Identification of quantitative trait loci for symbiotic nitrogen fixation in common bean

Authors: KAMFWA, KELVIN - University Of Zambia; Cichy, Karen; KELLY, JAMES - Michigan State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2019
Publication Date: 2/22/2019
Citation: Kamfwa, K., Cichy, K.A., Kelly, J. 2019. Identification of quantitative trait loci for symbiotic nitrogen fixation in common bean. Theoretical and Applied Genetics. 132(5):1375-1387. https://doi.org/10.1007/s00122-019-03284-6.
DOI: https://doi.org/10.1007/s00122-019-03284-6

Interpretive Summary: Common bean (Phaseolus vulgaris L.) is a staple food crop for millions of people in East Africa and Latin America. Like other legumes, common bean is able to convert atmospheric nitrogen (N2) to NH3 through symbiotic nitrogen fixation (SNF) with soil bacteria from the Rhizobium genus. SNF plays an important role in maintaining the productivity of common bean as it reduces the amount of nitrogen (N) fertilizer required for common bean production thereby reducing production costs. When compared to other grain legumes such as soybeans and cowpeas, common bean is considered weak in N fixation. However, numerous studies have reported adequate genetic variability for SNF within common bean. The amount of N fixed by common bean varies from 0 kg ha-1 to 150 kg ha-1, depending on the environment and genotype. This genetic variability suggests genetic improvement of common bean for SNF is possible. The current study was conducted to expand the current knowledge of the genetic basis of SNF in the Andean genepool of common bean. The objective of this study was to identify regions of the bean genome controlling SNF in a bi-parental mapping population derived from two bean lines Solwezi and AO-1012-29-3-3A, contrasting in SNF capacity. Multiple genomic regions were found to be important and the major finding was a quantitative trait loci (QTL) Ndfa7.1DB, SA (R2=14.9%) was consistently identified in two greenhouse studies and overlapped with previously reported QTL. Once these QTL are validated further, they could potentially be deployed in marker-assisted breeding to accelerate development of bean cultivars with enhanced SNF.

Technical Abstract: Common bean (Phaseolus vulgaris L.) productivity can be improved through the genetic enhancement of its symbiotic nitrogen fixation (SNF) capacity. This study was aimed at understanding the genetic architecture of SNF through QTL analysis of a recombinant inbred line (RIL) population contrasting for SNF potential. The mapping population consisted of 188 F4:5 RILs derived from a cross of Solwezi and AO-1012-29-3-3A that were evaluated for SNF in the greenhouse and field in Zambia. The population was genotyped with 5398 single nucleotide polymorphism (SNP) markers. QTL for shoot biomass, nitrogen percentage in shoot biomass, nitrogen percentage in seed, total nitrogen derived from atmosphere (Ndfa) and percentage of nitrogen derived from the atmosphere (%Ndfa) were identified. Three QTL for %Ndfa were identified on chromosomes Pv01, Pv04 and Pv09. Five QTL for Ndfa were identified on Pv04, Pv06, Pv07, Pv09 and Pv11. The QTL Ndfa9.1SA identified in the current study overlapped with previously reported QTL for SNF. A major QTL Ndfa7.1DB, SA (R2=14.9%) was consistently identified in two greenhouse studies and overlapped with previously reported QTL. The QTL Ndfa4.2SA identified from the greenhouse experiment is novel and overlapped with the QTL %NB4.3SA, %NS4.2SA and %Ndfa4.2SA from the field experiment. The QTL that have been identified in both greenhouse and field experiments, and those that overlap with previously reported QTL are stable across environments and genetic backgrounds. Once these QTL are validated further, they could potentially be deployed in marker-assisted breeding to accelerate development of bean cultivars with enhanced SNF.