Association Analysis and Identification of SNP Markers for Stemphylium Leaf Spot (<i>Stemphylium botryosum</i> f. sp. <i>spinacia</i>) Resistance in Spinach (<i>Spinacia oleracea</i>) — Oak Academic Publishing
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Association Analysis and Identification of SNP Markers for Stemphylium Leaf Spot (<i>Stemphylium botryosum</i> f. sp. <i>spinacia</i>) Resistance in Spinach (<i>Spinacia oleracea</i>)
Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
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US Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, USA
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Department of Plant Pathology, University of Arkansas, Fayetteville, USA
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University of California Cooperative Extension, Salinas, USA
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Vegetable Research Center, University of Arkansas, Alma, USA
,
Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
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Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
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Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
1 Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
2 US Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, USA
3 Department of Plant Pathology, University of Arkansas, Fayetteville, USA
4 University of California Cooperative Extension, Salinas, USA
5 Vegetable Research Center, University of Arkansas, Alma, USA
6 Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
7 Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
8 Department of Horticulture, 316 PTSC, University of Arkansas, Fayetteville, USA
Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia , is an important fungal disease of spinach ( Spinacia oleracea L.). The aim of this study was to conduct association analysis to identify single nucleotide polymorphism (SNP) markers associated with Stemphylium leaf spot resistance in spinach. A total of 273 spinach genotypes, including 265 accessions from the USDA spinach germplasm collection and eight commercial cultivars, were used in this study. Phenotyping for Stemphylium leaf spot resistance was evaluated in greenhouse; genotyping was conducted using genotyping by sequencing (GBS) with 787 SNPs; and single marker regression, general linear model, and mixed linear model were used for association analysis of Stemphylium leaf spot. Spinach genotypes showed a skewed distribution for Stemphylium leaf spot resistance, with a range from 0.2% to 23.5% disease severity, suggesting that Stemphylium leaf spot resistance in spinach is a complex, quantitative trait. Association analysis indicated that eight SNP markers, AYZV02052595_115, AYZV02052595_122, AYZV02057770_10404, AYZV02129827_205, AYZV0-2152692_182, AYZV02180153_337, AYZV02225889_197, and AYZV02258563_213 were strongly associated with Stemphylium leaf spot resistance, with a Log of the Odds (LOD) of 2.5 or above. The SNP markers may provide a tool to select for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection (MAS).
Morelock, T.E. and Correll, J.C. (2008) Spinach. In: Prohens, J. and Nuez, F., Eds., Vegetables I: Asteraceae, Brassicaceae, Chenopodiaceae, and Cucurbitaceae, Springer, New York, 189-218. http://dx.doi.org/10.1007/978-0-387-30443-4_6
Correll, J.C., Bluhm, B.H., Feng, C., Lamour, K., du Toit, L.J. and Koike, S.T. (2011) Spinach: Better Management of Downy Mildew and White Rust through Genomics. European Foundation for Plant Pathology, 129, 193-205. http://dx.doi.org/10.1007/s10658-010-9713-y
Correll, J.C., Morelock, T.E., Black, M.C., Koike, S.T., Brandenberger, L.P. and Dainello F.J. (1994) Economically Important Diseases of Spinach. Plant Disease, 78, 653-660. http://dx.doi.org/10.1094/PD-78-0653
Koike, S.T., Henderson, D.M. and Butler, E.E. (2001) Leaf Spot Disease of Spinach in California Caused by Stemphylium botryosum. Plant Disease, 85, 126-130. http://dx.doi.org/10.1094/PDIS.2001.85.2.126
Koike, S.T., Henderson, D.M. and Butler, E.E. (2001) Host-Specific Strain of Stemphylium Causes Leaf Spot Disease of California Spinach. California Agriculture, 55, 31-34. http://dx.doi.org/10.3733/ca.v055n05p31
du Toit, L.J. and Derie, M.L. (2001) Stemphylium botryosum Pathogenic on Spinach Seed Crops in Washington. Plant Disease, 85, 920. http://dx.doi.org/10.1094/PDIS.2001.85.8.920B
du Toit, L.J. and Hernandez-Perez, P. (2005) Efficacy of Hot Water and Chlorine for Eradication of Cladosporium variabile, Stemphylium botryosum, and Verticillium dahliae from Spinach Seed. Plant Disease, 89, 1305-1312. http://dx.doi.org/10.1094/PD-89-1305
Everts, K.L. and Armentrout, D.K. (2001) Report of Leaf Spot of Spinach Caused by Stemphylium botryosum in Maryland and Delaware. Plant Disease, 85, 1209. http://dx.doi.org/10.1094/PDIS.2001.85.11.1209B
Raid, R.N. (2004) Management of Stemphylium Leaf Spot on Baby Spinach Harvested for Spring Mix Production in the Everglades Agricultural Area of Florida. Summaries and Program of the 17th International Lettuce and Leafy Vegetable Conference, Quebec, 28-31 August 2004, 24.
Koike, S.T., Matheron, M.E. and du Toit, L.J. (2005) First Report of Leaf Spot of Spinach Caused by Stemphylium botryosum in Arizona. Plant Disease, 89, 1359. http://dx.doi.org/10.1094/PD-89-1359A
Morelock, T.E. and Correll, J.C. (2006) History of Spinach Production in the United States. Processing of the International Spinach Conference, La Conner, WA, 13-14 July 2006, 16.
Hernandez-Perez, P. and du Toit, L.J. (2006) Seedborne Cladosporium variabile and Stemphylium botryosum in spinach. Plant Disease, 90, 137-145. http://dx.doi.org/10.1094/PD-90-0137
Hernandez-Perez, P. (2005) Management of Seedborne Stemphylium botryosum and Cladosporium variabile Causing Leaf Spot of Spinach Seed Crops in Western Washington. M.S. Thesis, Washington State University, Pullman.
Koike, S.T., O’Neill, N.R. and Camara, M.P.S. (2001) Further Characterization of the Pathogen That Causes Stemphylium Leaf Spot of Spinach in California. Abstracts of the National Spinach Conference, Fayetteville, AR, 14-15 November 2001, 7.
Mou, B., Koike, S.T. and du Toit, L.J. (2008) Screening for Resistance to Leaf Spot Diseases of Spinach. HortScience, 43, 1706-1710.
Netzer, D., Globerson, D., Weintal, C.H. and Elyassi, R. (1985) Sources and Inheritance of Resistance to Stemphylium Leaf Spot of Lettuce. Euphytica, 34, 393-396. http://dx.doi.org/10.1007/BF00022934
Collard, B.C.Y. and Mackill D.J. (2008) Marker-Assisted Selection: An Approach for Precision Plant Breeding in the Twenty-First Century. Philosophical Transactions of the Royal Society B, 363, 557-572. http://dx.doi.org/10.1098/rstb.2007.2170
Xu, Y. and Crouch, J.H. (2008) Marker-Assisted Selection in Plant Breeding: From Publications to Practice. Crop Science, 48, 391-407. http://dx.doi.org/10.2135/cropsci2007.04.0191
Elshire, R.J., Glaubitz, J.C. and Sun, Q. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE, 6, e19379. http://dx.doi.org/10.1371/journal.pone.0019379
He, J., Zhao, X., Laroche, A., Lu, Z., Liu, H. and Li, Z. (2014) Genotyping-by-Sequencing (GBS), an Ultimate Marker-Assisted Selection (MAS) Tool to Accelerate Plant Breeding. Frontiers in Plant Science, 5, 484. http://dx.doi.org/10.3389/fpls.2014.00484
Sonah, H., Bastien, M., Iquira, E., Tardivel, A. and Legare, G. (2013) An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping. PLoS ONE, 8, e54603. http://dx.doi.org/10.1371/journal.pone.0054603
Dohm, J.C., et al. (2014) The Genome of the Recently Domesticated Crop Plant Sugar Beet (Beta vulgaris). Nature, 505, 546-549. http://dx.doi.org/10.1038/nature12817
Minoche, A.E., Dohm, J.C., Schneider, J., Holtgrawe, D., Viehover, P., Montfort, M., Sorensen, T.R., Weisshaar, B. and Himmelbauer, H. (2015) Exploiting Single-Molecule Transcript Sequencing for Eukaryotic Gene Prediction. Genome Biology, 16, 184. http://dx.doi.org/10.1186/s13059-015-0729-7
Van Deynze, A. (2014) A de Novo Draft Assembly of Spinach Using Pacific Biosciences Technology. Plant & Animal Genomics XXII Conference, San Diego, 10-15 January 2014. http://aa314.gondor.co/webinar/a-de-novo-draft-assembly-of-spinach-using-pacific-biosciences-technology/
van Deynze, A., Ashrafi, H., Hickey, L., Peluso, P., Rank, D., Chin, J., Rapicavoli, N., Drake, J., Garvin, T. and Schatz, M. (2015) Using Spinach to Compare Technologies for Whole Genome Assemblies. Plant & Animal Genomics XXIII Conference, San Diego, 10-14 January 2015.
Kisha, T., Sneller, C.H. and Diers B.W. (1997) Relationship between Genetic Distance among Parents and Genetic Variance in Populations of Soybean. Crop Science, 37, 1317-1325. http://dx.doi.org/10.2135/cropsci1997.0011183X003700040048x
Li, H. (2011) A Statistical Framework for SNP Calling, Mutation Discovery, Association Mapping and Population Genetic Parameter Estimation from Sequencing Data. Bioinformatics, 27, 2987-2993. http://dx.doi.org/10.1093/bioinformatics/btr509
Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K. and Wang, J. (2009) SOAP2: An Improved Ultrafast Tool for Short Read Alignment. Bioinformatics, 25, 1966-1967. http://dx.doi.org/10.1093/bioinformatics/btp336
Pritchard J.K., Stephens, M. and Donnelly, P. (2000) Inference of Population Structure Using Multilocus Genotype Data. Genetics, 155, 945-959.
Lv, J., Qi, J., Shi, Q., Shen, D., Zhang, S., Zhang, A., Shao, G., Li, H., Sun, Z., Weng, Y., Shang, Y., Gu, X., Li, X., Zhu, X., Zhang, J., van Treuren, R., van Dooijeweert, W., Zhang, Z. and Huang, S. (2012) Genetic Diversity and Population STRUCTURE of Cucumber (Cucumis sativus L). PLoS ONE, 7, e46919. http://dx.doi.org/10.1371/journal.pone.0046919
Evanno, G., Regnaut, S. and Goudet, J. (2005) Detecting the Number of Clusters of Individuals Using the Software STRUCTURE: A Simulation Study. Molecular Ecology, 14, 2611-2620. http://dx.doi.org/10.1111/j.1365-294X.2005.02553.x
Earl, D.A. and von Holdt, B.M. (2012) STRUCTURE HARVESTER: A Website and Program for Visualizing STRUCTURE Output and Implementing the Evanno Method. Conservation Genetics Research, 4, 359-361. http://dx.doi.org/10.1007/s12686-011-9548-7
Tamura, K., Stecher, G., Peterson, D., Ailipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30, 2725-2729. http://dx.doi.org/10.1093/molbev/mst197
Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S. (2007) TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. Bioinformatics, 23, 2633-2635. http://dx.doi.org/10.1093/bioinformatics/btm308
Lander, E.S. and Botstein, D. (1989) Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps. Genetics, 121, 185-199
Churchill, G.A. and Doerge, R.W. (1994) Empirical Threshold Values for Quantitative Trait Mapping. Genetics, 138, 963-971
Behare, J., Laterrot, H., Sarfatti, M. and Zamir, D. (1991) Restriction Fragment Length Polymorphism Mapping of the Stemphylium Resistance Gene in Tomato. Molecular Plant-Microbe Interaction, 4, 489-492. http://dx.doi.org/10.1094/MPMI-4-489
Kumar, P. (2007) Genetics of Resistance to Stemphylium Leaf Blight of Lentil (Lens culinaris) in the Cross Barimasur-4 × CDC Milestone. MSc Thesis, University of Saskatchewan, Saskatoon.
Saha, G.C., Sarker, A., Chen, W., Vandemark, G.J. and Muehlbauer, F.J. (2010) Inheritance and Linkage Map Positions of Genes Conferring Resistance to Stemphylium Blight in Lentil. Crop Science, 50, 1831-1839. http://dx.doi.org/10.2135/cropsci2009.12.0709