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Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula

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Abstract

Eragrostis curvula (Schrad.) Nees is a forage grass native to the semiarid regions of Southern Africa, which reproduces mainly by pseudogamous diplosporous apomixis. A collection of ESTs was generated from four cDNA libraries, three of them obtained from panicles of near-isogenic lines with different ploidy levels and reproductive modes, and one obtained from 12 days-old plant leaves. A total of 12,295 high-quality ESTs were clustered and assembled, rendering 8,864 unigenes, including 1,490 contigs and 7,394 singletons, with a genome coverage of 22%. A total of 7,029 (79.11%) unigenes were functionally categorized by BLASTX analysis against sequences deposited in public databases, but only 37.80% could be classified according to Gene Ontology. Sequence comparison against the cereals genes indexes (GI) revealed 50% significant hits. A total of 254 EST-SSRs were detected from 219 singletons and 35 from contigs. Di- and tri- motifs were similarly represented with percentages of 38.95 and 40.16%, respectively. In addition, 190 SNPs and Indels were detected in 18 contigs generated from 3 to 4 libraries. The ESTs and the molecular markers obtained in this study will provide valuable resources for a wide range of applications including gene identification, genetic mapping, cultivar identification, analysis of genetic diversity, phenotype mapping and marker assisted selection.

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Abbreviations

EST:

Expressed sequence tags

2,4-D:

2,4 Dichlorophenoxyacetic acid

BAP:

6-Benzylamino purine

DMSO:

Dimethyl sulfoxide

IPTG:

Isopropyl-beta-D-thiogalactopyranoside

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Acknowledgments

The project was supported by the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Grants PAV 137/4 and PICT 14625 and Secretaría de Ciencia y Tecnología (SECyT UNS) PGI 24/A133 (Argentina).

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Authors and Affiliations

  1. Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS)–CONICET, Camino de La Carrindanga Km 7.0, Bahia Blanca, 8000, Argentina

    Gerardo D. L. Cervigni, Marina Díaz, Juan P. Selva, Diego Zappacosta & Viviana Echenique

  2. Instituto de Biotecnología, CICVyA, INTA-Castelar, Buenos Aires, Argentina

    Norma Paniego & Viviana Echenique

  3. Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, San Juan 670, Bahia Blanca, 8000, Argentina

    Marina Díaz

  4. Departamento de Agronomía, Universidad Nacional del Sur, CERZOS–CONICET, San Andrés 800, Bahia Blanca, 8000, Argentina

    Juan P. Selva, Diego Zappacosta & Viviana Echenique

  5. Bioaxioma, Venezuela 110-1P, Buenos Aires, C1095AAD, Argentina

    Darío Zanazzi & Iñaki Landerreche

  6. Facultad de Ingeniería, Universidad de Buenos Aires, Av. Paseo Colón 850, Buenos Aires, C1063ACV, Argentina

    Darío Zanazzi & Iñaki Landerreche

  7. Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, S2125ZAA, Argentina

    Luciano Martelotto, Silvina Felitti & Silvina Pessino

  8. Primary Industries Research Victoria, Plant Biotechnology Centre, La Trobe University, Bundoora, VIC, 3086, Australia

    Germán Spangenberg

Authors
  1. Gerardo D. L. Cervigni
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  2. Norma Paniego
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  3. Marina Díaz
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  4. Juan P. Selva
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  5. Diego Zappacosta
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  6. Darío Zanazzi
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  7. Iñaki Landerreche
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  8. Luciano Martelotto
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  9. Silvina Felitti
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  10. Silvina Pessino
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  11. Germán Spangenberg
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  12. Viviana Echenique
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Corresponding author

Correspondence to Viviana Echenique.

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Gerardo D. L. Cervigni and Norma Paniego contributed equally to this manuscript.

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Cervigni, G.D.L., Paniego, N., Díaz, M. et al. Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula . Plant Mol Biol 67, 1–10 (2008). https://doi.org/10.1007/s11103-007-9282-4

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