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The marker SCK13603 associated with resistance to ascochyta blight in chickpea is located in a region of a putative retrotransposon

  • Genetics and Genomics
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Abstract

The sequence characterized amplified region (SCAR) marker SCK13603, associated with ascochyta blight resistance in a chickpea recombinant inbred line (RIL) population, was used as anchored sequence for genome walking. The PCRs performed in the walking steps to walk in the same direction produced eight bands in 5′ direction and five bands in 3′ direction with a length ranking from 530 to 2,871 bp. The assembly of the bands sequences along with the sequence of SCK13603 resulted in 7,815 bp contig. Blastn analyses showed stretches of DNA sequence mainly distributed from the nucleotides 1,500 to 4,500 significantly similar to Medicago truncatula genomic DNA. Three open reading frames (ORFs) were identified and blastp analysis of predicted amino acids sequences revealed that ORF1, ORF2 and ORF3 had significant similarity to a CCHC zinc finger protein, to an integrase, and to a precursor of the glucoamylase s1/s2, respectively, from M. truncatula. The high homology of the putative proteins derived from ORF1 and ORF2 with retrotransposon proteins and the prediction of the existence of conserved domains usually present in retrotransposon proteins indicate that the marker SCK13603 is located in a region of a putative retrotransposon. The information generated in this study has contributed to increase the knowledge of this important region for blight resistance in chickpea.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

BAC:

Bacterial artificial chromosome

Blastn:

Nucleotide basic local alignment search tool

Blastp:

Protein basic local alignment search tool

bp:

Bases pairs

DAF:

DNA amplification fingerprinting

EST:

Expressed sequence tag

LG:

Linkage group

LINE:

Long interspersed nuclear elements

LTR:

Long terminal repeat

MAS:

Marker-assisted selection

NCBI:

National Centre for Biotechnology Information

ORF:

Open reading frame

PCR:

Polymerase chain reaction

PPT:

Polypurine tract

PR:

Pathogenesis-related

QTL:

Quantitative trait loci

RAPD:

Random amplified polymorphic DNA

RGA:

Resistance gene analogue

RIL:

Recombinant inbred line

SCAR:

Sequence characterized amplified region

SNP:

Single nucleotide polymorphism

STMS:

Sequence tagged microsatellite sites

STS:

Sequence-tagged site

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Acknowledgments

This work has been supported by the European Union project: GLIP, contract no. FOOD-CT-2004-506223, and the national project: CICYT, contract no. AGL2005-07497-CO2-01/AGR. M. Iruela acknowledges grant support from IFAPA-CICE Junta de Andalucía (Spain).

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Authors and Affiliations

  1. Dpto. Mejora Genética Vegetal, IAS-CSIC, Córdoba, 14080, Córdoba, Spain

    Marta Iruela, Fernando Pistón & Francisco Barro

  2. Departamento de Genética, Universidad de Córdoba, Campus Rabanales Edif. C-5, 14071, Córdoba, Spain

    José Ignacio Cubero, Teresa Millán & Juan Gil

Authors
  1. Marta Iruela
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  2. Fernando Pistón
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  3. José Ignacio Cubero
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  4. Teresa Millán
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  5. Francisco Barro
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  6. Juan Gil
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Corresponding author

Correspondence to Juan Gil.

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Communicated by K. Toriyama.

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Iruela, M., Pistón, F., Cubero, J.I. et al. The marker SCK13603 associated with resistance to ascochyta blight in chickpea is located in a region of a putative retrotransposon. Plant Cell Rep 28, 53–60 (2009). https://doi.org/10.1007/s00299-008-0609-7

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  • DOI: https://doi.org/10.1007/s00299-008-0609-7

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