Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice

Arbelaez, J D and Tandayu, E and Reveche, M Y and Jarana, A and van Rogen, P and Sandager, L and Stolt, P and Ng, E and Varshney, R K and Kretzschmar, T and Cobb, J (2019) Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice. Plant Methods (TSI), 15(1) (78). pp. 1-11. ISSN 1746-4811

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Background Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. Results Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. Conclusion This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.

Item Type: Article
Divisions: Research Program : Genetic Gains
Uncontrolled Keywords: Seed DNA extraction, Single nucleotide polymorphism (SNP), Rice (Oryza sativa L.), Marker-assisted selection (MAS), Forward breeding, Breeding, Genotyping, Rapid generation advancement
Subjects: Others > Molecular Biology
Others > Plant Breeding
Others > Rice
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 09 Sep 2019 11:30
Last Modified: 09 Sep 2019 11:30
Official URL:
Projects: Transformation of Rice Breeding in South Asia and Sub-Saharan Africa, High Throughput Genotyping Services
Funders: Bill and Melinda Gates Foundation
Acknowledgement: The authors are grateful to Dr. Jerome Bartholome for his invaluable comments and advise and to all members of the Genotyping Service Lab, and the Favorable Environments Breeding program, Eraño Ramos, Stephen Eunice Manansala, Krizzel Jessica Llantada, Vitaliano Lopena, Holden Verdeprado and Princess Lilia Dela Cruz at IRRI for their support during the development and testing of the single seed-based MAS strategy. Funding The Bill and Melinda Gates Foundation (OPP1194925) projects “Transformation of Rice Breeding in South Asia and Sub-Saharan Africa” (TRB OPP1076488) and “High Throughput Genotyping Services” (HTPG OPP1130244) sponsored and funded this work.
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