Michigan has been a leader in organic dry bean (Phaseolus vulgaris L) production. Previous research has found that dry bean yields were substantially lower under organic conditions compared with adjacent conventional production. Since pests are controlled with approved methods in each respective system, fertility appears to be an issue where the two systems may differ. Seventy-nine black and navy bean elite breeding lines and commercial checks, and a nonnodulating check were evaluated for yield under organic conditions in 3 MI locations in 2011 through 2013. These same genotypes were also assayed for nodulation characteristics, N fixation, and shoot and root growth in the greenhouse under N free conditions. Several traits measured in the greenhouse were significantly correlated to traits measured in the field. In particular, percent N derived from the atmosphere (%Ndfa) in the greenhouse was correlated with seed yield, N yield, and %Ndfa in the field for most site years, suggesting that enhancing symbiotic nitrogen fixation (SNF) traits could improve productivity in organic bean systems. Variability for SNF ability has been reported within P. vulgaris. The black bean landrace selection ‘Puebla 152’ has been identified as having high SNF ability, however is poorly adapted to cultivation in northern latitudes due to long season maturity and indeterminate type III growth habit. The recombinant inbred line (RIL) population developed by crossing Puebla 152 with the commercial black bean cultivar ‘Zorro’ was used to investigate the inheritance of enhanced SNF ability. The RIL population consisted of 122 lines and was evaluated in the greenhouse under N free conditions, and under low N conditions in the field in East Lansing (EL), MI and in Isabela, Puerto Rico (PR). The %Ndfa averaged between 12.7 % up to 66.6 %, although individual RILs ranged up to 90.5 %Ndfa. Traits measured in the greenhouse such as shoot biomass and biomass difference correlated moderately with yield and %Ndfa traits measured in the field.A quantitative trait loci (QTL) analysis of the phenotypic data from the field and greenhouse was conducted using single-nucleotide polymorphism (SNP) markers developed through the BeanCAP. The phenotypic data included traits for yield, nodule rating, biomass growth, agronomic traits, and N fixation. A total of 19 QTL associated with SNF traits were identified on all 11 chromosomes except Pv02 and large clusters of QTL were discovered on Pv01, Pv06, and Pv08. Many of the QTL associated with %Ndfa, N harvest index, and %N in biomass were also associated with candidate genes expressed in the nodules and roots. Candidate genes such as Phvul.006G146400, which is a chitin elicitor receptor kinase is involved in recognition of rhizobia in the early establishment of the symbiotic relationship. Other candidate genes are transcription factors, such as Phvul.006G034400 that is associated with %Ndfa determined by natural abundance δ15N analysis, is a MADS-box family gene and is expressed in young and mature green pods. The majority of QTL associated with genes expressed in the root or nodule are derived from Puebla 152 while QTL associated with genes with enhanced expression in stems and pods are associated with Zorro. This follows a pattern where Puebla 152 has superior SNF ability, whereas Zorro is highly efficient in partitioning the fixed-N into the seed. The QTL described serve as potential targets for improvement of SNF characteristics in adapted commercial dry bean genotypes.
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