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Capturing pair-wise epistatic effects associated with three agronomic traits in barley

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Abstract

Genetic association mapping has been widely applied to determine genetic markers favorably associated with a trait of interest and provide information for marker-assisted selection. Many association mapping studies commonly focus on main effects due to intolerable computing intensity. This study aims to select several sets of DNA markers with potential epistasis to maximize genetic variations of some key agronomic traits in barley. By doing so, we integrated a MDR (multifactor dimensionality reduction) method with a forward variable selection approach. This integrated approach was used to determine single nucleotide polymorphism pairs with epistasis effects associated with three agronomic traits: heading date, plant height, and grain yield in barley from the barley Coordinated Agricultural Project. Our results showed that four, seven, and five SNP pairs accounted for 51.06, 45.66 and 40.42% for heading date, plant height, and grain yield, respectively with epistasis being considered, while corresponding contributions to these three traits were 45.32, 31.39, 31.31%, respectively without epistasis being included. The results suggested that epistasis model was more effective than non-epistasis model in this study and can be more preferred for other applications.

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Acknowledgements

The author of this research paper wants to express our gratitude to those scientists who helped phenotype and genotypes these barley cultivars and prepare the data for public use. This study was partially supported by USDA-NIFA Hatch Project (1005459), South Dakota State University Research Scholarship Support Fund, and the Agricultural Experiment Station at South Dakota State University.

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  1. Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Box 2140C, Brookings, SD, 57007, USA

    Yi Xu & Jixiang Wu

  2. Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA

    Yajun Wu

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  1. Yi Xu
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Xu, Y., Wu, Y. & Wu, J. Capturing pair-wise epistatic effects associated with three agronomic traits in barley. Genetica 146, 161–170 (2018). https://doi.org/10.1007/s10709-018-0008-0

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