Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean.  The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem.  In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line (RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the T₁ stage, and the six-leaf stage as the flowering critical stage was designated as the T₂ stage.  In total, 200 single nucleotide polymorphism (SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the T₁ stage, and 109 detected at the T₂ stage.  Among these SNP loci, one SNP cluster (s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the T₁ stage, and the elite haplotype showed significantly greater plant height than the others.  Meanwhile, one pleiotropic SNP cluster (ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the T₂ stage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition.  Furthermore, four co-associated SNP loci (ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the T₁ and T₂ stages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population.  More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by qRT-PCR.  Thus, these genetic loci and candidate genes could be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.

GmPHR1 from soybean (Glycine max) was isolated and characterized. This novel homolog of the AtPHR1 transcription factor confers tolerance to inorganic phosphate (Pi)-starvation. The gene is 2751 bp long, with an 819-bp open reading frame and five introns. Analysis of transcription activity in yeast revealed that the full-length GmPHR1 and its C-terminal activate the reporter genes for His, Ade and Ura, suggesting that the C-terminal peptide functions as a transcriptional activator. Quantitative real-time PCR indicated that patterns of GmPHR1 expression differed. For example, under low-Pi stress, this gene was quickly induced in the tolerant JD11 after 0.5 h, with expression then decreasing slowly before peaking at 12-24 h. By contrast, induction in the sensitive Niumaohuang (NMH) was slow, peaking at 6 h before decreasing quickly at 9 h. GmPHR1 showed sub-cellular localization in the nuclei of onion epidermal cells and Arabidopsis roots. Growth parameters in wild-type (WT) Arabidopsis plants as well as in overexpression (OE) transgenic lines were examined. Under low-Pi conditions, values for shoot, root and whole-plant dry weights, root to shoot ratios, and lengths of primary roots were significantly greater in OE lines than in the WT. These data demonstrate that GmPHR1 has an important role in conferring tolerance to phosphate starvation.