Identification of Candidate Genes Underlying an Iron Efficiency Quantitative Trait Locus in Soybean

Abstract

Prevalent on calcareous soils in the United States and abroad, iron deficiency is among the most common and severe nutritional stresses in plants. In soybean (Glycine max) commercial plantings, the identification and use of iron-efficient genotypes has proven to be the best form of managing this soil-related plant stress. Previous studies conducted in soybean identified a significant iron efficiency quantitative trait locus (QTL) explaining more than 70% of the phenotypic variation for the trait. In this research, we identified candidate genes underlying this QTL through molecular breeding, mapping, and transcriptome sequencing. Introgression mapping was performed using two related near-isogenic lines in which a region located on soybean chromosome 3 required for iron efficiency was identified. The region corresponds to the previously reported iron efficiency QTL. The location was further confirmed through QTL mapping conducted in this study. Transcriptome sequencing and quantitative real-time-polymerase chain reaction identified two genes encoding transcription factors within the region that were significantly induced in soybean roots under iron stress. The two induced transcription factors were identified as homologs of the subgroup lb basic helix-loop-helix (bHLH) genes that are known to regulate the strategy I response in Arabidopsis (Arabidopsis thaliana). Resequencing of these differentially expressed genes unveiled a significant deletion within a predicted dimerization domain. We hypothesize that this deletion disrupts the Fe-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT)/bHLH heterodimer that has been shown to induce known iron acquisition genes.

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves

“…By comparing the sequences of the molecular markers used in these studies to the introgressed regions, only the QTL identified on chromosome 3 [47–49] corresponded to an introgressed region (data not shown). Five DEGs corresponded to the region on chromosome 3 [14]. In six hour leaves we identified a S-adenosyl-L-methionine-dependent methyltransferases superfamily protein (Glyma03g28490).…”

Molecular mechanisms governing Arabidopsis iron uptake

“…Such a scenario might explain why Bur-0 requires lower levels of IRT1 transcripts when grown on standard growth medium [69] (Table 1). Studies exploiting natural variation have already provided important knowledge about Fe uptake and homeostasis [70,71] and are likely to remain an important research strategy in the future. In summary, the expression of IRT1 requires more than just the core strategy I transcriptional regulators, which may explain the strong connection between Fe uptake and other stress responses [72][73][74][75] and its integration into the plant developmental program [76][77][78].…”

Feruloyl-CoA 6'-Hydroxylase1-Dependent Coumarins Mediate Iron Acquisition from Alkaline Substrates in Arabidopsis

“…Although calcareous growth conditions generally reduce the productivity of strategy I plants, there are large differences among strategy I species and genotypes in their tolerance to Fe deficiencyinduced chlorosis. To a certain extent, these differences may relate to sequence deviations in FIT-and bHLHtype transcription factors that are primarily thought to drive IRT1-and FRO2-dependent Fe uptake (Peiffer et al, 2012). However, to date, it still remains unknown how nongraminaceous plants access ferric Fe in the rhizosphere and overcome the problem of low Fe solubility and impeded Fe reducibility in high pH soils.…”