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Genome-wide association analyses reveal the genetic basis of biomass accumulation under symbiotic nitrogen fixation in African soybean

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We explored the genetic basis of SNF-related traits through GWAS and identified 40 candidate genes. This study provides fundamental insights into SNF-related traits and will accelerate efforts for SNF breeding.

Abstract

Symbiotic nitrogen fixation (SNF) increases sustainability by supplying biological nitrogen for crops to enhance yields without damaging the ecosystem. A better understanding of this complex biological process is critical for addressing the triple challenges of food security, environmental degradation, and climate change. Soybean plants, the most important legume worldwide, can form a mutualistic interaction with specialized soil bacteria, bradyrhizobia, to fix atmospheric nitrogen. Here we report a comprehensive genome-wide association study of 11 SNF-related traits using 79K GBS-derived SNPs in 297 African soybeans. We identified 25 QTL regions encompassing 40 putative candidate genes for SNF-related traits including 20 genes with no prior known role in SNF. A line with a large deletion (164 kb), encompassing a QTL region containing a strong candidate gene (CASTOR), exhibited a marked decrease in SNF. This study performed on African soybean lines provides fundamental insights into SNF-related traits and yielded a rich catalog of candidate genes for SNF-related traits that might accelerate future efforts aimed at sustainable agriculture.

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Acknowledgements

We thank the Global Affairs Canada, Canadian Field Crop Research Alliance, and International Institute of Tropical Agriculture (IITA). We thank Fausta Karaboneye for her help on greenhouse phenotyping. We also thank sequencing platform of Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Canada.

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Authors and Affiliations

  1. Département de Phytologie, Université Laval, Quebec City, QC, Canada

    Davoud Torkamaneh, François-P. Chalifour, Chantal J. Beauchamp & François Belzile

  2. Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada

    Davoud Torkamaneh, Halim Maaroufi & François Belzile

  3. Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada

    Davoud Torkamaneh & Istvan Rajcan

  4. International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria

    Hesham Agrama & Steve Boahen

  5. Sultan Qaboos University, Muscat, Oman

    Hesham Agrama

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  1. Davoud Torkamaneh
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  2. François-P. Chalifour
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  3. Chantal J. Beauchamp
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  4. Hesham Agrama
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  6. Halim Maaroufi
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  7. Istvan Rajcan
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  8. François Belzile
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Contributions

DT and FB conceptualized the project. FC, CB, HA, and SB prepared the plant materials and performed sample selection. DT, FC, and CB conducted greenhouse phenotyping. HA and SB conducted field phenotyping. DT, IR, and HM formal analysis. DT and FB wrote the original draft. DT and FB wrote review and editing.

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Correspondence to François Belzile.

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Communicated by Albrecht E. Melchinger.

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Torkamaneh, D., Chalifour, FP., Beauchamp, C.J. et al. Genome-wide association analyses reveal the genetic basis of biomass accumulation under symbiotic nitrogen fixation in African soybean. Theor Appl Genet 133, 665–676 (2020). https://doi.org/10.1007/s00122-019-03499-7

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