Targeted Next-Generation Sequencing Identification of Mutations in Disease Resistance Gene Analogs (RGAs) in Wild and Cultivated Beets
Open Access
- 11 October 2017
- Vol. 8 (10), 264
- https://doi.org/10.3390/genes8100264
Abstract
Resistance gene analogs (RGAs) were searched bioinformatically in the sugar beet (Beta vulgaris L.) genome as potential candidates for improving resistance against different diseases. In the present study, Ion Torrent sequencing technology was used to identify mutations in 21 RGAs. The DNA samples of ninety-six individuals from six sea beets (Beta vulgaris L. subsp. maritima) and six sugar beet pollinators (eight individuals each) were used for the discovery of single-nucleotide polymorphisms (SNPs). Target amplicons of about 200 bp in length were designed with the Ion AmpliSeq Designer system in order to cover the DNA sequences of the RGAs. The number of SNPs ranged from 0 in four individuals to 278 in the pollinator R740 (which is resistant to rhizomania infection). Among different groups of beets, cytoplasmic male sterile lines had the highest number of SNPs (132) whereas the lowest number of SNPs belonged to O-types (95). The principal coordinates analysis (PCoA) showed that the polymorphisms inside the gene Bv8_184910_pkon (including the CCCTCC sequence) can effectively differentiate wild from cultivated beets, pointing at a possible mutation associated to rhizomania resistance that originated directly from cultivated beets. This is unlike other resistance sources that are introgressed from wild beets. This gene belongs to the receptor-like kinase (RLK) class of RGAs, and is associated to a hypothetical protein. In conclusion, this first report of using Ion Torrent sequencing technology in beet germplasm suggests that the identified sequence CCCTCC can be used in marker-assisted programs to differentiate wild from domestic beets and to identify other unknown disease resistance genes in beet.This publication has 31 references indexed in Scilit:
- Comparison of Next-Generation Sequencing SystemsJournal of Biomedicine and Biotechnology, 2012
- A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencersBMC Genomics, 2012
- Phytozome: a comparative platform for green plant genomicsNucleic Acids Research, 2011
- Sequencing technologies — the next generationNature Reviews Genetics, 2009
- Beet mild yellowing virus resistance derived from wild and cultivated Beta germplasmPlant Breeding, 2008
- Recent Progress in Elucidating the Structure, Function and Evolution of Disease Resistance Genes in PlantsJournal of Genetics and Genomics, 2007
- Clustal W and Clustal X version 2.0Bioinformatics, 2007
- GenABEL: an R library for genome-wide association analysisBioinformatics, 2007
- Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgarisL.)Genome, 2003
- The Bagplot: A Bivariate BoxplotThe American Statistician, 1999