments is needed. In that light, we are sequencing the genomes of a collection of 800 genetically diverse accessions (diversity panel) from the widest available germplasm worldwide to use as a resource for genetic improvement, and preparing materials for genetic and phenotypic analysis.
This research relates to objective 1 of the inhouse project, “Develop genotyping-by-sequencing methods for diverse cotton, oilseed, and industrial crop germplasm, and map genetic markers for economically and agronomically important traits in these crops". This project is associated with oilseed production, and builds upon our parent project by performing genome sequencing of, and molecular marker identification within, a large Brassica napus diversity panel.
Our collaborator at Cornell has made excellent progress in sequencing of all accessions in the diversity panel, completing a first pass Single nucleotide polymorphism (SNP) sequencing. Based on this data, our collaborator has been able to identify the most genetically diverse collection of Brassica napus, based on sequence. These lines are now being grown and Deoxyribonucleic acid (DNA) samples sent to KeyGene, Inc. to complete a full sequencing to identify haplotypes and for use in the imputation of sequence to the rest of the diversity panel.