1. Zhu J, Patzoldt WL, Shealy RT, Vodkin LO, Clough SJ, Tranel PJ. Transcriptome response to glyphosate in sensitive and resistant soybean. J Agric Food Chem. 2008 Aug 13;56(15):6355-63. Epub 2008 Jul 18.
2. Zou J, Rodriguez-Zas S, Aldea M, Li M, Zhu J, Gonzalez DO, Vodkin LO, DeLucia E, Clough SJ.Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific downregulation of photosynthesis.Mol Plant Microbe Interact. 2005 Nov;18(11):1161-74.
3. Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G.Transcription profiling of soybean nodulation by Bradyrhizobium japonicum.Mol Plant Microbe Interact. 2008 May;21(5):631-45.
4. Zhu, J., Patzoldt, W.L., Radwan, O., Tranel, P.J., Clough, S.J. 2009. Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome. The Plant Genome. 2:191-205.
5. Calla, B., Vuong, T., Radwan, O., Hartman, G.L., Clough, S.J. 2009. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and in Silico Mapping in Relation to Resistance Markers. The Plant Genome. 2:149-166.
Nodule
Root
Young leaf
Flower
1 cm pod
Pod shell 10 DAF
Pod shell 14 DAF
Seed 10 DAF
Seed 14 DAF
Seed 21 DAF
Seed 25 DAF
Seed 28 DAF
Seed 35 DAF
Seed 42 DAF
Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol. 2010 Aug 5;10:160.
Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010 Jul 1;63(1):86-99.
Oswaldo Valdes-Lopez, Saad M Khan, Robert J. Schmitz, Shiqi Cui, Jing Qiu, Trupti Joshi, Dong Xu, Brian Diers, Joseph R. Ecker, and Gary Stacey (2014) Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources. (in press)
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Shostak B, Induri SP, Sen S, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. Differential transpiration between pods and leaves during stress combination in soybean. Plant Physiol. 2023 Feb 22:kiad114. doi: 10.1093/plphys/kiad114. Epub ahead of print. PMID: 36810691.
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Zandalinas SI, Fichman Y, Sen S, Zeng S, Gómez-Cadenas A, Joshi T, Fritschi FB, Mittler R. Differential regulation of flower transpiration during abiotic stress in annual plants. New Phytol. 2022 Jul;235(2):611-629. doi: 10.1111/nph.18162. Epub 2022 May 12. PMID: 35441705; PMCID: PMC9323482.
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191.
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191.
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191.
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Shostak B, Induri SP, Sen S, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. Differential transpiration between pods and leaves during stress combination in soybean. Plant Physiol. 2023 Feb 22:kiad114. doi: 10.1093/plphys/kiad114. Epub ahead of print. PMID: 36810691.
Control vs Drought
Control vs Heat
Control vs Heat&Drought
Sinha R, Induri SP, Peláez-Vico MÁ, Tukuli A, Shostak B, Zandalinas SI, Joshi T, Fritschi FB, Mittler R. The transcriptome of soybean reproductive tissues subjected to water deficit, heat stress, and a combination of water deficit and heat stress. Plant J. 2023 Apr 3. doi: 10.1111/tpj.16222. Epub ahead of print. PMID: 37006191.
1. Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley RJ, Bilgin DD, Radwan O, Neece DJ, Clough SJ, May GD, Stacey G. Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection.Plant Physiol. 2010 Feb;152(2):541-52. Epub 2009 Nov 20.
1. Radwan O, Liu Y, Clough SJ. Transcriptional analysis of soybean root response to Fusarium virguliforme, the causal agent of sudden death syndrome.Mol Plant Microbe Interact. 2011 Aug;24(8):958-72.
1. Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum TJ, Mitchum MG.Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean.Mol Plant Microbe Interact. 2007 Mar;20(3):293-305.
2. Ithal N, Recknor J, Nettleton D, Maier T, Baum TJ, Mitchum MG.Developmental transcript profiling of cyst nematode feeding cells in soybean roots.Mol Plant Microbe Interact. 2007 May;20(5):510-25.
3. Kandoth PK, Ithal N, Recknor J, Maier T, Nettleton D, Baum TJ, Mitchum MG.The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells.Plant Physiol. 2011 Apr;155(4):1960-75. doi: 10.1104/pp.110.167536. Epub 2011 Feb 18.
Hajduch M, Ganapathy A, Stein JW, Thelen JJ. A systematic proteomic study of seed filling in soybean. Establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. Plant Physiol. 2005 Apr;137(4):1397-419.
Brechenmacher L, Lei Z, Libault M, Findley S, Sugawara M, Sadowsky MJ, Sumner LW, Stacey G. Soybean metabolites regulated in root hairs in response to the symbiotic bacterium Bradyrhizobium japonicum. Plant Physiol. 2010 Aug;153(4):1808-22.
Version 1.0
Metabolomics (LCMS, GCMS)
Root polar
Seed Nonpolar
Seed polar
Control
Water Stressed
Nguyen Lab (unpublished)
Version 1.0
Metabolomics (GCMS)
Root Hair and Stripped Root Heat Stress Time Points
Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S14.
Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics. 2010 Aug 11;11:469.
Version 1.0
SNP
Magellan vs PI567516C
Nguyen Lab (unpublished)
Version 1.0
SNP
41 NAM parents
Bilyeu Lab (unpublished)
Version 1.0
SNP
SNP50K Array
Song Q1, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB.
Development and evaluation of SoySNP50K, a high-density genotyping array for soybean.
PLoS One. 2013; 8(1):e54985. doi: 10.1371/journal.pone. 0054985. Epub 2013 Jan 25.
Version 1.0
Gene family
Transcription factors
Wang Z, Libault M, Joshi T, Valliyodan B, Nguyen HT, Xu D, Stacey G, Cheng J. SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol. 2010 Jan 18;10:14.
Version 1.0
Gene family
Cytochrome P450
Guttikonda SK, Trupti J, Bisht NC, Chen H, An YQ, Pandey S, Xu D, Yu O. Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450monooxygenases. BMC Plant Biol. 2010 Nov 9;10:243.
Version 1.0
G.Soja
SNP, Inversion/Deletion
Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7. Epub 2010 Dec 3.
Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010 Dec;42(12):1053-9. Epub 2010 Nov 14.
Version 1.0
Small RNA Data
Tag
seg_length
sequence
dcl4s_mutant_leaf_13_rep1
dcl4s_mutant_leaf_48_rep2
wide_type_leaf_37_rep1
wide_type_leaf_47_rep2
p_value
Chung WH1, Jeong N, Kim J, Lee WK, Lee YG, Lee SH, Yoon W, Kim JH, Choi IY, Choi HK, Moon JK, Kim N, Jeong SC.
Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes.
DNA Res. 2013 Nov 21. [Epub ahead of print]