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Rapid identification of angulata leaf mutations using next-generation sequencing

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Abstract

Map-based (positional) cloning has traditionally been the preferred strategy for identifying the causal genes underlying the phenotypes of mutants isolated in forward genetic screens. Massively parallel sequencing technologies are enabling the rapid cloning of genes identified in such screens. We have used a combination of linkage mapping and whole-genome re-sequencing to identify the causal mutations in four loss-of-function angulata (anu) mutants. These mutants were isolated in a screen for mutants with defects in leaf shape and leaf pigmentation. Our results show that the anu1-1, anu4-1, anu9-1 and anu12-1 mutants carry new alleles of the previously characterized SECA2, TRANSLOCON AT THE OUTER MEMBRANE OF CHLOROPLASTS 33 (TOC33), NON-INTRINSIC ABC PROTEIN 14 (NAP14) and CLP PROTEASE PROTEOLYTIC SUBUNIT 1 (CLPR1) genes. Re-sequencing the genomes of fine mapped mutants is a feasible approach that has allowed us to identify a moderate number of candidate mutations, including the one that causes the mutant phenotype, in a nonstandard genetic background. Our results indicate that anu mutations specifically affect plastid-localized proteins involved in diverse processes, such as the movement of peptides through chloroplast membranes (ANU1 and ANU4), metal homeostasis (ANU9) and protein degradation (ANU12).

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Abbreviations

ANU :

ANGULATA

das:

Days after stratification

EMS:

Ethylmethane sulfonate

NGS:

Next-generation sequencing

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Acknowledgments

We thank J.M. Serrano, F.M. Lozano, T. Trujillo, R. Sarmiento-Mañús, D. Navarro, L. Serna, J.M. Sánchez-Larrosa and A. Torregrosa for their excellent technical assistance. Research in the laboratory of J.L.M. is supported by Grants from the Ministerio de Economía y Competitividad of Spain [BFU2011-22825 and CSD2007-00057 (TRANSPLANTA)], the Generalitat Valenciana (PROMETEO/2009/112) and the European Commission [LSHG-CT-2006-037704 (AGRON-OMICS)]. HC is a recipient of a Marie Curie International Reintegration Grant (PIRG03-GA-2008-231073). RCS holds a fellowship from the Ministerio de Economía y Competitividad of Spain (BES-2009-014106). EMB holds a predoctoral fellowship from the Universidad Miguel Hernández.

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  1. Rubén Casanova-Sáez

    Present address: Department of Forest Genetics and Plant Physiology, Umeä Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umea, Sweden

Authors and Affiliations

  1. Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Alicante, Spain

    Eduardo Mateo-Bonmatí, Rubén Casanova-Sáez, Héctor Candela & José Luis Micol

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  1. Eduardo Mateo-Bonmatí
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  2. Rubén Casanova-Sáez
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Correspondence to José Luis Micol.

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E. Mateo-Bonmatí and R. Casanova-Sáez have contributed equally to this work.

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Mateo-Bonmatí, E., Casanova-Sáez, R., Candela, H. et al. Rapid identification of angulata leaf mutations using next-generation sequencing. Planta 240, 1113–1122 (2014). https://doi.org/10.1007/s00425-014-2137-8

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