Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice
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 short...
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doaj-26c7cb57b2c14444af83f8d4fbbc60ea2020-11-25T03:22:49ZengBMCPlant Methods1746-48112019-07-0115111110.1186/s13007-019-0464-2Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in riceJuan David Arbelaez0Erwin Tandayu1Maria Ymber Reveche2Annalhea Jarana3Petra van Rogen4Line Sandager5Patrik Stolt6Enghwa Ng7Rajeev K. Varshney8Tobias Kretzschmar9Joshua Cobb10International Rice Research InstituteInternational Rice Research InstituteInternational Rice Research InstituteInternational Rice Research InstituteIntertek - AgriTechIntertek - AgriTechIntertek - AgriTechInternational Rice Research InstituteInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Southern Cross Plant Science, Southern Cross UniversityInternational Rice Research InstituteAbstract 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.http://link.springer.com/article/10.1186/s13007-019-0464-2Seed DNA extractionSingle nucleotide polymorphism (SNP)Rice (Oryza sativa L.)Marker-assisted selection (MAS)Forward breedingBreeding |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Juan David Arbelaez Erwin Tandayu Maria Ymber Reveche Annalhea Jarana Petra van Rogen Line Sandager Patrik Stolt Enghwa Ng Rajeev K. Varshney Tobias Kretzschmar Joshua Cobb |
spellingShingle |
Juan David Arbelaez Erwin Tandayu Maria Ymber Reveche Annalhea Jarana Petra van Rogen Line Sandager Patrik Stolt Enghwa Ng Rajeev K. Varshney Tobias Kretzschmar Joshua Cobb Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice Plant Methods Seed DNA extraction Single nucleotide polymorphism (SNP) Rice (Oryza sativa L.) Marker-assisted selection (MAS) Forward breeding Breeding |
author_facet |
Juan David Arbelaez Erwin Tandayu Maria Ymber Reveche Annalhea Jarana Petra van Rogen Line Sandager Patrik Stolt Enghwa Ng Rajeev K. Varshney Tobias Kretzschmar Joshua Cobb |
author_sort |
Juan David Arbelaez |
title |
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
title_short |
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
title_full |
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
title_fullStr |
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
title_full_unstemmed |
Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
title_sort |
methodology: ssb-mass: a single seed-based sampling strategy for marker-assisted selection in rice |
publisher |
BMC |
series |
Plant Methods |
issn |
1746-4811 |
publishDate |
2019-07-01 |
description |
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 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. |
topic |
Seed DNA extraction Single nucleotide polymorphism (SNP) Rice (Oryza sativa L.) Marker-assisted selection (MAS) Forward breeding Breeding |
url |
http://link.springer.com/article/10.1186/s13007-019-0464-2 |
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