Association Mapping for Enhancing Maize (Zea mays L.) Genetic Improvement

Association mapping through linkage disequilibrium (LD) analysis is a powerful tool for the dissection of complex agronomic traits and for the identifi cation of alleles that can contribute to the enhancement of a target trait. With the developments of high throughput genotyping techniques and advanced statistical approaches as well as the assembling and characterization of multiple association mapping panels, maize has become the model crop for association analysis. In this paper, we summarize progress in maize association mapping and the impacts of genetic diversity, rate of LD decay, population size, and population structure. We also review the use of candidate genes and gene-based markers in maize association mapping studies that has generated particularly promising results. In addition, we examine recent developments in genome-wide genotyping techniques that promise to improve the power of association mapping and signifi cantly refi ne our understanding of the genetic architecture of complex quantitative traits. The new challenges and opportunities associated with genome-wide analysis studies are discussed. In conclusion, we review the current and future impacts of association mapping on maize improvement along with the potential benefi ts for poor people in developing countries who are dependent on this crop for their food security and livelihoods. J. Yan, National Maize Improvement Center of China, China Agricultural Univ., Beijing 100193, China; J. Yan and J. Crouch, International Maize and Wheat Improvement Center (CIMMYT), Apartado Postal 6-640, 06600 Mexico, DF, Mexico; M. Warburton, USDA-ARS, Corn Host Plant Resistance Research Unit, Box 9555, Mississippi State, MS 39762. Received 27 Apr. 2010. *Corresponding author ([email protected]). Abbreviations: CGIAR, Consultative Group on International Agricultural Research; crtRB1, β-carotene hydroxylase gene; GWA, genome-wide association; GWS, genome-wide selection; LD, linkage disequilibrium; MAF, minor allelic frequency; MAGIC, multiparent advanced generation intercross; MARS, marker-assisted recurrent selection; MAS, marker-assisted selection; NAM, nested association mapping; nMDS, nonmetric multidimensional scaling; PCA, principal components analysis; QTL, quantitative trait locus or loci; SNP, single nucleotide polymorphism. Published in Crop Sci. 51:433–449 (2011). doi: 10.2135/cropsci2010.04.0233 Published online 29 Dec. 2010. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA 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.