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Developing core marker sets for effective genomic-assisted selection in wheat and barley breeding programs.

Goro Ishikawa1, Hiroaki Sakai2, Nobuyuki Mizuno1

  • 1Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.

Breeding Science
|November 21, 2022
PubMed
Summary

Researchers developed core marker sets for barley and wheat to accelerate crop breeding. These sets effectively capture genetic diversity, improving genomic selection accuracy and enabling cost-effective advancements in plant breeding.

Keywords:
barleybreedinggenotyping platformnext-generation sequencingwheat

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Area of Science:

  • Agricultural Science
  • Genetics
  • Plant Breeding

Background:

  • Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are vital temperate crops.
  • Genomic-assisted selection (GAS) requires efficient marker sets for effective breeding.

Purpose of the Study:

  • To develop and validate core marker sets for genomic-assisted selection in barley and wheat.
  • To assess the utility of these core sets for capturing genomic polymorphisms and predicting trait values.

Main Methods:

  • Selection of core marker sets (768 for barley, 960 for wheat) from genome-wide amplicon sequencing markers.
  • Evaluation of marker distribution, minor allele frequency, and polymorphism capture across diverse accessions.
  • Assessment of trait value predictability using fivefold cross-validation.

Main Results:

  • Core marker sets effectively capture polymorphisms across the entire genomes of barley and wheat.
  • Prediction accuracies for six barley traits averaged 0.62 (range 0.56-0.74).
  • Prediction accuracies for eight wheat traits averaged 0.65 (range 0.44-0.83).

Conclusions:

  • Established core marker sets accelerate crop breeding in a cost-effective manner.
  • These sets provide a strong foundation for genomic selection research in temperate crops.
  • The marker sets are applicable to advanced breeding materials with high relatedness.