Ries, David; Holtgräwe, Daniela; Viehöver, Prisca; Weisshaar, Bernd: Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels. In: BMC Genomics. Jg.17 H. 1. 2016
Inhalt
- Results and discussion
- Improvement of InDel detection
- Improvement of variant calling and variant filtering
- Identification of a 31 kbp interval containing the RED gene
- Identification of the causal gene from three genes in the interval
- The number of accessions used has a high influence on mapping resolution
- About 30 fold coverage is sufficient for interval detection
- Conclusions
- Methods
- Selection of plant material
- Plant growth and DNA isolation
- Library preparation and sequencing
- Generation of a reference sequence with pseudo-chromosomes
- Postprocessing and mapping of reads from pools
- InDel realignment
- Base Quality Score Recalibration
- Variation calling
- Calculation of allele frequencies
- Generation of an error file for the reference genotype
- Interval identification and prediction of causal variations
- Calculation of mean allele frequencies for single breeding panel pools
- Comparison of mapping resolution from 360 versus 120 accessions
- Generation and comparison of reduced coverage data subsets
- Availability of supporting data
- Additional files
- Abbreviations
- Competing interests
- Authors’ contributions
- Acknowledgements
- References