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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #333856

Research Project: Development and Application of Genetic, Genomic, and Bioinformatic Resources in Maize

Location: Plant, Soil and Nutrition Research

Title: Genome-wide association for plant height and flowering time across 15 tropical maize populations under managed drought stress and well-watered conditions in sub-Saharan Africa

Author
item WALLACE, JASON - CORNELL UNIVERSITY - NEW YORK
item ZHANG, XUECAI - INTERNATIONAL MAIZE & WHEAT IMPROVEMENT CENTER (CIMMYT)
item BEYENE, YOSEPH - INTERNATIONAL MAIZE & WHEAT IMPROVEMENT CENTER (CIMMYT)
item SEMAGN, KASSA - UNIVERSITY OF ALBERTA
item OLSEN, MICHAEL - INTERNATIONAL MAIZE & WHEAT IMPROVEMENT CENTER (CIMMYT)
item PRASANNA, BODDUPALLI - INTERNATIONAL MAIZE & WHEAT IMPROVEMENT CENTER (CIMMYT)
item Buckler, Edward - Ed

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/6/2016
Publication Date: 7/28/2016
Citation: Wallace, J., Zhang, X., Beyene, Y., Semagn, K., Olsen, M., Prasanna, B., Buckler IV, E.S. 2016. Genome-wide association for plant height and flowering time across 15 tropical maize populations under managed drought stress and well-watered conditions in sub-Saharan Africa. Crop Science. 56:2365.

Interpretive Summary: Developing crops that can deal with drought is one of the major challenges that plant breeding faces in this century of rapidly changing climate. This study develops statistical and genomic methods for combining maize drought studies coming from 15 different families of maize that were adapted to African environments. The study identified several hundred genetic variants that are associated with plant height and flowering under various drought stresses. These results can be used going forward to enhance breeding efforts for drought in Sub-Saharan Africa. However, as breeding and genomics continues to generate large diverse datasets, this study provides a model to combine data from diverse families and field trials.

Technical Abstract: Genotyping breeding materials is now relatively inexpensive but phenotyping costs have remained the same. One method to increase gene mapping power is to use genome-wide genetic markers to combine existing phenotype data for multiple populations into a unified analysis. We combined data from 15 biparental populations of maize (Zea mays L.) (>2500 individual lines) developed under the Water-Efficient Maize for Africa project to perform genome-wide association analysis. Each population was phenotyped in multilocation trials under water-stressed and well-watered environments and genotyped via genotyping-by-sequencing. We focused on flowering time and plant height and identified clear associations between known genomic regions and the traits of interest. Out of ~380,000 single-nucleotide polymorphisms (SNPs), we found 115 and 108 that were robustly associated with flowering time under well-watered and drought stress conditions, respectively, and 143 and 120 SNPs, respectively, associated with plant height. These SNPs explained 36 to 80% of the genetic variance, with higher accuracy under well-watered conditions. The same set of SNPs had phenotypic prediction accuracies equivalent to genome-wide SNPs and were significantly better than an equivalent number of random SNPs, indicating that they captured most of the genetic variation for these phenotypes. These methods could potentially aid breeding efforts for maize in Sub-Saharan Africa and elsewhere. The methods will also help in mapping drought tolerance and related traits in this germplasm. We expect that analyses combining data across multiple populations will become more common and we call for the development of algorithms and software to enable routine analyses of this nature.