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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #316515
Title: Genome-wide association analysis of symbiotic nitrogen fixation in common bean

Author
item KAMFWA, KELVIN - Michigan State University
item Cichy, Karen
item KELLY, JAMES - Michigan State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/13/2015
Publication Date: 7/2/2015
Citation: Kamfwa, K., Cichy, K.A., Kelly, J.D. 2015. Genome-wide association analysis of symbiotic nitrogen fixation in common bean. Theoretical and Applied Genetics. 128(10):1999-2017.

Interpretive Summary: Nitrogen is frequently the most limiting nutrient for crop productivity. The two major sources of N for crop production are synthetic fertilizers and symbiotic nitrogen fixation (SNF) by legumes. SNF is the result of a symbiotic relationship between legumes and a diverse group of bacteria called Rhizobium. Common bean is considered weak in SNF in comparison with other major grain legumes. A genome-wide association study was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation and related traits in 259 common bean (Phaseolus vulgaris) genotypes. Significant single nucleotide polymorphisms (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. Significant SNPs identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of common bean for SNF.

Technical 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) comprised of 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.