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Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses

Euphytica volume 204, pages 473–485 (2015)Cite this article

Abstract

A recombinant inbred line population (RIP-9) derived from an interspecific cross (ILC72 × Cr5-10) was evaluated for growth habit during 2 years (2003 and 2004). This RIP was used to develop a pair of near isogenic lines (NILs) for erect vs prostrate growth habit in chickpea. Molecular characterization of the identified pair of NILs was performed using 52 sequence tagged microsatellite site markers distributed over different chickpea linkage groups (CaLG) of the genetic map. It revealed polymorphic markers in CaLG1 and CaLG3. Starting from a previous data base simple linear regression was applied to detect association between markers and growth habit. The RAPD (random amplified polymorphic DNA) marker OPAD091053 mapped on CaLG1 explained the highest percentage (maximum 15.4 %) of the total phenotypic variation for growth habit and it was used to develop a SCAR (sequence characterized amplified region) marker (SCAD091053). New markers were developed from sequences surrounding SCAD091053 in the physical map. QTL (quantitative trait loci) analysis revealed a new QTL (QTLHg2) in CaLG1. The Indel marker (deletion/insertion) Indel 3 and the predicted gene Ca_07000 (14,5 Mb of Ca1) and (15,3 Mb of Ca1) had the highest LOD values explaining 24.6 and 23.4 % of the phenotypic variation in years 2003 and 2004, respectively. To confirm these results, another RIP (RIP-5) derived from an intraspecific cross (WR315 × ILC3279) and segregating for erect vs semi-erect growth habit was employed. RIP-5 allowed mapping the gene (Hg2/hg2) on CaLG1 that was flnaked by two Indel markers (Indel 1 and Indel 2) in the range of 12,3 and 16,2 Mb. So, Hg2/hg2 gene corresponds to QTLHg2 region. The annotated genes Ca_07000 and Ca_06999 were homologues to predicted zinc finger genes in Glycine max and Pisum sativum, respectively. Hence, they could be considered as possible candidate genes.

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Acknowledgments

This work has been supported by the project INIA contract RTA2010-00059, co-financed by EU funds (FEDER). Ali L. acknowledges Ph.D. fellowship from Syrian Ministry of High Education and ICRISAT for supporting six months stay at the Center of Excellence in Genomic (ICRISAT, Patancheru, India).

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Authors and Affiliations

  1. Departamento de Genética, Universidad de Córdoba, Campus Rabanales, Edif. C5, 14071, Córdoba, Spain

    L. Ali, J. Gil & T. Millan

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India

    S. Azam, H. Kudapa & R. K. Varshney

  3. Área de Mejora y Biotecnología, IFAPA Centro “Alameda del Obispo”, Apdo 3092, 14080, Córdoba, Spain

    J. Rubio

  4. Institute for Sustainable Agriculture, CSIC, 4084, 14080, Córdoba, Spain

    E. Madrid

  5. Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, 10300 Baltimore Ave., Building 010A, Beltsville, MD, 20705, USA

    P. Castro

  6. Grain Legume Genetics and Physiology Research Unit USDA-ARS, Washington State University, Pullman, WA, 99164, USA

    W. Chen

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  1. L. Ali
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  2. S. Azam
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  3. J. Rubio
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  4. H. Kudapa
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  7. P. Castro
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  9. J. Gil
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  10. T. Millan
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Correspondence to L. Ali.

Electronic supplementary material

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Supplementary material 1 (XLSX 12 kb) The primer sequences of the markers developed in this study

10681_2015_1369_MOESM2_ESM.docx

Supplementary material 2 (DOCX 15 kb) Microsatellite markers screened in RIP-1 parental lines, their 635 physical positions, primer pairs sequences, PCR predicted size and the obtained size

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Ali, L., Azam, S., Rubio, J. et al. Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses. Euphytica 204, 473–485 (2015). https://doi.org/10.1007/s10681-015-1369-4

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  • DOI: https://doi.org/10.1007/s10681-015-1369-4

Keywords

  • Linkage analysis
  • Cicer
  • Erect
  • Prostrate
  • Semi-erect
  • Physical map

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