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Fine mapping for double podding gene in chickpea

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Abstract

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For the first time, fine mapping for sfl locus was carried out using a battery of new STMS and SNP markers. The target region was delimited to 92.6 Kb where seven annotated genes were found that could be candidate genes for the simple/double podding trait in chickpea.

Abstract

Four recombinant inbred populations (RIP-1, RIP-7, RIP-11, and CPR-01) were used to map the double podding gene (sfl) in chickpea. In RIP-1, the gene was initially mapped on linkage group (LG) 6 between the two sequence-tagged microsatellite site (STMS) markers TA120 and TR1. Eight new STMS markers were added onto LG6 in the target region and sfl locus was finally located between CAGM27819 and CAGM27777 markers within an interval of 2 cM. Seven out of the eight markers were mapped in RIP-7 and its reciprocal RIP-11 confirming the location of the sfl locus to a 4.8 cM interval flanked by TR44 and CAGM27705. Furthermore, using a high-density single nucleotide polymorphism (SNP) map of CPR-01, sfl was mapped to the same genomic region in a 5.1 cM interval between TR44 and the SNP scaffold1646p97220. Five pairs of near isogenic lines (NILs) and eight recombinant inbred lines (RILs) were used to refine this region in the chickpea physical map. Combining data from linkage analysis in four RIPs, marker physical positions and recombination events obtained in both pairs of NILs and selected RILs, sfl could be placed within a genomic window of 92.6 Kb. Seven annotated genes were extracted from this region. The regulator of axillary meristem-predicted gene could be a candidate gene for the simple/double podding gene. This study provides additional set of markers flanking and tightly linked to sfl locus that are useful for marker-assisted selection.

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Acknowledgments

This work has been supported by the project INIA contract RTA2013-00025, co-financed by the European Union through the ERDF 2014–2020 “Programa Operativo de Crecimiento Inteligente”. Ali L acknowledges PhD fellowship from Syrian Ministry of High Education. Funding for the Canadian research component was provided by the Agriculture Development Fund of the Saskatchewan Ministry of Agriculture and by the Saskatchewan Pulse Growers. The authors would like to thank Dr. F Madueño from the IBMCP (CSIC-UPV, Spain) for helpful comments.

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Authors and Affiliations

  1. Department of Genetics, University of Córdoba, Campus Rabanales Ed. C-5, 14071, Córdoba, Spain

    L. Ali, J. Gil & T. Millan

  2. Crop Development Center, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada

    A. Deokar & B. Tar’an

  3. Área de Mejora y Biotecnología, IFAPA, Apdo 3092, 14080, Córdoba, Spain

    C. Caballo & J. Rubio

  4. 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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  3. C. Caballo
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Correspondence to T. Millan.

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Ali, L., Deokar, A., Caballo, C. et al. Fine mapping for double podding gene in chickpea. Theor Appl Genet 129, 77–86 (2016). https://doi.org/10.1007/s00122-015-2610-1

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