Genome-Wide Association Mapping for Leaf Tip Necrosis and Pseudo-black Chaff in Relation to Durable Rust Resistance in Wheat

The partial rust resistance genes Lr34 and Sr2 have been used extensively in wheat (Triticum aestivum L.) improvement, as they confer exceptional durability. Interestingly, the resistance of Lr34 is associated with the expression of leaf tip necrosis (LTN) and Sr2 with pseudo-black chaff (PBC). Genome-wide association mapping using CIMMYT’s stem rust resistance screening nursery (SRRSN) wheat lines was done to identify genotyping-bysequencing (GBS) markers linked to LTN and PBC. Phenotyping for these traits was done in Ithaca, New York (fall 2011); Njoro, Kenya (main and off-seasons, 2012), and Wellington, India (winter, 2013). Using the mixed linear model (MLM), 18 GBS markers were significantly associated with LTN. While some markers were linked to loci where the durable leaf rust resistance genes Lr34 (7DS), Lr46 (1BL), and Lr68 (7BL) were mapped, significant associations were also detected with other loci on 2BL, 5B, 3BS, 4BS, and 7BS. Twelve GBS markers linked to the Sr2 locus (3BS) and loci on 2DS, 4AL, and 7DS were significantly associated with PBC. This study provides insight into the complex genetic control of LTN and PBC. Further efforts to validate and study these loci might aid in determining the nature of their association with durable resistance. The rust diseases, which include leaf rust caused by Puccinia triticina Eriks., stem rust caused by P. graminis Pers. f. sp. tritici, and stripe rust caused by P. striiformis West. f. sp. tritici., are the major biotic stresses that affect global wheat production. Although several rust resistance genes have been identified, most of them are race specific and can be easily overcome by new virulent races of the pathogen (Samborski, 1985; McIntosh et al., 1995; Pretorius et al., 2000; Wanyera et al., 2006). To circumvent this challenge, rust resistance breeding has shifted its focus to achieving nonrace-specific, widespread, prolonged resistance, also known as durable resistance (Johnson, 1984). This is usually characterized by slow rusting, partial, and adult plant resistance (APR) expressed at the postseedling stage with extended latent periods that delay the spread of the disease (Caldwell, 1968; Parlevliet, 1975; Kolmer, 1996). Among the cataloged rust resistance genes, Lr34/Yr18/Sr57/Pm38/Sb1/Ltn1 (hereafter referred to as Lr34) and Sr2/Yr30/Lr27/Pbc1 (hereafter referred to as Sr2) have been deployed widely for several decades due to their exceptional durability. Published in The Plant Genome 8 doi: 10.3835/plantgenome2015.01.0002 © 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. P. Juliana, J.E. Rutkoski, H. Barbier, and M.E. Sorrells, Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY 14853; J.A. Poland, Dep. of Agronomy, Kansas State University, Manhattan, KS 66506, and USDA–ARS, Manhattan, KS 66502; R.P. Singh, International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600 Mexico, D.F., Mexico; S. Natesan, Agricultural Univ., Madurai 641003, India; S. Murugasamy, Wheat Research Station, Indian Agricultural Research Institute, Wellington–643231, Nilgiris, India. Received 16 Jan. 2015. Accepted 30 Mar. 2015. *Corresponding author (mes12@cornell.edu). Abbreviations: ABC, adenosine triphosphate-binding cassette; APR, adult plant resistance; DArT, diversity array technology; FDR, false discovery rate; GBS, genotyping-by-sequencing; GLM, generalized linear model; LD, linkage disequilibrium; LTN, leaf tip necrosis; MLM, mixed linear model; PBC, pseudo-black chaff; PC, principal component; Q-Q, quantile–quantile; QTL, quantitative trait loci; SNP, single nucleotide polymorphisms; SRRSN, stem rust resistance screening nursery. Published July 10, 2015