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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01390

GWAS to identify genetic loci for resistance to yellow rust in wheat pre-breeding lines derived from diverse exotic crosses

  • 1Other, United States
  • 2Department of Immunology, Institute of Biomedical Research, National Autonomous University of Mexico, Mexico
  • 3Roque Institute of Technology, Mexico
  • 4Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Mexico
  • 5International Maize and Wheat Improvement Center (Mexico), Mexico
  • 6Universidad Autónoma Agraria Antonio Narro, Mexico

Yellow rust (YR) or stripe rust, caused by Puccinia striformis f. sp tritici Eriks (Pst), is a major challenge to resistance breeding in wheat. A genome wide association study (GWAS) was performed using 22,415 single nucleotide polymorphism (SNP) markers and 591 haplotypes to identify genomic regions associated with resistance to yellow rust in a subset panel of 419 pre-breeding lines (PBLs) developed at International Center for Maize and Wheat Improvement (CIMMYT). The 419 PBLs were derived from an initial set of 984 PBLs generated by a three-way crossing scheme (exotic/elite1//elite2) among 25 best elites and 244 exotics (synthetics, landraces) from CIMMYT’s germplasm bank. For the study, 419 PBLs were characterized with 22,415 high-quality DArTseq-SNPs and phenotyped for severity of yellow rust disease at five locations in Mexico. A population structure was evident in the panel with three distinct subpopulations, and a genome-wide linkage disequilibrium (LD) decay of 2.5 cM was obtained. Across all five locations, 14 SNPs and 7 haplotype blocks were significantly (P < 0.001) associated with the disease severity explaining 6.0 to 14.1% and 7.9 to 19.9% of variation, respectively. Based on average LD decay of 2.5 cM, identified 14 SNP-trait associations were delimited to seven quantitative trait loci (QTLs) in total. Seven SNPs were part of the two haplotype blocks on chromosome 2A identified in haplotypes-based GWAS. In silico analysis of the identified SNPs showed hits with interesting candidate genes, which are related to pathogenic process or known to regulate induction of genes related to pathogenesis such as those coding for glunolactone oxidase, quinate O-hydroxycinnamoyl transferase or two-component histidine kinase. The two-component histidine kinase, for example, acts as a sensor in the perception of phytohormones ethylene and cytokinin. Ethylene plays a very important role in regulation of multiple metabolic processes of plants, including induction of defense mechanisms mediated by jasmonate. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

Keywords: bread wheat, Yellow rust resistance, Pre-breeding lines, Linked Top-cross Population, DArTseq

Received: 13 Jun 2019; Accepted: 08 Oct 2019.

Copyright: © 2019 SINGH, Ledesma-Ramírez, Solís-Moya, Iturriaga, Sehgal, Reyes-Valdes, Montero-Tavera, Sansaloni, Burgueño, Ortiz, Aguirre-Mancilla, Ramírez-Pimentel and Vikram. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
PhD. SUKHWINDER SINGH, Other, Pullman, WA, United States, sukh@geneshifters.com
Dr. Ernesto Solís-Moya, Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Celaya, Mexico, solis.ernesto@inifap.gob.mx