Theoretical and Applied Genetics

, Volume 126, Issue 3, pp 693–710 | Cite as

Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping

  • Gregory L. BergerEmail author
  • Shuyu Liu
  • Marla D. Hall
  • Wynse S. Brooks
  • Shiaoman Chao
  • Gary J. Muehlbauer
  • B.-K. Baik
  • Brian Steffenson
  • Carl A. Griffey
Original Paper


Genome-wide association studies (GWAS) provide an opportunity to examine the genetic architecture of quantitatively inherited traits in breeding populations. The objectives of this study were to use GWAS to identify chromosome regions governing traits of importance in six-rowed winter barley (Hordeum vulgare L.) germplasm and to identify single-nucleotide polymorphisms (SNPs) markers that can be implemented in a marker-assisted breeding program. Advanced hulled and hulless lines (329 total) were screened using 3,072 SNPs as a part of the US. Barley Coordinated Agricultural Project (CAP). Phenotypic data collected over 4 years for agronomic and food quality traits and resistance to leaf rust (caused by Puccinia hordei G. Otth), powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal], net blotch (caused by Pyrenophora teres), and spot blotch [caused by Cochliobolus sativus (Ito and Kuribayashi) Drechsler ex Dastur] were analyzed with SNP genotypic data in a GWAS to determine marker-trait associations. Significant SNPs associated with previously described quantitative trait loci (QTL) or genes were identified for heading date on chromosome 3H, test weight on 2H, yield on 7H, grain protein on 5H, polyphenol oxidase activity on 2H and resistance to leaf rust on 2H and 3H, powdery mildew on 1H, 2H and 4H, net blotch on 5H, and spot blotch on 7H. Novel QTL also were identified for agronomic, quality, and disease resistance traits. These SNP-trait associations provide the opportunity to directly select for QTL contributing to multiple traits in breeding programs.


Quantitative Trait Locus Powdery Mildew Leaf Rust Test Weight Powdery Mildew Resistance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This study was supported with funding provided by the Virginia Small Grains Board, the Maryland Grain Producers Utilization Board, and the Kentucky Small Grains Grower Association. This material is based on work supported by USDA-CSREES-NRI Grant no. 2006-55606-16722 and USDA-NIFA Grant no. 2009-85606-05701, “Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement”, and Specific Cooperative Agreement (58-6645-0-108). Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the authors and do not necessarily reflect the view of the US Department of Agriculture.

Supplementary material

122_2012_2011_MOESM1_ESM.docx (13 kb)
Supplementary material 1 (DOCX 13 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Gregory L. Berger
    • 1
    Email author
  • Shuyu Liu
    • 2
  • Marla D. Hall
    • 3
  • Wynse S. Brooks
    • 1
  • Shiaoman Chao
    • 4
  • Gary J. Muehlbauer
    • 5
  • B.-K. Baik
    • 6
  • Brian Steffenson
    • 7
  • Carl A. Griffey
    • 1
  1. 1.Crop and Soil Environmental SciencesVirginia TechBlacksburgUSA
  2. 2.Texas AgriLife ResearchTexas A&M UniversityAmarilloUSA
  3. 3.Limagrain Cereal SeedsWichitaUSA
  4. 4.USDA-ARS Biosciences Research LabFargoUSA
  5. 5.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA
  6. 6.Department of Soil and Crop ScienceWashington State UniversityPullmanUSA
  7. 7.Department of Plant PathologyUniversity of MinnesotaSt. PaulUSA

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