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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice
Plant Methods, Vol.15(1), pp.1-11
24/07/2019
PMCID: PMC6652012
PMID: 31367224
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Abstract
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 geno-typing 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 (F 6) 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.
Details
- Title
- Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice
- Creators
- Juan David Arbelaez - International Rice Research InstituteErwin Tandayu - International Rice Research InstituteMaria Ymber Reveche - International Rice Research InstituteAnnalhea Jarana - International Rice Research InstitutePetra van Rogen - IntertekLine Sandager - IntertekPatrik Stolt - IntertekEnghwa Ng - International Rice Research InstituteRajeev K Varshney - International Crops Research Institute for the Semi-Arid TropicsTobias Kretzschmar - Southern Cross UniversityJoshua Cobb - International Rice Research Institute
- Publication Details
- Plant Methods, Vol.15(1), pp.1-11
- Publisher
- BioMed Central Ltd.; London
- Grant note
- 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.
- Identifiers
- 991012925555202368
- Copyright
- © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Academic Unit
- Faculty of Science and Engineering; School of Environment, Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article