Molecular Breeding

, Volume 31, Issue 1, pp 163–180 | Cite as

Identifying quantitative trait loci for symbiotic nitrogen fixation capacity and related traits in common bean

  • Lara Ramaekers
  • Carlos H. Galeano
  • Nayibe Garzón
  • Jozef Vanderleyden
  • Matthew W. Blair


Symbiotic nitrogen fixation (SNF) through association with root-nodulating rhizobia effectively contributes to improved nitrogen nutrition of leguminous plants and is an ecologically sound and low-cost strategy for improving pulse productivity. One of the main factors determining the efficiency of SNF is the plant genotype, but little is known about the plants’ genetic contribution to SNF in the case of common bean. Therefore, quantitative trait loci (QTL) analysis for SNF and related growth traits was performed in a common bean recombinant inbred line (RIL) population under both greenhouse and field conditions. The RIL population was generated from the cross G2333 × G19839. Additionally, the existing genetic map of the population was improved through the mapping of 42 markers out of a set of 108 nodulation gene-based markers. All greenhouse and field experiments showed significant differences between RIL genotypes for most SNF and related growth traits. In the first greenhouse experiment, two QTL for percent nitrogen (N%) fixed were identified on linkage groups b01 and b04, explaining 21 and 20 % of the observed phenotypic variance, respectively. The QTL on linkage group b01 overlapped with a QTL detected for total N content at harvest in the field experiment (R 2 = 14 %). In the second greenhouse experiment, two QTL for total plant N fixed were identified on linkage groups b04 and b10 (R 2 = 18 and 17 %, respectively). The field experiment also yielded one QTL for the N% fixed at harvest on linkage group b04 and another for the total N fixed in the shoot at late pod-filling stage on linkage group b01. The latter two QTL identified in the field explained 19 and 21 %, respectively, of the observed phenotypic variance. DNA sequence comparison of markers closely linked to QTL identified some potential candidate genes underlying the QTL. One of these genes encodes for an auxin-responsive transcription factor which could explain differences in growth and possibly yield and N accumulation between climbing beans and bush beans. Another putative gene was identified for an AP2/ERF-domain-containing transcription factor underlying the QTL for the total amount of symbiotic nitrogen fixed in the field.


QTL analysis Symbiotic nitrogen fixation Common bean Climbing bean Putative genes 



Days after planting


Linkage group


Meters above sea level




N derived from air (N fixed)


N derived from soil


Nodule dry weight


Nodule number




Nitrogen use efficiency


Shoot dry weight


Symbiotic nitrogen fixation


Soil and plant analysis development


Quantitative trait loci


Recombinant inbred lines


Root dry weight


Single strand conformation polymorphism


Total dry weight


Transcription factor



We are grateful to Yercil Viera and Agobardo Hoyos for seed preparations and field management, and Steve Beebe and Alcides Hincapie for population development. This study was financed by a grant from the Flemish Interuniversity Council (VLIR) to L. R. and by the International Center for Tropical Agriculture (CIAT). C. H. G. is supported by a doctoral research fellowship from IRO (Interfaculty Council for Development Co-operation of the KU Leuven). This study was part of a PhD dissertation by L. R. at the KU Leuven.

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Department of Microbial and Molecular SystemsCentre of Microbial and Plant GeneticsHeverleeBelgium
  2. 2.Universidad Nacional de ColombiaValle de CaucaColombia
  3. 3.Department of Plant Breeding and GeneticsHall, Cornell UniversityIthacaUSA

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