2012 Annual Report 4.Accomplishments 1. New tools for studying gene expression in pea and lentil. The ability to precisely detect differences in gene expression between plants requires the use of “reference” genes, which should be stably expressed across different lines and treatments, and serve to normalize data for other genes. ARS scientists in Pullman, Washington identified five different genes in pea and lentil that can be used as reference genes. The reference genes (TIF, 18S rRNA, actin, B-tubulin 2 and B-tubulin. 3)were used to normalize data from pea seedlings that were inoculated with the root rot pathogen Aphanomyces euteiches. Several genes, including callose synthase and B-1-3 glucanase, were identified that were expressed at higher levels in tolerant peas, suggesting these genes have a role in defense against disease. PCR primers and protocols developed during this study are useful tools for amplifying reference genes that can be applied to gene expression studies across a broad range of plant materials and growing conditions. Review Publications Fortuna, A., Honeycutt, C.W., Vandemark, G.J., Griffin, T.S., Larkin, R.P., He, Z., Wienhold, B.J., Sistani, K.R., Albrecht, S.L., Woodbury, B.L., Torbert III, H.A., Powell, J.M., Hubbard, R.K., Eigenberg, R.A., Wright, R.J., Allredge, R.J. 2012. Links among nitrification, nitrifier communities and edaphic properties in contrasting soils receiving dairy slurry. Journal of Environmental Quality. 41:262-272. Abi-Ghanem, R., Carpenter-Boggs, L., Smith, J.L., Vandemark, G.J. 2012. Nitrogen fixation by U.S. and Middle Eastern chickpeas with commercial and wild Middle Eastern inocula. International Scholarly Research Network (ISRN). Volume 2012, Article ID 981842, 5 pages. Mcgee, R.J., Coyne, C.J., Pilet Nayel, M., Moussart, A., Tivoli, B., Baranger, A., Hamon, C., Mcphee, K., Vandemark, G.J. 2012. Registration of Pea Germplasm Partially Resistant to Aphanomyces Root Rot for Breeding Fresh or Freezer Pea and Dry Pea Types. Journal of Plant Registrations. 6:203-207. Peever, T., Chen, W., Adbo, Z., Kaiser Jr, W.J. 2012. Genetic of virulence in Ascochyta rabiei. Plant Pathology. 61: 754-760. DOI: 10.1111/j.1365-3059.2011.02566.x. Ali, H., Haq, A., Shah, T., Chen, W. 2012. Validation of molecular markers for resistance among Pakistani chickpea germplasm to races of Fusarium oxysporum f. sp. ciceris. European Journal of Plant Pathology. 132:237-244. DOI 10.1007/s10658-011-9868-1. Attanayake, R., Porter, L., Johnson, D., Chen, W. 2012. Genetic and phenotypic diversity and random association of DNA markers of the fungal plant pathogen Sclerotinia sclerotiorum from soil on a fine geographic scale.. Soil Biology and Biochemistry. 55:28-36. Yang, L., Li, G., Zhang, J., Jiang, D., Chen, W. 2011. Compatibility of Coniothyrium minitans with Compound Fertilizer in Suppressionof Sclerotinia sclerotiorum. Biological Control. 59:221-227. Ali, H., Alam, S., Attanayake, R., Rahman, Chen, W. 2012. Population structure and mating type distribution of the chickpea blight pathogen Ascochyta rabiei from Pakistan and United States. Journal of Plant Pathology. 94: 99-108. Kwon, S.J., Brown, A.F., Hu, J., Mcgee, R.J., Watt, C., Kisha, T.J., Timmerman-Vaughan, G., Grusak, M.A., Mcphee, K., Coyne, C.J. 2012. Genetic diversity, population structure and genome-wide marker-trait association analysis of the USDA pea (Pisum sativum L.) core collection. Genes and Genomics. 10.1007/s13258-011-0213-z. Dugan, F.M., Lupien, S.L., Chen, W. 2012. Clonostachys rhizophaga and other fungi from chickpea debris in the Palouse region of the Pacific Northwest, USA. North American Fungi. 7(6): 1-11. Madrid, E., Rajesh, P., Millan, T., Chen, W. 2011. Characterization and genetic analysis of an EIN4-like sequence (CaETR-1) located in QTL ARI implicated in Ascochyta blight resistance in chickpea. Plant Cell Reports. 31:1033-1042. DOI 10.1007/s00299-011-1221-9. Njambere, E., Chen, W., Frate, C., Temple, S. 2011. Ascospore dimorphism-associated mating types of Sclerotinia trifoliorum equally capable of infecting chickpea. Australasian Plant Pathology. 40:648-655. DOI 10.1007/s13313-011-0069-3. Attanayake, R., Glawe, D., Mcphee, K., Dugan, F.M., Chen, W. 2011. Potential alternative hosts for the pea powdery mildew pathogen Erysiphe trifolii. Pisum Genetics. 42:18-20. Saha, G., Vandemark, G.J. 2012. Evaluation of expression stability of candidate references genes among green and yellow pea cultivars (Pisum sativum L.) subjected to abiotic and biotic stress. American Journal of Plant Sciences. 5:235-242.