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Genome-wide association study for resistance to the southern root-knot nematode (Meloidogyne incognita) in soybean

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Abstract

Soybean [Glycine max (L.) Merrill] is one of the most important traded commodities for the world’s economy. However, soybean cultivation is often affected by biotic and abiotic factors that prevent the crop from attaining its full yield potential. With the advent of new tools for next-generation sequencing, the genomic knowledge gained from the study of this major oilseed crop has increased considerably in recent years. In this study, we performed a genotypic characterization of 188 plant introductions (PIs) and five cultivars using a genotyping-by-sequencing (GBS) approach and a phenotypic characterization for resistance/tolerance to the southern root-knot nematode, Meloidogyne incognita. We then performed a genome-wide association study (GWAS) for this important trait. From 46,196 SNP markers identified and validated on this set of genotypes, three were significantly associated with nematode resistance. Remarkably, all of these were in a single, very small (3.4 kb) region of chromosome 10. Most lines (48 out of 57) with the highest level of resistance shared the haplotype composed of the alleles associated with resistance at these three SNP loci. Interestingly, nine of the lines exhibiting a high level of resistance did not exhibit the “resistant haplotype” on Gm10. This suggests either that recombination has broken the association between the SNPs and the resistance locus or that resistance is conferred by a different locus altogether. In the latter case, these lines represent a putative alternative source of resistance, an important information for breeding programs.

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Acknowledgments

We greatly appreciate the financial support of the Coordination for the Improvement of Higher Level for Education program (CAPES), National Counsel of Technological and Scientific Development (CNPq), and Emerging Leaders in the Americas Program (ELAP). We thank the members of the plant biotechnology laboratory at Embrapa Soja, Brazil. Furthermore, we thank the Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS) at Université Laval, Canada, for supporting the doctoral student exchange program and this research. This paper was approved for publication by the Editorial Board of Embrapa Soja as manuscript number 119/2016.

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Authors and Affiliations

  1. Londrina State University, Londrina, PR, Brazil

    André L. de L. Passianotto

  2. Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, Quebec, G1V 0A6, Canada

    Huma Sonah & François Belzile

  3. Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa – Soja), P.O. Box 231, Londrina, PR, Brazil

    Waldir P. Dias, Francismar C. Marcelino-Guimarães & Ricardo V. Abdelnoor

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  1. André L. de L. Passianotto
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  3. Waldir P. Dias
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  6. Ricardo V. Abdelnoor
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Correspondence to Francismar C. Marcelino-Guimarães.

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Passianotto, A.L.d.L., Sonah, H., Dias, W.P. et al. Genome-wide association study for resistance to the southern root-knot nematode (Meloidogyne incognita) in soybean. Mol Breeding 37, 148 (2017). https://doi.org/10.1007/s11032-017-0744-3

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