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Crop productivity is severely reduced by water deficit and drought in many plant species including soybean. Improved root and shoot traits can contribute to drought tolerance ability of the plant. This research was conducted to identify QTL that underlie several root and shoot traits in the 'Essex' by 'Forrest' (ExF RILs, n=94) recombinant inbred line (RIL) soybean population. Field collected samples were used for gathering phenotypic data of basal root thickness (BRT), lateral root number (LRN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), and calculating RFW/SFW, and RDW/SDW ratios. All traits and ratios were compared against DNA markers using the composite interval mapping (CIM). A total of 12 QTL: 3 for MRL, 1 QTL for LRN, 1 QTL for BRT, 2 QTL for RFW, 2 QTL for RDW, 4 QTL for SFW, 3 QTL for SDW, and 3 QTL for SFW/SDW were identified and mapped on different linkage groups (LGs) A2, B2, C2, D1a, F, G, and N. The LOD scores of these QTL ranged from 2.5 to 6.0. No QTL were associated with RFW/RDW. The root and shoot trait QTL of this study may benefit breeding programs for producing cultivars tolerant to water deficit and high yield. Preliminary analyses of genes the QTL regions using GO annotation gave insight into genes that may underlie some of these QTLs.

Research of quantitative trait loci (QTL) for macronutrient accumulation in soybean seed is limited. Therefore, the objective of this research was to identify QTL related to macronutrients (N, C, S, P, K, Ca, and Mg) in seeds in 92 F 5:7 recombinant inbred lines (RILs) developed from a cross between MD 96-5722 (MD) and Spencer using a total 5,376 Single Nucleotide Polymorphism (SNP) markers. A genetic linkage map based on SNP markers was constructed using the Illumina Infinium SoySNP6K BeadChip Array. The RILs were genotyped using 537 polymorphic, reliably segregating SNP markers. A total of 8 QTL for K (qPOT001-qPOT008) were identified on LGs D1b (Chr 1), N (Chr 3), A1 (Chr 5), O (Chr 10), F (Chr 13), B2 (Chr 14), and J (Chr 16). Four QTL for Mg (qMAG001-qMAG004) were identified on LGs N (Chr 3), A1 (Chr 5), J (Chr 16), and G (Chr 18). One QTL for P (qPHO001), one for C on LG J (Chr 16), one for N (qNIT001) and S (qSUL001) on the same LG J (Chr 16), and one QTL for Ca (qCAL001) on LG G (Chr 18). K and Mg QTL were clustered together on LG A1 (Chr 5) with a peak position of 9.50 cM and LOD support interval of 8.50-9.50 cM. Similar observation was noticed for P, K, Mg, C, N, and S, where the QTL were clustered on LG J (Chr 16) with peak position of 11 cM for K, P, and S, and 10 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.cM for C and N, and 12 cM for Mg. The LOD support intervals for all these clustered QTL were between 8.90 and 12.30 cM. The QTL clustering of these nutrients suggests possible common physiological and genetic relationships, suggesting possible similar metabolic processes and pathways for these nutrients. The inverse relationships between N:S ratio and all nutrients suggest possible use of N:S ratio as a measure for higher nutrients accumulation in seed. Since most of QTL identified in this study were not previously reported, this research will further help breeders to improve nutrient accumulation in seeds and contribute to our understanding of the physiological and genetic bases of seed nutrition quality.

Phytophthora sojae causes Phytophthora root and stem rot disease of soybean (Glycine max), leading to huge annual yield loss worldwide, but resistance to Phytophthora sojae (Rps) genes remain elusive. Soybean cultivar ‘Yudou 29’ is resistant to P. sojae strain PsMC1, and this study aimed to clone, identify, and characterize the Rps gene in Yudou 29 (RpsYD29) and clarify its functional mechanism. We map-based cloned RpsYD29 (ZINC FINGER PROTEIN03, GmZFP03) using the families of a cross between Yudou 29 and a P. sojae-susceptible soybean cultivar ‘Jikedou 2’. P. sojae-resistance of GmZFP03 was functionally validated by stable soybean genetic transformation and allele-phenotype association analysis. GmZFP03 was identified as a C2H2-type zinc finger protein transcription factor, showing four-amino acid residue polymorphisms (V79F, G122-, G123-, and D125V) and remarkably different expression patterns between resistant and susceptible soybeans. Notably boosted activity and gene expression of superoxide dismutase (SOD) in resistant-type GmZFP03-expressed transgenic soybean, substantial enhancement of P. sojae resistance of wild-type soybean by exogenous SOD treatment, and GmZFP03 binding to and activation of two SOD1 (Glyma.03g242900 and Glyma.19g240400) promoters demonstrated the involvement of SOD1s in GmZFP03-mediated resistance to P. sojae strain PsMC1. Thus, this study cloned the soybean P. sojae-resistant GmZFP03, the product of which specifically targets two SOD1 promoters. GmZFP03 can be directly used for precise P. sojae-resistance soybean breeding.

Mycotoxin deoxynivalenol (DON), produced by Gibberella zeae (Schwein.) Petch (teleomorph of Fusarium graminearum Schwabe) was known to be both a virulence factor in the pathogenesis of Triticum aestivum L. (wheat) and an inhibitor of Arabidopsis thaliana L. seed germination. Fusarium graminearum causes both Gibberella ear rot in maize (Zea mays L.) and Fusarium head blight (FHB) in wheat and barley. Arabidopsis thaliana was also a host for the related root rot pathogen F. virguliforme Aoki. A. thaliana seedling growth was reduced by the pathogen in a proportional response to increasing spore concentrations. Here, the changes in transcript abundances corresponding to 10,560 A. thaliana expressed sequence tags (ESTs) was compared with changes in 192 known plant defense and biotic/abiotic stress related genes in soybean roots after infestation with F. virguliforme. A parallel comparison with a set of resistance pathways involved in response to the DON toxicity in A. thaliana was performed. A. thaliana data was obtained from the AFGC depository. The variations of transcript abundances in Arabidopsis and soybean treated with pathogen suggest that both plants respond to the pathogen mainly by common, possibly global responses with some specific secondary metabolic pathways involved in defense. In contrast, DON toxin appeared to impact central metabolisms in Arabidopsis plants with significant alterations ranging from the protein metabolism to redox production. Several new putative resistance pathways involved in responding to both pathogen and DON infestation in soybean and A. thaliana were identified.