Development of SSR Markers in Oilseed Crop Camelina sativa

Camelina sativa has been recognized to adapt well to a wide range of environment conditions including drought and low nutrient soils. The annual oilseed crop has advantage of higher oil content up to 45%, of which unsaturated α-linolenic acid (18:3) comprises about 35-45% of total fatty acid. It is important to understand the genome of the crop to improve its agricultural values, especially yield, oil content and lodging tolerance. Total RNA was extracted from tissues grown at well watered (2.2 kPa) soil, 10 kPa (3 days after drought treatment; DADT), 100 kPa (20 DADT), and rehydrated soil By using next generation sequencing technology, we obtained more than 275 K transcripts which are responsible for about 60,171 loci, corresponding to 4.58 transcripts per locus in the Camelina genic regions. Read mapping was conducted by using a Bowtie 2 software and an average mapping of those reads was found to be 93%. Simple sequence repeats were explored from the assembled transcripts and more than 37,000 microsatellites were identified. Among them, a majority (58%) is a di-nucleotide motif, followed by tri-nucleotide repeats (41%), and others (1%). Some amplification primers from the SSR motifs were designed and found to be successfully applied to identify hybrids from the mapping populations so that the polymorphic SSR loci will be used for QTL mapping to identify yield, oil content and lodging traits.