• Nov 1 2016

    Applied Bean Genomics project a resounding success!

    By: Lori Wright

    Project Success!  We have been busy!

    • 7 Book chapters
    • 44 publications in peer reviewed journals
    • 50 abstracts and papers published in conference proceedings
    • 184 Oral or Poster Presentations at conferences and symposia
    • 14 graduate students completed their degree
    • 31 undergraduates gained and added valuable experience working on the project
    • 88 invention disclosures of advanced Phaseolus germplasm were made to the Catalyst Centre (Office of Research, University of Guelph)
    • 31 lines were supported for registration by the Ontario Pulse Committee
    • 9 lines were licenced for sale by companies, including: SeCan, Cooks, Parish and Heimbecker, Bolton Seeds, and Hensall District Co-Op.  Our most recently developed lines combine resistance to both Common Bacterial Blight and Anthracnose - certain to be valued by Ontario Growers.

    During the 6 year tenure of the project our knowledge of bean genomics and the genetics was considerably advanced in areas that relate directly to the utilization of beans by producers and the industry. Significant research accomplishments include:

    • sequencing the entire (>600 mB) genome of OAC Rex, the first common bacterial blight variety developed by the Guelph bean breeding program;
    • characterization of a 380 kbp fragment containing the CBB disease resistance marker SU91, a cluster with TIR-NBS-LRR (toll interleukin 1 receptor-nucleotide binding site-leucine rich repeat) resistance proteins a modified Niemann-Pic gene that may be responsible for the majority of the resistance in OAC Rex;
    • identification of additional molecular markers for CBB resistance, including polymorphisms in the Niemann-Pic gene;
    • identification of quantitative trait loci (QTL) for additional CBB resistance loci, Anthracnose resistance loci, nitrogen fixation loci, and yield;
    • resequencing the genomes of bean lines (SMARC1-PN1, SARC1, SMARC1N-PN1) integrating mutations conferring deficiencies in the storage protein synthesis      compositions, that gave insight into the genetic causes of the mutations and the mechanisms leading to improved sulphur amino acid compositions in these lines
    • sequencing the entire genomes of 7 isolates (fuscans and non-fuscans) of the disease causing organism of CBB (namely: Xanthomonas axonopodis pv. phaseoli [Xap]), identifying polymorphisms in type III effectors, that may be associated with differential aggressiveness of the isolates;
    • demonstration that the genetic gains achieved in selecting with the molecular marker SU91 in four BC1F1 families, with different genetic backgrounds, ranged from 6% and 21 %;
    • development of a model to estimate the effectiveness of marker assisted selection;
    • determination that protein isolates from the mutant lines (SMARC1-PN1, SMARC1N-PN1 and SARC1) produced biofilms with interesting physical differences that may be related to their unique protein compositions
    • characterization of the genomic locations of more than 100 structural and regulatory genes in the phenylpropanoid pathway in bean involved in seed coat colour and antioxidant levels,
    • identified the genomic location of the nondarkening gene on chromosome 10 in a pinto mapping population
    • determination of: differences in proanthocyanin content between darkening and nondarkening cranberry beans, measurement of the antioxidant values of various bean seed fractions from darkening and nondarkening cranberry beans; heat induced degradation of free flavonoids but relative stability of bound phenolics in regular and nondarkeneing beans.
    • determination of the health promoting properties of bean diets, including the demonstration of their effectiveness in reducing colon inflammation and their protective effect against severe colitis; as well as the demonstration that consumption of navy beans as a supplement to a high-fat diet, reduced the obese phenotype by improving the gut barrier integrity barrier and promoting a shift in the gut microbiota community such that key “anti-obesity” microbes were increased in bean-fed mice, compared to high-fat diet controls.

    Total Book Chapters: 7

    1. De Ron, AM, González, AM, Papa R, Bitocchi E, Debouck DG, Brick MA, Fourie D, Marsolais F, Beaver J, Geffroy V, McClean P, Lozano R, Yuste-Lisbona F, Casquero PA (2015) Common bean. In Grain Legumes. De Ron AM (ed.). Series Handbook of Plant Breeding. Springer Science + Business Media, New York. Vol 10. pp. 1-36. Springer Verlag, New York. doi: 10.1007/978-1-4939-2797-5_1   http://www.springer.com/us/book/9781493927968
    2. Pandurangan, S. and Marsolais, F. (2015). "Determining sulfur-limiting conditions for studies of seed composition in common bean Phaseolus vulgaris. Molecular Physiology and Ecophysiology of Sulfur.", in De Kok, LJ, Hawkesford, M.J., Rennenberg, H., Saito, K., and Schnug, E. (eds.) - Series Proceedings of the International Plant Sulfur Workshop, Springer, pp. 207-213.
    3. Perry, G and Pauls, K.P. (2011) Common Bacterial Blight In Phaseolus vulgaris. In Agricultural Research Updates. Editor P. Hendriks, Nova Science Publishers Inc.
    4. Reinprecht, Y., Perry G.E, and Pauls, K.P. (2016) A comparison of phenylpropanoid pathway gene families in common bean (Phaseolus vulgaris L.) with an emphasis on P450 genes and a focus on cinnamate 4-hydroxylase (C4H) genes. In The Common bean (Phaseolus vulgaris L.) Genome, Compendium of Plant Genomes, eds.Marta Santalla, Frederic Marsolais, Marcelino Pérez de la Vega. Springer
    5. Schernthaner J, Singh J, Labbé N, Liao D, Marsolais, F (2012) The unfolded protein response in plant seeds. In Agricultural Research Updates, Vol 2. Hendricks, BP, ed. Nova Science Publishers, Hauppauge, NY, pp. 429-454
    6. Yu, K., Shi, C. and Zhang, B. 2012. Development and   application of molecular markers to breed common  bean for resistance to common bacterial blight-current status and future directions, in M. Najafpour (ed.) Photosynthesis / Book 2, InTech Open Access  publisher, University Campus, STeP Ri, Slavka Krautzeka 83/A, 51000 Rijeka, Croatia. Chapter 18 pp. 365-388.
    7. Zhang C, Zarepoor L, Lu J, Power KA (2014). Functional foods and gut health. In: Nutraceuticals and Functional Foods: Natural Remedy. Nova Science Publishers, Inc. (Dr. SK. Brar, Dr. S Kaur and GS Dhillon; Eds).,  Chapter 15; pp. ISBN: 978-1-62948-793-9

    Total Peer reviewed Papers (those accepted for publication and those published): 44

    1. Burt, AJ, William, HM, Perry, G, Khanal, R, Pauls, KP, Kelly, JD and Navabi, A (2015) Candidate gene identification with SNP marker-based fine mapping of anthracnose resistance gene Co-4 in common bean PLoS ONE 10/2015; 10(10):e0139450
    2. Chen PX, Bozzo GG,  Freixas Coutin JA, Marcone, MF, Pauls PK,Tang Y, Zhang B, Liu R,  Tsao R (2014) Free and conjugated phenolic compounds and their antioxidant activities in regular and non-darkening cranberry bean (Phaseolus vulgaris L.) seed coats. Journal of  Functional  Foods. 10/2014; doi:10.1016/j.jff.2014.10.032
    3. Chen, P, Dupuis, J, Marcone, M, Pauls, KP, Liu, R, Liu, Q, Tang, Y, Zhang, B andTsao, R (2015) Physicochemical properties and in vitro digestibility of cooked regular and non-darkening cranberry beans (Phaseolus vulgaris L) and their effects on bioaccessibility, phenolic composition and antioxidant activity. Journal of Agricultural and Food Chemistry, 63(48): 10448-10458 Publication Date (Web): October 19, 2015
    4. Chen, P.X., Tang, Y., Marcone, M.F., Pauls, P.K., Zhang, B., Liu, R., Tsao, R. 2015. Characterization of free, conjugated and bound phenolics and lipophilic antioxidants in regular and non-darkening cranberry beans (Phaseolus vulgaris L.). Food Chemistry, 185(15), 298-308
    5. Chen, P.X., Tang, Y., Zhang, B., Liu, R., Marcone, M.F., Li, X., Tsao, R. 2014. 5-Hydroxymethyl-2-furfural and Derivatives Formed during Acid Hydrolysis of Conjugated and Bound Phenolics in Plant Foods and the Effects on Phenolic Content and Antioxidant Capacity. Journal of Agricultural and Food Chemistry, 62(20): 4754-4761
    6. Dezfulian, M.H., Soulliere, D., Dhaliwal, R.K., Madhulika, S. and Crosby, W.L. (2012). The SKP1-like gene Family of Arabidopsis Exhibits a High Degree of Differential Gene Expression and Gene Product Interaction During Development.  PLoSOne 7(11) e50984
    7. Durham, K. M., W. Xie, K. Yu, K. P. Pauls, E. Lee, and A. Navabi. Interaction of common bacterial blight Quantitative trait loci in a resistant inter-cross population of common bean. Plant Breeding (Accepted, 2012)
    8. Khanal R, Burt AJ, Woodrow L, Balasubramanian P and Navabi A. Genotypic association of parameters commonly used to predict canning quality of dry beans (Phaseolus vulgaris L.(2014) Crop Science 54:2564–2573. .
    9. Khanal, R, Rupert, T, Navabi, A, Smith, TH, Burt, A and Pauls, KP (2016) Mist Common Bean. Can J Plant Science Accepted Sept 2015
    10. Khanal, R, Smith, TH, Michaels, TE and Pauls, KP (2016) Dynasty Kidney Bean Can J. Plant Science 96: 215–217
    11. Khanal, R., Rupert, T., Navabi, A., Smith, T.H., Burt, A., and Pauls, K.P (2016) Fathom Common Bean. Canadian Journal Plant Science 96: 276–279 Accepted  Sept 2015. 
    12. Khanal, R., Rupert, T., Navabi, A., Smith, T.H., Michaels, T.E., Burt, A., and Pauls, K.P. (2016) Bolt Common Bean. Canadian Journal Plant Science Science 96: 218-221
    13. Khanal, R., Rupert, T., Navabi, A., Smith, T.H., Michaels, T.E., Burt, A., and Pauls, K.P. (2015) Yeti Kidney Bean. Can J Plant Science 96: 280–282
    14. Khanal, R., Smith, T.H. and Pauls, K.P (2016) OAC Spark Common Bean. Canadian Journal Plant Science Accepted 11-Apr-2016.
    15. Khanal, R., Smith, T.H., Michaels, T.E., and Pauls, K.P (2016) Lighthouse Common Bean. Canadian Journal Plant Science Accepted 11-Apr-2016.
    16. Khanal, S., J. Xue, R. Khanal,W. Xie, J. Shi, K. P. Pauls, and A. Navabi. 2013. Quantitative Trait Loci Analysis of Folate Content in Dry Beans, Phaseolus vulgaris L. International Journal of Agronomy (Open Access: http://www.hindawi.com/journals/ija/2013/983641/) 2013: doi:10.1155/2013/983641.
    17. Liao D, Cram D, Sharpe AG, Marsolais F. (2013) Transcriptome profiling identifies candidate genes associated with the accumulation of distinct sulfur γ-glutamyl dipeptides in Phaseolus vulgaris and Vigna mungo seeds. Front Plant Sci 4, 60 (Frontiers in Plant Genetics and Genomics, Research Topic The Legume Genome), accepted
    18. Liao D, Pajak A, Karcz SR, Chapman BP, Sharpe AG, Austin RS, Datla R, Dhaubhadel S, Marsolais F. (2012) Transcripts of sulphur metabolic genes are coordinately regulated in developing seeds of common bean lacking phaseolin and major lectins. J Exp Bot 63, 6283-6295
    19. Lin Y, Pajak A, Marsolais, F, McCourt P, Riggs D. Characterization of a cruciferin deficient mutant of Arabidopsis and its utility for overexpression of foreign proteins in plants. Submitted to PLoS ONE, PONE-D-12-33842R1, accepted April 19, 2013
    20. Liu, S., Yu, K., Haffner, M., Park, S.J., Banik, M., Crosby, W.L., and Pauls, K.P. 2010. Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.). Genetica. 138:709-716
    21. Marsolais F, Pajak A, Yin F, Taylor M, Gabriel M, Merino DM, Ma V, Kameka A, Vijayan P, Pham H, Huang S, Rivoal J, Bett K, Hernández-Sebastià C, Liu Q, Bertrand A, Chapman R. (2010) Proteomic analysis of common bean seed with storage protein deficiency reveals up-regulation of sulfur-rich proteins and starch and raffinose metabolic enzymes, and down-regulation of the secretory pathway. J Proteomics 73: 1587-1600 (1 citation)
    22. Monk JM, Zhang CP, Wu W, Zarepoor L, Lu JT, Liu R, Pauls P, Wood GA, Tsao R, Robinson LE, Power KA. (2015) White and dark kidney beans reduce colonic mucosal damage and inflammation in response to dextran sodium sulfate. Journal of Nutritional Biochemistry. 26:752-760.
    23. Monk, J.M., Lepp, D., Zhang, C., Wu, W., Zarepoor, L., Lu, J., Pauls, K.P., Tsao, R., Wood, G.A., Robinson, L.E., and Power, K.A. (2016).  Diets enriched with cranberry beans alter the microbiota and mitigate colitis severity and associated inflammation. Journal of Nutritional Biochemistry 28pp. 129-139. doi : 10.1016/j.jnutbio.2015.10.014
    24. Monk, Jennifer, Claire Zhang, Wendy Wu, Geoffrey A. Wood, Lindsay E. Robinson, and Krista A. Power (2014). Kidney bean diets enhance microbial activity and gut barrier integrity, priming the colon to attenuate intestinal inflammation during colitis. Canadian Nutrition Society Conference, St. John’s, Newfoundland, June 2014. Applied Physiology, Nutrition, and Metabolism, 2014, 39(5): 631
    25. Navabi A., Bett, K., Balasubramanian, P., Hou, A., Pauls, K. P. (2014).  Genetic diversity of the Canadian dry bean varieties released since 1930: a pedigree analysis.  Crop Science, 54, 993-1003
    26. Navabi A., Rupert, T., Park, S. J, Yu, K., Smith, T. H. and Pauls, K. P. 2013. Apex common bean. Can. J. Plant Sci. 93: 131-135
    27. Pandurangan S, Diapari M, Yin F, Munholland S, Perry G, Chapman BP, Huang S, Sparvoli F, Bollini R, Crosby WL, Pauls KP, Marsolais F.(2016) Genomic analysis of storage protein deficiency in common bean (Phaseolus vulgaris. Front Plant Sci 7, 389. doi: 10.3389/fpls.2016.00389 (Specialty section Plant Genetics and Genomics, Research Topic: Genomics assisted breeding for legume crops)
    28. Pandurangan S, Sandercock M, Beyaert R, Conn KL, Hou A, Marsolais F (2015) Differential response to sulfur nutrition of two common bean genotypes differing in storage protein composition. Front Plant Sci 6, 92, doi: 10.3389/fpls.2015.00092 (Specialty section Frontiers in Plant Physiology, Research Topic: Frontiers of sulfur metabolism in plant growth, development and stress response)
    29. Perry GE, Dinatale C, Xie W, Navabi A, Crosby W, Yu K, Shi M, and Pauls KP (2013). A Comparison of the Molecular Organization of Genomic Regions Associated with Resistance to Common Bacterial Blight in Two Phaseolus vulgaris Genotypes. Frontiers in Plant Science, doi: 10.3389/fpls.2013.00318.
    30. Rajsic P., A. Weersink, A. Navabi and P. Pauls. (2016)  Economics of Genomic Selection: The Role of Prediction Accuracy and Relative Genotyping Costs. Euphytica 210: 259-276.
    31. Reinprecht, Y.,Yadegari, Z., Perry, G.E.,Siddiqua, M., Wright, L.C., McClean, P.E. and Pauls, K.P.,  (2013) A comparison of genomic regions containing genes coding for enzymes and transcription factors for  the phenylpropanoid pathway in Phaseolus vulgaris and Glycine max. Frontiers in Plant Science, doi: 10.3389/fpls.2013.00317.
    32. Ropeke J, Bozzo GG (2015) Arabidopsis thaliana β-glucosidase BGLU15 attacks flavonol 3-O-β-glucoside-7-O-α-rhamnosides. Phytochemistry. 109: 14-24 (doi:10.1016/j.phytochem.2014.10.028).
    33. Shi, C., Chaudhary, S., Yu, K., Park, S. J., Navabi, A., and McClean, P. E. 2011. Identification of candidate genes associated with CBB resistance in common bean HR45 (Phaseolus vulgaris L.) using cDNA-AFLP. Molecular Biology Report 38:75–81. (4 citations)
    34. Shi, C., Navabi, A., and Yu, K. (2011). "Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations.", BMC Plant Biology (E-journal), 11:52. doi: 10.1186/1471-2229-11-52.
    35. Shi, C., Yu, K., Xie, W., Perry, G.E., Navabi, A., Pauls, K.P., Miklas, P.N., and Deidré, F. (2012). "Development of candidate gene markers associated to common bacterial blight resistance in common bean.", Theoretical and Applied Genetics (TAG), 125(7), pp. 1525-1537. doi : 10.1007/s00122-012-1931-6
    36. Smith, T.H., T. E. Michaels, A. Navabi, and K. P. Pauls. 2012. OAC Inferno common bean. Canadian Journal Plant Science 92: 589-592
    37. Smith, T.H., T. E. Michaels, A. Navabi, and K. P. Pauls. 2012. Rexeter common bean. Canadian Journal Plant Science.  92: 351–353
    38. Xie, W., Yu, K., Pauls, K. P., and Navabi, A. 2012. Application of image analysis in genetic studies of quantitative disease resistance: exemplified using common bacterial blight-common bean pathosystem. Phytopathology 102:434-442.
    39. Yin F, Pajak A, Chapman R, Sharpe A, Huang S, Marsolais F. (2011) Analysis of common bean expressed sequence tags identifies sulfur metabolic pathways active in seed and sulfur-rich proteins highly expressed in the absence of phaseolin and major lectins. BMC Genomics 12, 268
    40. Yu, K. Bacterial chromosome libraries of pulse crops-characteristics and applications. Journal of Biomedicine and Biotechnology Volume 2012, Article ID 493186, 8 pages doi:10.1155/2012/493186
    41. Yu, K., Shi, C. and Zhang, B. 2012. Development and   application of molecular markers to breed common  bean for resistance to common bacterial blight-current status and future directions, in M. Najafpour (ed.) Photosynthesis / Book 2, InTech Open Access  publisher, University Campus, STeP Ri, Slavka Krautzeka 83/A, 51000 Rijeka, Croatia. Chapter 18 pp. 365-388.
    42. Zhang C, Monk JM, Lu JT, Zarepoor L, Wu W, Liu R, Pauls KP, Wood GA, Robinson L, Tsao R, Power KA. Cooked navy and black bean diets improve biomarkers of colon health and reduce inflammation during colitis. Br J Nutr. 2014 May;111(9):1549-63. doi: 10.1017/S0007114513004352. Epub 2014 Feb 13. PMID: 24521520
    43. Zhang C, Monk JM, Lu JT, Zarepoor L, Wu W, Liu R, Pauls KP, Wood GA, Robinson L, Tsao R, Power KA. Cooked navy and black bean diets improve biomarkers of colon health and reduce inflammation during colitis. Br J Nutr. 2014 May; 111(9):1549-63.
    44. Zou, X., Shi, C., Austin, R. S., Merico, D., Munholland, S., Marsolais, F., Navabi, A., Crosby, W. L., Pauls, K. P., Yu, K. and Cui, Y. 2013. Genome-wide single nucleotide polymorphism and insertion-deletion discovery through next-generation sequencing of reduced representation libraries in common bean. Mol. Breeding. DOI: 10.1007/s11032-013-9997-7.
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