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

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

Research output: Contribution to journalArticle

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.
Original languageEnglish (US)
Article number78
JournalPlant Methods
Volume15
Issue number1
DOIs
StatePublished - Jul 24 2019
Externally publishedYes

Fingerprint

marker-assisted selection
Seeds
rice
seeds
Breeding
sampling
Costs and Cost Analysis
methodology
breeding
Gene Frequency
genotyping
gene frequency
Oryza
leaves
Cotyledon
DNA
cost benefit analysis
quantitative traits
Cost-Benefit Analysis
Single Nucleotide Polymorphism

Keywords

  • Seed DNA extraction
  • Single nucleotide polymorphism (SNP)
  • Rice (Oryza sativa L.)
  • Marker-assisted selection (MAS)
  • Forward breeding
  • Breeding
  • Genotyping
  • Rapid generation advancement

Cite this

Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice. / Arbelaez, Juan David; Tandayu, Erwin; Reveche, Maria Ymber; Jarana, Annalhea; Van Rogen, Petra; Sandager, Line; Stolt, Patrik; Ng, Enghwa; Varshney, Rajeev K.; Kretzschmar, Tobias; Cobb, Joshua.

In: Plant Methods, Vol. 15, No. 1, 78, 24.07.2019.

Research output: Contribution to journalArticle

Arbelaez, JD, Tandayu, E, Reveche, MY, Jarana, A, Van Rogen, P, Sandager, L, Stolt, P, Ng, E, Varshney, RK, Kretzschmar, T & Cobb, J 2019, 'Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice', Plant Methods, vol. 15, no. 1, 78. https://doi.org/10.1186/s13007-019-0464-2
Arbelaez, Juan David ; Tandayu, Erwin ; Reveche, Maria Ymber ; Jarana, Annalhea ; Van Rogen, Petra ; Sandager, Line ; Stolt, Patrik ; Ng, Enghwa ; Varshney, Rajeev K. ; Kretzschmar, Tobias ; Cobb, Joshua. / Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice. In: Plant Methods. 2019 ; Vol. 15, No. 1.
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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 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.",
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AU - Arbelaez, Juan David

AU - Tandayu, Erwin

AU - Reveche, Maria Ymber

AU - Jarana, Annalhea

AU - Van Rogen, Petra

AU - Sandager, Line

AU - Stolt, Patrik

AU - Ng, Enghwa

AU - Varshney, Rajeev K.

AU - Kretzschmar, Tobias

AU - Cobb, Joshua

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N2 - 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.

AB - 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.

KW - Seed DNA extraction

KW - Single nucleotide polymorphism (SNP)

KW - Rice (Oryza sativa L.)

KW - Marker-assisted selection (MAS)

KW - Forward breeding

KW - Breeding

KW - Genotyping

KW - Rapid generation advancement

U2 - 10.1186/s13007-019-0464-2

DO - 10.1186/s13007-019-0464-2

M3 - Article

VL - 15

JO - Plant Methods

JF - Plant Methods

SN - 1746-4811

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ER -