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      GWAS to Identify Genetic Loci for Resistance to Yellow Rust in Wheat Pre-Breeding Lines Derived From Diverse Exotic Crosses

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          Abstract

          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 YR 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 YR 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 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.

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          ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense.

          Cross-talk between ethylene and jasmonate signaling pathways determines the activation of a set of defense responses against pathogens and herbivores. However, the molecular mechanisms that underlie this cross-talk are poorly understood. Here, we show that ethylene and jasmonate pathways converge in the transcriptional activation of ETHYLENE RESPONSE FACTOR1 (ERF1), which encodes a transcription factor that regulates the expression of pathogen response genes that prevent disease progression. The expression of ERF1 can be activated rapidly by ethylene or jasmonate and can be activated synergistically by both hormones. In addition, both signaling pathways are required simultaneously to activate ERF1, because mutations that block any of them prevent ERF1 induction by any of these hormones either alone or in combination. Furthermore, 35S:ERF1 expression can rescue the defense response defects of coi1 (coronative insensitive1) and ein2 (ethylene insensitive2); therefore, it is a likely downstream component of both ethylene and jasmonate signaling pathways. Transcriptome analysis in Col;35S:ERF1 transgenic plants and ethylene/jasmonate-treated wild-type plants further supports the notion that ERF1 regulates in vivo the expression of a large number of genes responsive to both ethylene and jasmonate. These results suggest that ERF1 acts downstream of the intersection between ethylene and jasmonate pathways and suggest that this transcription factor is a key element in the integration of both signals for the regulation of defense response genes.
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            Epidemiology and control of stripe rust [Puccinia striiformisf. sp.tritici] on wheat

            X.M. Chen (2005)
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              The AP2/ERF domain transcription factor ORA59 integrates jasmonic acid and ethylene signals in plant defense.

              Plant defense against pathogens depends on the action of several endogenously produced hormones, including jasmonic acid (JA) and ethylene. In certain defense responses, JA and ethylene signaling pathways synergize to activate a specific set of defense genes. Here, we describe the role of the Arabidopsis (Arabidopsis thaliana) APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain transcription factor ORA59 in JA and ethylene signaling and in defense. JA- and ethylene-responsive expression of several defense genes, including PLANT DEFENSIN1.2 (PDF1.2), depended on ORA59. As a result, overexpression of ORA59 caused increased resistance against the fungus Botrytis cinerea, whereas ORA59-silenced plants were more susceptible. Several AP2/ERF domain transcription factors have been suggested to be positive regulators of PDF1.2 gene expression based on overexpression in stably transformed plants. Using two different transient overexpression approaches, we found that only ORA59 and ERF1 were able to activate PDF1.2 gene expression, in contrast to the related proteins AtERF1 and AtERF2. Our results demonstrate that ORA59 is an essential integrator of the JA and ethylene signal transduction pathways and thereby provide new insight into the nature of the molecular components involved in the cross talk between these two hormones.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/753061
                URI : https://loop.frontiersin.org/people/327815
                URI : https://loop.frontiersin.org/people/165361
                URI : https://loop.frontiersin.org/people/519850
                URI : https://loop.frontiersin.org/people/355431
                URI : https://loop.frontiersin.org/people/755289
                URI : https://loop.frontiersin.org/people/811004
                URI : https://loop.frontiersin.org/people/275495
                URI : https://loop.frontiersin.org/people/753844
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                30 October 2019
                2019
                : 10
                : 1390
                Affiliations
                [1] 1Departamento de estudios e investigación de Posgrado, Tecnológico Nacional de México/Instituto Tecnológico de Roque , Celaya, Mexico
                [2] 2Programa de mejoramiento genetico de trigo, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío , Celaya, Mexico
                [3] 3Department of Bioscience, Centro Internacional de Mejoramiento de Maíz y Trigo , Texcoco, Mexico
                [4] 4Departamento de Fitomejoramiento, Universidad Autónoma Agraria Antonio Narro , Saltillo, Mexico
                [5] 5Department of Biotechnology, Geneshifters , Pullman, WA, United States
                Author notes

                Edited by: Sukhjiwan Kaur, Department of Economic Development Jobs Transport and Resources, Australia

                Reviewed by: Rosy Raman, New South Wales Department of Primary Industries, Australia; Ambuj Bhushan Jha, University of Saskatchewan, Canada

                *Correspondence: Ernesto Solís-Moya, solis.ernesto@ 123456inifap.gob.mx ; Deepmala Sehgal, d.sehgal@ 123456cgiar.org ; Sukhwinder Singh, suksinghseedwheat@ 123456gmail.com

                This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2019.01390
                6831551
                31781137
                492d63e3-5fe6-45ba-932c-580d73db9db4
                Copyright © 2019 Ledesma-Ramírez, Solís-Moya, Iturriaga, Sehgal, Reyes-Valdes, Montero-Tavera, Sansaloni, Burgueño, Ortiz, Aguirre-Mancilla, Ramírez-Pimentel, Vikram and Singh

                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.

                History
                : 13 June 2019
                : 08 October 2019
                Page count
                Figures: 7, Tables: 2, Equations: 2, References: 67, Pages: 14, Words: 6174
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                dartseq,linked top-cross population,pre-breeding lines,yellow rust resistance,gbs,bread wheat

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