Association Mapping and Nucleotide Sequence Variation in Five Drought Tolerance Candidate Genes in Spring Wheat

Functional markers are needed for key genes involved in drought tolerance to improve selection for crop yield under moisture stress conditions. The objectives of this study were to (i) characterize five drought tolerance candidate genes, namely dehydration responsive element binding 1A (DREB1A), enhanced response to abscisic acid (ERA1-B and ERA1-D), and fructan 1-exohydrolase (1-FEH-A and 1-FEH-B), in wheat (Triticum aestivum L.) for nucleotide and haplotype diversity, Tajima’s D value, and linkage disequilibrium (LD) and (ii) associate withingene single nucleotide polymorphisms (SNPs) with phenotypic traits in a spring wheat association mapping panel (n = 126). Field trials were grown under contrasting moisture regimes in Greeley, CO, and Melkassa, Ethiopia, in 2010 and 2011. Genome-specific amplification and DNA sequence analysis of the genes identified SNPs and revealed differences in nucleotide and haplotype diversity, Tajima’s D, and patterns of LD. DREB1A showed associations (false discovery rate adjusted probability value = 0.1) with normalized difference vegetation index, heading date, biomass, and spikelet number. Both ERA1-A and ERA1-B were associated with harvest index, flag leaf width, and leaf senescence. 1-FEH-A was associated with grain yield, and 1-FEH-B was associated with thousand kernel weight and test weight. If validated in relevant genetic backgrounds, the identified marker–trait associations may be applied to functional marker-assisted selection. D tolerance is a complex trait that involves the expression of many genes. A better understanding of the roles and relative importance of those genes would aid the development of drought tolerant crop cultivars. A drought tolerance candidate gene is a DNA sequence that co-maps with a drought tolerance quantitative trait locus (QTL) and encodes a protein that can be functionally associated with the stress response or adaptation process (Cattivelli et al., 2008). In plants, the construction of molecular linkage maps based on candidate genes is one way of identifying the genes underlying QTL instead of time-consuming fine mapping. This candidate gene strategy shows promise for bridging the gap between quantitative genetic and molecular genetic approaches to study complex traits such as drought tolerance. Candidate gene association mapping is aimed at linking phenotypic variation with polymorphic sites in candidate genes to identify causative polymorphisms (Martinez-Gonzalez et al., 2008). Drought stress induces a large number of genes that have been identified and characterized for their function (Shinozaki and Yamaguchi-Shinozaki, 2007). There are two categories of genes in terms of response to the phytohormone abscisic acid (ABA): ABA-independent and ABA-dependent. For example, ABA-independent dehydration responsive element binding (DREB) genes are Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.04.0010 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. E.A. Edae, P.F. Byrne, H. Manmathan, S.D. Haley, and M. Moragues, Dep. of Soil and Crop Sciences, Colorado State Univ., Fort Collins, CO 80523; M.S. Lopes and M.P. Reynolds, CIMMYT, Int., Apdo. Postal 6-641, 06600 Mexico, DF, Mexico. Received 22 Apr. 2013. *Corresponding author ([email protected]). Abbreviations: 1-FEH, fructan 1-exohydrolase; ABA, abscisic acid; DArT, Diversity Array Technology; dNTP, deoxyribonucleotide triphosphate; DREB, dehydration responsive element binding; ERA1, enhanced response to abscisic acid; h2, broad-sense heritability; LD, linkage disequilibrium; MAF, minor allele frequency; NDVI, normalized difference vegetation index; PCR, polymerase chain reaction; π, nucleotide diversity; QTL, quantitative trait locus or loci; SNP, single nucleotide polymorphism; q, diversity parameter.