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Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Abstract

Key message

We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species.

Abstract

Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F5 recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.

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Acknowledgments

H. Khazaei expresses his gratitude to the Emil Aaltonen Foundation (Emil Aaltosen Säätiö) and Niemi-säätiö for their financial support. The project was further supported by the University of Helsinki, Niemi-Säätiö and by “Legume Futures (Legume-supported cropping systems for Europe)”, a collaborative research project funding from the European Union’s Seventh Programme for research, technological development and demonstration under Grant Agreement No. 245216. In addition, we thank Markku Tykkyläinen, Sanna Peltola, Sini Lindström and Stefano Zanotto for their assistance in the glasshouse work. We thank Prof. Wolfgang Link (Georg-August-University, Göttingen, Germany) for providing the seeds of the parental lines.

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The authors declare that they have no conflict of interest.

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Communicated by Glenn James Bryan.

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Khazaei, H., O’Sullivan, D.M., Sillanpää, M.J. et al. Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.). Theor Appl Genet 127, 2371–2385 (2014). https://doi.org/10.1007/s00122-014-2383-y

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  • DOI: https://doi.org/10.1007/s00122-014-2383-y

Keywords

  • Quantitative Trait Locus
  • Linkage Group
  • Faba Bean
  • Composite Interval Mapping
  • Quantitative Trait Locus Region