OJGen  Vol.4 No.3 , June 2014
Localisation of Loci Involved in Resistance to Diaporthe toxica and Pleiochaeta setosa in White Lupin (Lupinus albus L.)
ABSTRACT

L. albus is an annual grain-legume crop mainly grown for high-protein fodder worldwide but also to produce large seeds for human consumption as a snack-food. In order to make genetic gains in grain yield, assessment of the genetic variation in the germplasm and identification of loci associated with agronomic traits are essential. Phomopsis blight (PB) and Pleiochaeta root rot (PRR), caused by the fungal pathogens Diaporthe toxica and, Pleiochaeta setosa respectively, are two major yield-limiting diseases of the L. albus crop. The extent of genetic diversity in 94 accessions of L. albus comprising: Australian and exotic cultivars, advanced breeding lines, and landraces originating from 26 different countries was determined utilizing PCR-based genic, and microarray-based Diversity Arrays Technology (DArT&#8482), markers. All accessions were evaluated for resistance to PB in two plant tissues (leaves and stems) using either sprayed or injected spore inoculum. A subset of 58 accessions was further evaluated for resistance to PRR by growing seedlings in spore-infested potting mix. The combined data of 724 (50 genic- and 674 DArT) markers were used for cluster analysis. A subset of 324 markers with call rate ≥95% and predicted disease scores of different genotypes were used to identify marker loci accounting for phenotypic variation in PB and PRR resistance using linear regression analysis. Several markers showed significant association with PB or PRR resistance at P < 0.05. Our results showed that favourable alleles for PB and PRR resistance are present in the diverse accessions investigated and they will provide valuable materials for lupin breeding.


Cite this paper
Raman, R. , Vipin, C. , Luckett, D. , Cowley, R. , Ash, G. , Harper, J. , Kilian, A. and Raman, H. (2014) Localisation of Loci Involved in Resistance to Diaporthe toxica and Pleiochaeta setosa in White Lupin (Lupinus albus L.). Open Journal of Genetics, 4, 210-226. doi: 10.4236/ojgen.2014.43022.
References
[1]   Argiriou, A., Kalivas, A., Michailidis, G. and Tsaftaris, A. (2012) Characterization of Profilin Genes from Allotetraploid (Gossypium hirsutum) Cotton and Its Diploid Progenitors and Expression Analysis in Cotton Genotypes Differing in Fiber Characteristics. Molecular Biology Reports, 39, 3523-3532.
http://dx.doi.org/10.1007/s11033-011-1125-3

[2]   Agrama, H.A. and Eizenga, G.C. (2008) Molecular Diversity and Genome-Wide Linkage Disequilibrium Patterns in a Worldwide Collection of Oryza sativa and Its Wild Relatives. Euphytica, 160, 339-355.
http://dx.doi.org/10.1007/s10681-007-9535-y

[3]   Ayers, N.M., McClung, A.M., Larkin, P.D., Bligh, H.F.J., Jones, C.A. and Park, W.D. (1997) Microsatellite and Single Nucleotide Polymorphism Differentiate Apparent Amylose Classes in an Extended Pedigree of US Rice Germplasm. Theor Appl Genet, 94, 773-781.
http://dx.doi.org/10.1007/s001220050477

[4]   Ali, M.L., Rajewski, J.F., Baenziger, P.S., Gill, K.S., Eskridge, K.M. and Dweikat, I. (2008) Assessment of Genetic Diversity and Relationship among a Collection of US Sweet Sorghum Germplasm by SSR Markers. Molecular Breeding, 21, 497-509.
http://dx.doi.org/10.1007/s11032-007-9149-z

[5]   Parzies, H.K., Spoor, W. and Ennos, R.A. (2000) Genetic Di-versity of Barley Landrace Accessions (Hordeum vulgare ssp. vulgare) Conserved for Different Lengths of Time in Ex Situ Gene Banks. Heredity, 84, 476-486.
http://dx.doi.org/10.1046/j.1365-2540.2000.00705.x

[6]   Raman, H., Raman, R., Nelson, M.N., Aslam, M.N., Rajasekaran, R., Wratten, N., Cowling, W.A., Kilian, A., Sharpe, A.G. and Schondelmaier, J. (2012) Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.). DNA Research, 19, 51-65.
http://dx.doi.org/10.1093/dnares/dsr041

[7]   Stodart, B.J., Mackay, M. and Raman, H. (2005) AFLP and SSR Analysis of Genetic Diversity among Landraces of Bread Wheat (Triticum aestivum L. Em. Thell) from Different Geographic Regions. Australian Journal of Agricultural Research, 56, 691-697.
http://dx.doi.org/10.1071/AR05015

[8]   Stodart, B.J., Mackay, M.C. and Raman, H. (2007) Assessment of Molecular Diversity in Landraces of Bread Wheat (Triticum aestivum L.) Held in an Ex Situ Collection with Diversity Arrays Technology (DArT). Australian Journal of Agricultural Research, 58, 1174-1182.
http://dx.doi.org/10.1071/AR07010

[9]   Takumi, S., E. Nishioka, H. Morihiro, Kawahara, T. and Matuoka, Y. (2009) Natural Variation of Morphological Traits in Wild Wheat Progenitor Aegilops tauschii Coss. Breeding Science, 59, 579-588.
http://dx.doi.org/10.1270/jsbbs.59.579

[10]   Botstein, D., White, R.l., Skolnick, M. and Davis, R.W. (1980) Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms. American Journal of Human Genetics, 32, 314-331.

[11]   Lander, E.S. and Botstein, D. (1989) Mapping Mendelian Factors Un-derlying Quantitative Traits Using RFLP Linkage Maps. Genetics, 121, 185-199.

[12]   Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Friters, A., Pot, J., Paleman, J., Kuiper, M. et al. (1995) AFLP: A New Technique for DNA Fingerprinting. Nucleic Acids Research, 23, 4407-4414.
http://dx.doi.org/10.1093/nar/23.21.4407

[13]   Weber, J. and May, P. (1989) Abundant Class of Human DNA Polymorphisms Which Can Be Typed Using the Polymerase Chain Reaction. American Journal of Human Genetics, 44, 388-396.

[14]   Jaccoud, D., Peng, K., Feinstein, D. and Kilian, A. (2001) Diversity Arrays: A Solid State Technology for Sequence Information Independent Genotyping. Nucleic Acids Research, 29, e25.
http://dx.doi.org/10.1093/nar/29.4.e25

[15]   Gupta, P.K., Rustgi, S. and Mir, R.R. (2008) Array-Based High-Throughput DNA Markers for Crop Improvement. Heredity, 101, 5-18.
http://dx.doi.org/10.1038/hdy.2008.35

[16]   Sorrells, M.E. (2007) Application of New Knowledge, Technologies, and Strategies to Wheat Improvement. Euphytica, 157, 299-306.
http://dx.doi.org/10.1007/s10681-007-9456-9

[17]   Ganal, M.W., Altmann, T. and Röder, M.S. (2009) SNP Identification in Crop Plants. Current Opinion in Plant Biology, 12, 211-217.
http://dx.doi.org/10.1016/j.pbi.2008.12.009

[18]   Nelson, M.N., Phan, H.T.T., Ellwood, S.R., Moolhuijzen, P.M., Hane, J., Williams, A., O‘Lone, C.E., Fosu-Nyarko, J., Scobie, M., Cakir, M., et al. (2006) The First Gene-Based Map of Lupinus angustifolius L.—Location of Domestication Genes and Conserved Synteny with Medicago truncatula. Theoretical and Applied Genetics, 113, 225-238.
http://dx.doi.org/10.1007/s00122-006-0288-0

[19]   Phan, H.T.T., Ellwood, S.R., Hane, J.K., Ford, R., Materne, M. and Oliver, R.P. (2007) Extensive Macrosynteny between Medicago truncatula and Lens culinaris ssp. culinaris. Theoretical and Applied Genetics, 114, 549-558.
http://dx.doi.org/10.1007/s00122-006-0455-3

[20]   Varshney, R.K., Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S., Baek, J., Rosen, B.D., Tar’an, B., et al. (2013) Draft Genome Sequence of Chickpea (Cicer arietinum) Provides a Resource for Trait Improvement. Nature Biotechnology, 31, 240-246.
http://dx.doi.org/10.1038/nbt.2491

[21]   Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J.A., Donoghue, M.T.A., Azam, S., Fan, G., Whaley, A.M., et al. (2012) Draft Genome Sequence of Pigeonpea (Cajanus cajan), an Orphan Legume Crop of Resource-Poor Farmers. Nature Biotechnology, 30, 83-89.
http://dx.doi.org/10.1038/nbt.2022

[22]   Parra-González, L., Aravena-Abarzúa, G., Navarro-Navarro, C., Udall, J., Maughan, J., Peterson, L., Salvo-Garrido, H. and Maureira-Butler, I. (2012) Yellow Lupin (Lupinus luteus L.) Transcriptome Sequencing: Molecular Marker Development and Comparative Studies. BMC Genomics, 13, 425.
http://dx.doi.org/10.1186/1471-2164-13-425

[23]   Yang, H., Tao, Y., Zheng, Z., Li, C., Sweetingham, M. and Howieson, J. (2012) Application of Next-Generation Sequencing for Rapid Marker Development in Molecular Plant Breeding: A Case Study on Anthracnose Disease Resistance in Lupinus angustifolius L. BMC Genomics, 13, 318.
http://dx.doi.org/10.1186/1471-2164-13-318

[24]   Yang, H., Tao, Y., Zheng, Z., Zhang, Q.F., Zhou, G., Sweetingham, M.W., Howieson, J.G. and Li, C. (2013) Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L. PLoS ONE, 8, e64799.
http://dx.doi.org/10.1371/journal.pone.0064799

[25]   Phan, H.T.T., Ellwood, S.R., Adhikari, K., Nelson, M.N. and Oliver, R.P. (2007) The First Genetic and Comparative Map of White Lupin (Lupinus albus L.): Identification of QTL for Anthracnose Resistance and Flowering Time, and a Locus for Alkaloid Content. DNA Research, 14, 59-70.
http://dx.doi.org/10.1093/dnares/dsm009

[26]   Croxford, A.E., Rogers, T., Caligari, P.D.S. and Wilkinson, M.J. (2008) High-Resolution Melt Analysis to Identify and Map Sequence-Tagged Site Anchor Points onto Linkage Maps: A White Lupin (Lupinus albus) Map as an Exemplar. New Phytologist, 180, 594-607.
http://dx.doi.org/10.1111/j.1469-8137.2008.02588.x

[27]   Lin, R., Renshaw, D., Luckett, D., Clements, J., Yan, G., Adhikari, K., Buirchell, B., Sweetingham, M. and Yang, H. (2009) Development of a Sequence-Specific Pcr Marker Linked to the Gene “Pauper” Conferring Low-Alkaloids in White Lupin (Lupinus albus L.) for Marker Assisted Selection. Molecular Breeding, 23, 153-161.
http://dx.doi.org/10.1007/s11032-008-9222-2

[28]   Raman, R., Cowley, R.B., Raman, H. and Luckett, D.J. (2014) Analyses Using SSR and DArT Molecular Markers Reveal That Ethiopian Accessions of White Lupin (Lupinus albus L.) Represent a Unique Genepool. Open Journal of Genetics, 4, 87-98.
http://dx.doi.org/10.4236/ojgen.2014.42012

[29]   Vipin, C., Luckett, D., Detering, F., Harper, J., Ash, G.J., Kilian, A., Ellwood, S.R., Phan, H.T.T. and Raman, H. (2013) Construction of Integrated Linkage Map of a Recombinant Inbred Line Population of White Lupin (Lupinus albus L.). Breeding Science, 63, 292-300.
http://dx.doi.org/10.1270/jsbbs.63.292

[30]   Luckett, D.J., Cowley, R.B., Richards, M.F. and Roberts, D.M. (2009) Breeding Lupinus albus for Resistance to the Root Pathogen Pleiochaeta setosa. European Journal of Plant Pathology, 125, 131-141.
http://dx.doi.org/10.1007/s10658-009-9465-8

[31]   Cowley, R.B., Ash, G., Harper, J.D.I. and Luckett, D.J. (2010) Evidence That Diaporthe toxica Infection of Lupinus albus Is an Emerging Concern for the Australian Lupin Industry. Australasian Plant Pathology, 39, 146-153.
http://dx.doi.org/10.1071/AP09067

[32]   Cowley, R., Ash, G., Harper, J., Smith, A., Cullis, B. and Luckett, D. (2012) Application of Multi-Phase Experiments in Plant Pathology to Identify Genetic Resistance to Diaporthe toxica in Lupinus albus. Euphytica, 186, 655-669.

[33]   Tanksley, S.D. and McCouch, S.R. (1977) Seed Banks and Molecular Maps: Unlocking Genetic Potential from the Wild. Science, 277, 1063-1066.

[34]   Cowley, R., Luckett, D.J., Ash, G., Harper, J., Vipin, C., Raman, H. and Ellwood, S. (2014) Identification of QTLs Associated with Resistance to Phomopsis Pod Blight (Diaporthe toxica) in Lupinus albus. Breeding Science, 64, 83-89.
http://dx.doi.org/10.1270/jsbbs.64.83

[35]   Breseghello, F. and Sorrells, M.E. (2006) Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars. Genetics, 172, 1165-1177.
http://dx.doi.org/10.1534/genetics.105.044586

[36]   Zhao, J., Paulo, M.-J., Jamar, D., Lou, P., van Eeuwijk, F., Bonnema, G., Vreugdenhil, D. and Koornneef, M. (2007) Association Mapping of Leaf Traits, Flowering Time, and Phytate Content in Brassica rapa. Genome, 50, 963-973.
http://dx.doi.org/10.1139/G07-078

[37]   Soto-Cerda, B.J. and Cloutier, S. (2012) Association Mapping in Plant Genomes. In: Caliskan, M., Ed., Genetic Diversity in Plants, InTech.
http://www.intechopen.com/books/howtoreference/genetic-diversity-in-plants/association-mapping-in-plant-genomes

[38]   Courtois, B., Audebert, A., Dardou, A., Roques, S., Ghneim-Herrera, T., Droc, G., Frouin, J., Rouan, L., Gozé, E., Kilian, A., et al. (2013) Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel. PLoS ONE, 8, e78037.
http://dx.doi.org/10.1371/journal.pone.0078037

[39]   Iqbal, M.J., Mamidi, S., Ahsan, R., Kianian, S.F., Coyne, C.J., Hamama, A.A., Narina, S.S. and Bhardwaj, H.L. (2012) Population Structure and Linkage Disequilibrium in Lupinus albus L. Germplasm and Its Implication for Association Mapping. Theoretical and Applied Genetics, 125, 517-530.
http://dx.doi.org/10.1007/s00122-012-1850-6

[40]   Peakall, R. and Smouse, P.E. (2006) GenALEx 6: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research. Molecular Ecology Notes, 6, 288-295.
http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x

[41]   Vekemans, X. (2002) Aflp-Surv Version 1.0. Distributed by the Author. Laboratoire De Génétique Et Ecologie Végétale, Université Libre De Bruxelles, Belgium.
http://www.ulb.ac.be/sciences/lagev

[42]   Coart, E., Van Glabeke, S., Petit, R.J., Van Bockstaele, E. and Roldán-Ruiz, I. (2005) Range Wide Versus Local Patterns of Genetic Diversity in Hornbeam (Carpinus betulus L.). Conservation Genetics, 6, 259-273.
http://dx.doi.org/10.1007/s10592-004-7833-7

[43]   Jaccard, P. (1908) Nouvelles Recherches Sur La Distribution Florale. Bulletin de la Société vaudoise des Sciences Naturelles, 44, 223-270.

[44]   Clarke, K.R. and Gorley, R.N. (2006) Primer V6: User Manual/Tutorial. PRIMER-E Ltd., Plymouth.

[45]   Cowley, R., Luckett, D., Harper, J. and Ash, G. (2012) Development of a Reliable and Rapid Detached Leaf Assay to Detect Resistance to the Fungal Disease Phomopsis Leaf Blight, Caused by Diaporthe toxica, in Lupinus albus. Canadian Journal of Plant Pathology, 34, 401-409.
http://dx.doi.org/10.1080/07060661.2012.705327

[46]   Cowley, R.B., Ash, G.J., Harper, J.D.I. and Luckett, D.J. (2012) Evaluation of Resistance to Phomopsis Stem Blight (Caused by Diaporthe toxica) in Lupinus albus. European Journal of Plant Pathology, 133, 631-644.
http://dx.doi.org/10.1007/s10658-012-9942-3

[47]   Coombes, N.E. (2002) The Reactive Tabu Search for Efficient Correlated Experimental Designs. Ph.D. Thesis, John Moores University, Liverpool.

[48]   Butler, D.G., Cullis, B.R., Gilmour, A.R. and Gogel, B.J. (2009) ASREML-R Reference Manual. Release 3.0. Technical Report, Queensland Department of Primary Industries, Australia.

[49]   Wunderlich, N., Ash, G.J., Harper, J.D.I., Cowley, R.B. and Luckett, D.J. (2008) Penetration and Symptom Development of Pleiochaeta Root Rot in Susceptible and Resistant Lupinus albus Cultivars. Australasian Plant Pathology, 37, 387-391.
http://dx.doi.org/10.1071/AP08014

[50]   Sweetingham, M. and Yang, H. (1998) New Sources of Resistance to Pleiochaeta and Eradu Patch Disease in Lupinus Species. GRDC Final Report, Project UWA 166, CLIMA, UWA, Perth, 49, 1213-1223.

[51]   Cullis, B.R., Smith, A.B. and Coombes, N.E. (2006) On the Design of Early Generation Cultivar Trials with Correlated Data. Journal of Agricultural, Biological, and Environmental Statistics, 11, 381-393.
http://dx.doi.org/10.1198/108571106X154443

[52]   Team, R.C. (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.

[53]   Sarkar, D. (2008) Lattice: Multivariate Data Visualization with R. Springer, New York.

[54]   Wickham, H. (2011) The Split-Apply-Combine Strategy for Data Analysis. Journal of Statistical Software, 40, Published Online.

[55]   Wickham, H. (2007) Reshaping Data with the Reshape Package. Journal of Statistical Software, 21, 1-20
http://www.jstatsoft.org/v21/i12/

[56]   Adhikari, K.N., Thomas, G., Diepeveen, D. and Trethowan, R. (2013) Overcoming the Barriers of Combining Early Flowering and Anthracnose Resistance in White Lupin (Lupinus albus L.) for the Northern Agricultural Region of Western Australia. Crop and Pasture Science, 64, 914-921.
http://dx.doi.org/10.1071/CP13249

[57]   Jing, R., Johnson, R., Seres, A., Kiss, G., Ambrose, M.J., Knox, M.R., Noel Ellis, T.H. and Flavell, A.J. (2007) Gene-Based Sequence Diversity Analysis of Field Pea (Pisum). Genetics, 177, 2263-2275.
http://dx.doi.org/10.1534/genetics.107.081323

[58]   Chen, Y., Lee, L.S., Luckett, D.J., Henry, R., Hill, H. and Edwards, M. (2007) A Quinolizidine Alkaloid O-Tigloyltransferase Gene in Wild and Domesticated White Lupin (Lupinus albus). Annals of Applied Biology, 151, 357-362.
http://dx.doi.org/10.1111/j.1744-7348.2007.00175.x

[59]   Adhikari, K., Buirchell, B.J., Thomas, G.J., Sweetingham, M.W. and Yang, H. (2009) Identification of Anthracnose Resistance in Lupinus albus L. and Its Transfer from Landraces to Modern Cultivars. Crop & Pasture Science, 60, 472-479.
http://dx.doi.org/10.1071/CP08092

[60]   Flint-Garcia, S.A., Thornsberry, J.M. and Buckler, E.S. (2003) Structure of Linkage Disequilibrium in Plants. Annual Review of Plant Biology, 54, 357-374.
http://dx.doi.org/10.1146/annurev.arplant.54.031902.134907

 
 
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