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Title: Quantitative trait loci mapping for spike characteristics using a genetic map with array-based and genotyping-by-sequencing (GBS) SNP markers in hexaploid wheat

Author
item ZHOU, YAOPENG - University Of Maryland
item CONWAY, BENJAMIN - Colorad0 State University
item MILLER, DANIELA - University Of Maryland
item Marshall, David
item COOPER, AARON - University Of Maryland
item MURPHY, J - North Carolina State University
item Chao, Shiaoman
item Brown-Guedira, Gina
item Costa, Jose

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2016
Publication Date: 7/1/2017
Citation: Zhou, Y., Conway, B., Miller, D., Marshall, D.S., Cooper, A., Murphy, J.P., Chao, S., Brown Guedira, G.L., Costa, J. 2017. Quantitative trait loci mapping for spike characteristics using a genetic map with array-based and genotyping-by-sequencing (GBS) SNP markers in hexaploid wheat. The Plant Genome. https://doi:10.3835/plantgenome2016.10.0101.
DOI: https://doi.org/10.3835/plantgenome2016.10.0101

Interpretive Summary: This research generated a genetic map that will help identify visual characteristics of wheat. It is important to understand the genetics of how visual characteristics are inherited, and this research examines the type of heritability in wheat. The most important location for these traits can be found at just three locations on the wheat chromosomes. These results provide valuable information for manipulating spike morphology for breeding purposes.

Technical Abstract: Wheat spike characteristics determine the number of grains produced on each spike and constitute key components of grain yield. However, understanding of the genetic basis of spike characteristics in wheat is limited. In this study, genotyping-by-sequencing (GBS) and iSelect 9K assay were used on a doubled haploid (DH) soft red winter wheat population that showed a wide range of phenotypic variation for spike traits. The constructed genetic map spanned 2934.1 cM with an average interval length of 3.4 cM. Quantitative trait loci (QTL) analysis involving additive effects, epistasis (QQ) and QTL-by-environment (QE) and epistasis-by-environment (QQE) interactions detected a total of 109 QTLs, 13 QE, and 20 QQ interactions in five environments. Spike characteristics were mainly determined by additive effects and were fine-tuned by QQ, QE, and QQE. Major QTL QSl.cz-1A/QFsn.cz-1A explained up to 30.9% of the phenotypic variation for spike length and fertile spikelet number, QGsp.cz-2B.1 explained up to 15.6% of the phenotypic variation of grain number per spikelet, and QSc.cz-5A.3 explained up to 80.2% of the phenotypic variation for spike compactness. Additionally, QTLs for correlated spike characteristics formed QTL clusters on chromosomes 1A, 5A, 2B, 3B, 5B, 1D, and 5D. This study expands the understanding of the genetic basis of spike characteristics in hexaploid wheat. A number of stable QTLs detected in this study have potential to be used in marker-assisted selection. Additionally, the genetic map generated in this study could be used to study other traits of economic importance.