ena-STUDY-CSU-20-06-2013-04:06:35:978-57
Transcritome re-sequencing defines genetic variation between and within barley varieties.
Genetic variation within domesticated crop plant varieties is not usually well characterized or quantified.   Intra-varietal genetic variation may be important for crop performance under stress. Improved understanding of intra-varietal variation could allow the production of crop varieties with improved resilience to changing climate and rapidly evolving pests and diseases.  The genetic variation in two typical barley varieties was defined generating a large set of single nucleotide polymorphisms with known allele frequencies.  The transcriptomes of two barley varieties, Baudin and Gairdner, were deep sequenced and assembled into unigenes by reference mapping to the HarvEST barley database.  A large number of SNPs were identified, with more than 200, 000 apparent SNPs between reads for variety Baudin and reference EST sequences.  The genetic variation in both varieties was concentrated in < 27% of the unigenes assembled as 73.08% of the unigenes had no SNPs (SNP allele frequency > 0.1). Putatively significant SNPs (SNP minor allele frequency > 0.1) represented 9.65% and 14.64% of Baudin and Gairdner genetic variation.  Background genetic diversity (SNP allele frequency = 0.1, including both low frequency alleles and sequencing errors) accounted for 90.23% and 85.52% of apparent genetic variation in Baudin and Gairdner respectively.  A small percentage (2.24%) of the total unigenes had a very high SNP density ( > 10 SNPs per unigene).  The SNP dataset was further refined to produce a dataset of very high quality SNPs for varietal genotyping.  Genome-wide marker sets such as these, may become a valuable and complementary addition to the plant breeding toolbox uniquely aiding both selection and management of diversity within varieties.
Genetic variation within domesticated crop plant varieties is not usually well characterized or quantified.   Intra-varietal genetic variation may be important for crop performance under stress. Improved understanding of intra-varietal variation could allow the production of crop varieties with improved resilience to changing climate and rapidly evolving pests and diseases.  The genetic variation in two typical barley varieties was defined generating a large set of single nucleotide polymorphisms with known allele frequencies.  The transcriptomes of two barley varieties, Baudin and Gairdner, were deep sequenced and assembled into unigenes by reference mapping to the HarvEST barley database.  A large number of SNPs were identified, with more than 200, 000 apparent SNPs between reads for variety Baudin and reference EST sequences.  The genetic variation in both varieties was concentrated in < 27% of the unigenes assembled as 73.08% of the unigenes had no SNPs (SNP allele frequency > 0.1). Putatively significant SNPs (SNP minor allele frequency > 0.1) represented 9.65% and 14.64% of Baudin and Gairdner genetic variation.  Background genetic diversity (SNP allele frequency = 0.1, including both low frequency alleles and sequencing errors) accounted for 90.23% and 85.52% of apparent genetic variation in Baudin and Gairdner respectively.  A small percentage (2.24%) of the total unigenes had a very high SNP density ( > 10 SNPs per unigene).  The SNP dataset was further refined to produce a dataset of very high quality SNPs for varietal genotyping.  Genome-wide marker sets such as these, may become a valuable and complementary addition to the plant breeding toolbox uniquely aiding both selection and management of diversity within varieties.