- Poster presentation
- Open Access
Genome-wide SNP discovery from a pooled sample of accessions of the biofuel plant Jatropha curcasbased on whole-transcriptome Illumina resequencing
© Silva-Junior et al; licensee BioMed Central Ltd. 2011
- Published: 13 September 2011
- Genomic Selection
- Draft Genome Sequence
- Amplification Bias
- Predict Gene Model
- Illumina GAIIx
Jatropha curcas(JC) is an oil-rich, drought-tolerant perennial shrub of the Euphorbiaceae family widely dispersed throughout the world. Thought to be native to Central America, it has been the object of an increasing number of studies in recent years for it exhibits a number of appealing attributes as a promising source of biodiesel. Although its undomesticated nature and preferential outcrossed mating system would suggest a high degree of genetic variation to be exploited in breeding, studies have shown limited genetic diversity in the existing germplasm collections . In spite of the increased interest in this bioenergy plant, challenges still exist to turn this species into a genuine crop and improved varieties that consolidate desirable traits are not yet available, making JC large scale plantation an uncertain business . Genomic studies to potentially assist JC breeding efforts have started in the last few years. JC is diploid (2n=22), with a haploid genome size estimated at 416 Mbp . EST databases focusing on gene discovery were constructed and a draft genome sequence was recently published covering 285 Mbp (~68%) of the genome in 120,586 contigs with 40,929 predicted gene models . The focus of our work with JC is to provide effective tools to accelerate breeding through Genomic Selection (GS)  and to help assess the levels, organization and enrichment strategies of genetic diversity in germplasm banks and breeding populations. To this end we have started the development of SNP markers. Available EST databases built from single individual plants do not provide the necessary sequence diversity for SNP discovery.In this work we report on the discovery of a set of SNPs for JC derived from a pool of genetically diverse accessions using Illumina sequencing and a SNP selection pipeline recently described .
Genetic diversity data was used to select twelve JC accessions that maximized genetic diversity out of a germplasm collection currently serving as the foundation of a breeding program . Total RNA of young expanding leaves was extracted from each individual plant and a pool of equimolar quantities of RNA was prepared. Two Illumina GAIIx single end lanes were sequenced following standard protocols. Raw reads were processed and aligned on the mapped reference genome using GSNAP . GATK Unified Genotyper  was used to estimate the allele frequency in the pooled samples and to provide an accurate posterior probability of there being a segregating variant allele at each locus using a Bayesian genotype likelihood model. SNPs were then specifically selected to design Illumina Golden Gate Genotyping Technology (GGGT) assays based on an in silico estimated minor allele frequency MAF >0.10 and at least 60 bases available on each SNP flank with no additional SNPs following a procedure described earlier .
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