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

Juan David Arbelaez1, Erwin Tandayu1,2,3, Maria Ymber Reveche1

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A new single rice seed sampling method provides accurate DNA for marker-assisted selection, significantly reducing costs and accelerating breeding. This efficient strategy bypasses traditional leaf sampling bottlenecks for faster genetic gain in rice varieties.

Keywords:
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Area of Science:

  • Plant breeding and genetics
  • Molecular biology and genomics

Background:

  • Marker-assisted selection (MAS) and rapid line fixation accelerate genetic gain in breeding programs.
  • Seed sampling is a bottleneck in MAS, especially in rice where seed symmetry complicates automated methods.
  • Current leaf-based sampling is costly and inefficient for large-scale rice breeding operations.

Purpose of the Study:

  • To develop and validate a single rice seed sampling strategy for MAS.
  • To create a more efficient, cost-effective, and convenient alternative to leaf-based sampling.
  • To ensure the accuracy of MAS results is maintained with the new method.

Main Methods:

  • DNA extraction from single rice seeds.
  • Genotyping using Polymerase Chain Reaction (PCR) for trait markers.
  • Large-scale comparison of single seed versus leaf-based sampling methodologies.
  • Cost-benefit analysis of the new sampling strategy.

Main Results:

  • A single rice seed yields sufficient DNA (7-8 ng/μL) for multiple PCR assays.
  • DNA quantity and quality were consistent across different seed types and harvest times.
  • Single seed sampling achieved ~99% genotypic concordance with leaf-based methods and higher SNP call rates (99.24% vs. 97.5%).
  • The single seed strategy reduced sampling costs fourfold and allows early selection before field planting.

Conclusions:

  • A cost-effective and simple single seed genotyping strategy for rice MAS has been developed.
  • This method facilitates wider adoption of MAS, increasing favorable allele frequency and accelerating varietal development.
  • The strategy enhances the efficiency of parental selection and rapid generation advancement in rice breeding.