Genetic factors associated with nodulation and nitrogen derived from atmosphere in a middle american common bean panel under low soil fertility

Authors: OLADZAD, ATENA - North Dakota State University; GONZALEZ, ABIEZER - University Of Puerto Rico; MACCHIAVELLI, RAUL - University Of Puerto Rico; ESTEVEZ DE JENSEN, CONSUELO - University Of Puerto Rico; BEAVER, JAMES - University Of Puerto Rico; Porch, Timothy - Tim; MCCLEAN, PHILLIP - North Dakota State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2020
Publication Date: 12/15/2020
Citation: Oladzad, A., Gonzalez, A., Macchiavelli, R., Estevez De Jensen, C., Beaver, J., Porch, T.G., Mcclean, P. 2020. Genetic factors associated with nodulation and nitrogen derived from atmosphere in a middle american common bean panel under low soil fertility. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.576078.
DOI: https://doi.org/10.3389/fpls.2020.576078

Interpretive Summary: Among grain legume crops, common beans are considered to have poor biological nitrogen fixation (BNF) capabilities although variation in nitrogen fixing capabilities exists within the species. The availability of a genetic panel varying in BNF capacity and a large-scale SNP data set for common bean provided an opportunity to discover genetic factors associated with nitrogen fixation among genotypes in the Middle American gene pool. Using nodulation and percentage of nitrogen derived from atmosphere (% NDFA) data collected from field trials, at least 11 genotypes with higher levels of BNF capacity were identified. Genome wide association studies (GWAS) detected both major and minor effects that control these traits. A major genetic factor affecting nodulation on chromosome Pv06 was discovered in the interval between 28.0-28.27 Mbp. In this interval, the peak SNP was located within a small GTPase that positively regulates cellular polarity and growth of root hair tips. Located 20kb upstream of this location is an auxin-responsive factor related gene involved in auxin transportation during root nodulation. For % NDFA, nitrate transporters, a squamosa promoter binding transcriptome factor, and MATE efflux family protein were identified as candidate genes. Three additional QTLs were identified on chromosomes Pv03, Pv09, and Pv11. These key candidate genes from both traits were integrated with previous studies on N2 fixation to describe a BNF pathway that could be used by breeders to develop markers for the selection of strong N2 fixing genotypes for low soil fertility conditions. These efforts could lead to improved biological nitrogen fixation in common bean and thus to reduced fertilizer inputs.

Technical Abstract: Among grain legume crops, common beans (Phaseolus vulgaris L.) are considered to have poor biological nitrogen fixation (BNF) capabilities although variation in nitrogen fixing capabilities exists within the species. The availability of a genetic panel varying in BNF capacity and a large-scale SNP data set for common bean provided an opportunity to discover genetic factors associated with nitrogen fixation among genotypes in the Middle American gene pool. Using nodulation and percentage of nitrogen derived from atmosphere (% NDFA) data collected from field trials, at least 11 genotypes with higher levels of BNF capacity were identified. Genome wide association studies (GWAS) detected both major and minor effects that control these traits. A major nodulation interval at Pv06:28.0-28.27 Mbp was discovered. In this interval, the peak SNP was located within a small GTPase that positively regulates cellular polarity and growth of root hair tips. Located 20kb upstream of this peak SNP is an auxin-responsive factor AUX/IAA-related gene involved in auxin transportation during root nodulation. For % NDFA, nitrate transporters, NRT1:2 and NRT1.7 (Pv02:8.64), squamosa promoter binding transcriptome factor (Pv08:28.42), and MATE efflux family protein (Pv06:10.91) were identified as candidate genes. Three additional QTLs were identified on chromosomes Pv03:5.24 Mbp, Pv09:25.89 Mbp, Pv11: 32.89 Mbp. These key candidate genes from both traits were integrated with previous results on N2 fixation to describe a BNF pathway that could be used by breeders to develop markers for the selection of strong N2 fixing genotypes for low soil fertility conditions.