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Genome-wide association analysis of symbiotic nitrogen fixation in common bean

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Abstract

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Significant SNPs and candidate genes for symbiotic nitrogen fixation (SNF) and related traits were identified on Pv03, Pv07 and Pv09 chromosomes of common bean.

Abstract

A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean Diversity Panel (ADP) comprising 259 common bean (Phaseolus vulgaris) genotypes. The ADP was evaluated for SNF and related traits in both greenhouse and field experiments. After accounting for population structure and cryptic relatedness, significant SNPs were identified on chromosomes Pv03, Pv07 and Pv09 for nitrogen derived from atmosphere (Ndfa) in the shoot at flowering, and for Ndfa in seed. The SNPs for Ndfa in shoot and Ndfa in seed co-localized on Pv03 and Pv09. Two genes Phvul.007G050500 and Phvul.009G136200 that code for leucine-rich repeat receptor-like protein kinases (LRR-RLK) were identified as candidate genes for Ndfa. LRR-RLK genes play a key role in signal transduction required for nodule formation. Significant SNPs identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of common bean for SNF.

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Abbreviations

ADP:

Andean Diversity Panel

BLASTn:

Basic local alignment search tool for nucleotide

GWAS:

Genome-wide association study

Ndfa:

Nitrogen derived from the atmosphere

GH:

Greenhouse

MLM:

Mixed linear model

LD:

Linkage disequilibrium

LRR-RLK:

Leucine-rich repeat receptor-like protein kinase

N:

Nitrogen

Pv:

Phaseolus vulgaris chromosome

SNF:

Symbiotic nitrogen fixation

SNP:

Single nucleotide polymorphism

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Acknowledgments

Research was supported by the Feed the Future Innovation Lab for Collaborative Research on Grain Legumes by the Bureau for Economic Growth, Agriculture, and Trade, US Agency for International Development, under the terms of Cooperative Agreement No. EDH-A-00-07-00005-00; and the US Department of Agriculture, Agricultural Research Service. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the US Agency for International Development or the US Government. We also thank Dr. Zixang Wen for his helpful comments on some aspects of data analyses.

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  1. Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA

    Kelvin Kamfwa & James D. Kelly

  2. USDA-ARS, Sugarbeet and Bean Research Unit, Michigan State University, 1066 Bogue St, East Lansing, MI, 48824, USA

    Karen A. Cichy

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  1. Kelvin Kamfwa
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All experiments described in this manuscript comply with the current US laws in which they were performed.

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Communicated by I. Rajcan.

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Kamfwa, K., Cichy, K.A. & Kelly, J.D. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Theor Appl Genet 128, 1999–2017 (2015). https://doi.org/10.1007/s00122-015-2562-5

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