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Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño

M. Rocío Aguilar-Rangel, Ricardo A. Chávez Montes, Eric Gonzalez-Segovia, View ORCID ProfileJeffrey Ross-Ibarra, View ORCID ProfileJune K. Simpson, Ruairidh J. H. Sawers
doi: https://doi.org/10.1101/152397
M. Rocío Aguilar-Rangel
1Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México.
2Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México.
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Ricardo A. Chávez Montes
1Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México.
3ABACUS: Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento del Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Carretera México-Toluca Km. 38.5, Ocoyoacac, Estado de México, México.
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Eric Gonzalez-Segovia
1Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México.
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Jeffrey Ross-Ibarra
4Department of Plant Sciences, Center for Population Biology, and Genome Center, University of California, Davis, CA, 95616, USA.
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  • ORCID record for Jeffrey Ross-Ibarra
June K. Simpson
2Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México.
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Ruairidh J. H. Sawers
1Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Guanajuato, México.
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ABSTRACT

Background Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.

Methods Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.

Results A total of 2386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles that mirrored the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a constitutive stress response. Constitutive stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.

Discussion Constitutive activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between PT and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in PT. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 20, 2017.
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Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
M. Rocío Aguilar-Rangel, Ricardo A. Chávez Montes, Eric Gonzalez-Segovia, Jeffrey Ross-Ibarra, June K. Simpson, Ruairidh J. H. Sawers
bioRxiv 152397; doi: https://doi.org/10.1101/152397
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Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
M. Rocío Aguilar-Rangel, Ricardo A. Chávez Montes, Eric Gonzalez-Segovia, Jeffrey Ross-Ibarra, June K. Simpson, Ruairidh J. H. Sawers
bioRxiv 152397; doi: https://doi.org/10.1101/152397

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