A targeted genotyping-by-sequencing tool (Rapture) for genomics-assisted breeding in oat
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We adapted and tested a Rapture assay as an enhancement of genotyping-by-sequencing (GBS) in oat (Avena sativa). This assay was based on an additional bait-based capture of specific DNA fragments representing approximately 10,000 loci within the enzyme-based complexity reduction provided by GBS. By increasing the specificity of GBS to include only those fragments that provided effective polymorphic markers, it was possible to achieve deeper sequence coverage of target markers, while simultaneously sequencing a greater number of samples on a single unit of next-generation sequencing. The Rapture assay consistently out-performed the GBS assay when filtering markers at 80% completeness or greater, even though the total number of reads per sample was only 25% that of GBS. The reduced sequencing cost per sample for Rapture more than compensated for the increased cost of the capture reaction. Thus, Rapture generated a more repeatable set of marker data at a cost per sample that was approximately 40% less than GBS. Additional advantages of Rapture included accurate identification of heterozygotes, and the possibility to increase the depth or length of sequence reads with less impact on the cost per sample. We tested Rapture for genomic selection and diversity analysis and concluded that it is an effective alternative to GBS or other SNP assays. We recommend the use of Rapture in oat and the development of similar assays in other crops with large complex genomes.
The authors gratefully acknowledge professional assistance from Matthew Hayes, Brad De Haan, Denis Green, Kali Stewart, Julie Chapados, Kasia Dadej, and Wayne McCormick, as well as useful discussions and input from Charlene Wight, Alireza Nakhforoosh, and Shiaoman Chao. This work was funded as part of the ‘Oat Project’ through the Agriculture and Agri-Food Canada AgriScience Program, with matching industry support from the Canadian Field Crop Research Alliance (CFCRA).
Author contribution statement
WAB, AI and NAT performed data analysis and wrote the manuscript; BB suggested the Rapture technique and advised on its development; AI and BB performed laboratory analyses; WY and JMF provided biological materials and advised on data interpretation. All authors edited and approved the final manuscript.
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
- Boudhrioua C, Bastien M, Légaré G, Pomerleau S, St-Cyr J, Boyle B, Belzile F (2017) Genotyping-by-sequencing in potato. In: Kumar Chakrabarti S, Xie C, Kumar Tiwari J (eds) The potato genome. Springer, ChamGoogle Scholar
- Chaffin AS, Huang Y-F, Smith S, Bekele WA, Babiker E, Gnanesh BN, Foresman BJ, Blanchard SG, Jay JJ, Reid RW, Wight CP, Chao S, Oliver R, Islamovic E, Kolb FL, McCartney C, Mitchell Fetch JW, Beattie AD, Bjørnstad Å, Bonman JM, Langdon T, Howarth CJ, Brouwer CR, Jellen EN, Esvelt Klos K, Poland JA, Hseih T-F, Brown R, Jackson E, Schlueter JA, Tinker NA (2016) A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement. Plant Genome. https://doi.org/10.3835/plantgenome2015.10.0102 CrossRefPubMedGoogle Scholar
- Dorant Y, Benestan L, Normandeau E, Boyle B, Rochette R, Bernatchez L (2019) Comparing Pool-seq, Rapture and GBS genotyping for inferring population structure; the American lobster (Homarus americanus) as a case study. Ecol Evolut 9(11):6606–6623Google Scholar
- Esvelt Klos K, Huang Y-F, Bekele WA, Obert DE, Babiker E, Beattie AD, Bjørnstad Å, Bonman JM, Carson ML, Chao S, Gnanesh BN, Griffiths I, Harrison SA, Howarth CJ, Hu G, Ibrahim A, Islamovic E, Jackson E, Jannink JL, Kolb FL, McMullen MS, Mitchell Fetch JW, Murphy JP, Ohm HW, Rines HW, Rossnagel BG, Schlueter JA, Sorrells ME, Wight CP, Yan W, Tinker NA (2016) Population genomics related to adaptation in elite oat germplasm. Plant Genome 9:2CrossRefGoogle Scholar
- Money D, Gardner K, Migicovsky Z, Schwaninger H, Zhong G-Y, Myles S (2015) LinkImpute: fast and accurate genotype imputation for nonmodel organisms. G3 Genes Genomes Genet 5:2383–2390Google Scholar
- Norman A, Taylor J, Edwards J, Kuchel H (2018) Optimising genomic selection in wheat: effect of marker density, population size and population structure on prediction accuracy. G3 Genes Genomes Genet 8:2889–2899Google Scholar
- Perrier X, Jacquemoud-Collet JP (2006) DARwin software http://darwin.cirad.fr/darwin. Accessed 2 Dec 2019
- R Core Team (2018) R: a language and environment for statistical computing. https://www.r-project.org/about.html. Accessed 2 Dec 2019
- Sunstrum FG, Bekele WA, Wight CP, Yan W, Chen Y, Tinker NA (2019) A genetic linkage map in southern-by-spring oat identifies multiple QTLs for adaptation and rust resistance. Plant Breed 138:82–94Google Scholar
- Tinker NA, Bekele WA, Hattori J (2016) Haplotag: software for haplotype-based genotyping-by-sequencing analysis. G3 Genes Genomes Genet 6:857–863Google Scholar
- Yan H, Bekele WA, Wight CP, Peng Y, Langdon T, Latta RG, Fu Y-B, Diederichsen A, Howarth CJ, Jellen EN, Boyle B, Wei Y, Tinker NA (2016) High-density marker profiling confirms ancestral genomes of Avena species and identifies d-genome chromosomes of hexaploid oat. Theor Appl Genet 129:2133–2149CrossRefGoogle Scholar