Preliminary QTL detection for Corynespora Leaf Fall disease resistance in rubber plant
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Abstract. Oktavia F, Sudarsono, Dinarti D. 2021. Preliminary QTL detection for Corynespora Leaf Fall disease resistance in rubber plant. Nusantara Bioscience 13: 53-61. Corynespora Leaf Fall (CLF) disease caused by Corynespora cassiicola fungus is one of the most important diseases of rubber trees. Conventional breeding to obtain the resistant rubber clones was constrained by the long time required for selection processes. This study was aimed to identify resistant loci linked with CLF disease on the rubber tree. Analysis was conducted on 104 F1 of BPM 1 x RRIM 600. The resistance evaluation of the population had been done against two C. cassiicola isolates and the molecular analysis was generated by using 28 selected SSR markers. There was a phenotypic variation in F1 resistance to both isolates with leaf wilting intensities ranged from 5.2% to 33.4% on CC-06 isolate, and from 3.5% to 36.4% on CC-22 isolate. There was no QTL identified on the genetic linkage map, but a single marker analysis showed that some loci associated with CLF disease. The associated loci can be used as a preliminary information to develop molecular markers linked with resistance to CLF disease to assist the rubber breeding programs.
2019-01-01
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References
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Cubry P, Pujade-Renaud V, Garcia D, Espeout S, Le Guen V, Granet F, Seguin M. 2014. Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.). Plant Breed 133(3):419-426. doi: 10.1111/pbr.12158
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Grattapaglia D, Sederoff R. 1994. Genetic linkage maps of Eucaliptus grandis and Eucaliptus urophylla using pseudo-test-cross-mapping strategy and RAPD markers. Genetics 137:1121-1137.
Hackett CA, Wachiraà FN, Paul S, Powell W, Waugh R. 2000. Construction of a genetic linkage map for Camellia sinensis (tea). Heredity 85:346-355.
Hadi H, Hartana A. 2004. Analysis of Molecular Marker for Hevea rubber Resistance to Corynespora Leaf Fall Disease. Indon Nat Rub Res 22(2):47-56.
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Lieberei R. 2007. South American Leaf Blight of the Rubber Tree (Hevea spp.): New Steps in Plant Domestication using Physiological Features and Molecular Markers. Annals of Bot 100(6):1125-1142. doi: 10.1093/aob/mcm133
Lincoln SE, Landers SL. 1993. Constructing Genetic Linkage Maps with MAPMAKER/EXP Version 3.0: A Tutorial and Reference Manual: A Whitehead Institute for Biomedical Research. Technical Report, Cambridge.
Ma JQ, Yao MZ, Wang XC, Jin JQ, Wang XM, Chen L. 2014. Construction of SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis). PLoS One 9(3):e93131.
Mantello CC, Cardoso-Silva CB, da-Silva CC, de-Souza LM, Scaloppi-Junior EJ, de Souza Gonçalves P, de Souza AP. 2014. De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS One 9(7):e102665. doi: 10.1371/journal.pone.0102665
McCouch SR, Tanksley SD. 1991. Development and use of Restriction Fragment Length Polymorphism in rice breeding and genetics. In GS. Khus & G. H. Toenissen (Eds.), Rice Biotechnology : Biotech Agr 8: 109-133). Phillipina: IRRI.
Novalina, Sagala AD. 2013. Construction of Hevea brasiliensis genetic linkage map and Identification of quantitative trait loci using RAPD markers. Inter J Adv Sci Engineer Inform Tech 3(1):71-75.
Orozco-Castillo, Chalmers C, Waugh R, Powell W. 1994. Detection of genetik diversity and selective gen introgression in coffee using RAPD markers. Theor Appl Genet 87:934-940.
Rattanawong R, Prapan K, Lekawipat N, Seguin M, Clement-Demange A. 2009. Detection of QTLs assotiation with growth, latex production and rubber quality for the development of Marker Asissted Selection (Hevea brasiliensis). IRRDB workshop on genome and transcriptome.
Rosa JRBF, Mantello CC, Garcia D. 2018. QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions. BMC Plant Biol 18(223):1-16. doi.org/10.1186/s12870-018-1450-y
Silva CC, Mantello CC, Campos T, Souza L. M, Gonçalves PS, Souza AP. 2014. Leaf-, panel and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. Mol Breed 34(3):1035-1053. doi: 10.1007/s11032-014-0095-2
Souza L, Gazaffi R, Mantello C, Silva C, Garcia D, Le Guen, V. 2013. QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate. PLoS One 8(4):1-10.
Souza L, Mantello C, Suzuki F, Rodrigo G, Le-Guen V. 2011. Development of a genetic linkage map of rubber (Hevea brasiliensis) based on microsatellite markers. Paper presented at the IUFRO tree biotechnology confrence. 26 Jun - 2 Jul 2011, Arraial D’Ajuda, Bahia, Brazil.
Tan A, Tan AM. 1996. Genetic studies of leaf diseases resistance in Hevea. J Nat Rubber Res 11(2):108-114.
Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Tangphatsornruang S. 2011. Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res. 18:471-482.
An Z, Zhao Y, Zhang X, Huang X, Hua Y, Cheng H, Li X, Huang H. 2019. A high-density genetic map and QTL mapping on growth and latex yield-related traits in Hevea brasiliensis Müll.Arg. Industrial Crops Prod 32:440-448. doi.org/10.1016/j.indcrop.2019.03.002
Breton F, Sanier C, d’Auzac A. 2000. Role of cassiicolin a host-selective toxin in pathogenicity of Corynespora cassiicola, causal agent of a leaf fall disease of Hevea. J. Rubb Res 3(2):115-128.
Champoux MC, Wang G, Sarkarung S, Mackill DJ, O'Toole JC, Huang N, McCouch SR. 1995. Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. Theor Appl Genet 90(7-8):969-981.
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK. 2005. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169-196.
Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF,de Souza Gonçalves P and de Souza AP. 2018. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. Front Plant Sci 9:1255. doi: 10.3389/fpls.2018.01255
Creste S, Neto AT, Figueira A. 2001. Detection of single sequence repeat polymorphism in denaturating polyacrylamide sequencing gels by silver staining. Plant Mol Bio Rep 19:299-306.
Cubry P, Pujade-Renaud V, Garcia D, Espeout S, Le Guen V, Granet F, Seguin M. 2014. Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.). Plant Breed 133(3):419-426. doi: 10.1111/pbr.12158
Feng SP, Li WG, Huang HS, Wang JY, Wu YT. 2009. Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85-97.
Grattapaglia D, Sederoff R. 1994. Genetic linkage maps of Eucaliptus grandis and Eucaliptus urophylla using pseudo-test-cross-mapping strategy and RAPD markers. Genetics 137:1121-1137.
Hackett CA, Wachiraà FN, Paul S, Powell W, Waugh R. 2000. Construction of a genetic linkage map for Camellia sinensis (tea). Heredity 85:346-355.
Hadi H, Hartana A. 2004. Analysis of Molecular Marker for Hevea rubber Resistance to Corynespora Leaf Fall Disease. Indon Nat Rub Res 22(2):47-56.
Joehanes R, Nelson JC. 2008. Genetics and population analysis : QGene 4.0, an extensible Java QTL-analysis platform. Bio Appl Note 24(23):2788–2789. doi: doi:10.1093/bioinformatics/btn523
Le-Guen V, Garcia D, Mattos C, Doare F, Lespinasse D, Seguin M. 2007. Bypassing of a phyllogenic Microcyclus ulei resistance in rubber tree analyzed by QTL detection. New Phytologist 173:335-345.
Le Guen V, Garcia D, Doaré F, Mattos C, Condina V, Couturier C, Seguin M. 2011. A rubber tree’s durable resistance to Microcyclus ulei is conferred by a qualitative gene and a major quantitative resistance factor. Tree Genet Genome 7:877–889.
Le Guen V, Garcia D, Mattos C, Fouet O, Doaré F, Condina V, Seguin M (2013). A newly identified locus controls complete resistance to Microcyclus ulei in the Fx2784 rubber clone. Tree Genet Genome 9(3):805-812. doi: 10.1007/s11295-013-0599-7
Le Guen V, Gay C, Xiong TC, Souza LM, Rodier-Goud M, Seguin M. 2011. Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis). Plant Breed 130(2):294-296. doi: 10.1111/j.1439-0523.2010.01774.x
Le Guen V, Lespinasse D, Oliver G, Rodier-Goud M, Pinard F, Seguin M. 2003. Molecular mapping of genes conferring field resistance to South American Leaf Blight (Microcyclus ulei) in rubber tree. Theor Appl Genet 108(1):160-167. doi: 10.1007/s00122-003-1407-9
Lespinasse D, Rodier-Goud M, Grivet L, Leconte A, Legnate H, Seguin M. 2000. A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite and isozyme markers. Theor Appl Genet 100:127-138.
Li D, Deng Z, Qin B, Liu X, Men Z. 2012. De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13(1):192-205.
Lieberei R. 2007. South American Leaf Blight of the Rubber Tree (Hevea spp.): New Steps in Plant Domestication using Physiological Features and Molecular Markers. Annals of Bot 100(6):1125-1142. doi: 10.1093/aob/mcm133
Lincoln SE, Landers SL. 1993. Constructing Genetic Linkage Maps with MAPMAKER/EXP Version 3.0: A Tutorial and Reference Manual: A Whitehead Institute for Biomedical Research. Technical Report, Cambridge.
Ma JQ, Yao MZ, Wang XC, Jin JQ, Wang XM, Chen L. 2014. Construction of SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis). PLoS One 9(3):e93131.
Mantello CC, Cardoso-Silva CB, da-Silva CC, de-Souza LM, Scaloppi-Junior EJ, de Souza Gonçalves P, de Souza AP. 2014. De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS One 9(7):e102665. doi: 10.1371/journal.pone.0102665
McCouch SR, Tanksley SD. 1991. Development and use of Restriction Fragment Length Polymorphism in rice breeding and genetics. In GS. Khus & G. H. Toenissen (Eds.), Rice Biotechnology : Biotech Agr 8: 109-133). Phillipina: IRRI.
Novalina, Sagala AD. 2013. Construction of Hevea brasiliensis genetic linkage map and Identification of quantitative trait loci using RAPD markers. Inter J Adv Sci Engineer Inform Tech 3(1):71-75.
Orozco-Castillo, Chalmers C, Waugh R, Powell W. 1994. Detection of genetik diversity and selective gen introgression in coffee using RAPD markers. Theor Appl Genet 87:934-940.
Rattanawong R, Prapan K, Lekawipat N, Seguin M, Clement-Demange A. 2009. Detection of QTLs assotiation with growth, latex production and rubber quality for the development of Marker Asissted Selection (Hevea brasiliensis). IRRDB workshop on genome and transcriptome.
Rosa JRBF, Mantello CC, Garcia D. 2018. QTL detection for growth and latex production in a full-sib rubber tree population cultivated under suboptimal climate conditions. BMC Plant Biol 18(223):1-16. doi.org/10.1186/s12870-018-1450-y
Silva CC, Mantello CC, Campos T, Souza L. M, Gonçalves PS, Souza AP. 2014. Leaf-, panel and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. Mol Breed 34(3):1035-1053. doi: 10.1007/s11032-014-0095-2
Souza L, Gazaffi R, Mantello C, Silva C, Garcia D, Le Guen, V. 2013. QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate. PLoS One 8(4):1-10.
Souza L, Mantello C, Suzuki F, Rodrigo G, Le-Guen V. 2011. Development of a genetic linkage map of rubber (Hevea brasiliensis) based on microsatellite markers. Paper presented at the IUFRO tree biotechnology confrence. 26 Jun - 2 Jul 2011, Arraial D’Ajuda, Bahia, Brazil.
Tan A, Tan AM. 1996. Genetic studies of leaf diseases resistance in Hevea. J Nat Rubber Res 11(2):108-114.
Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Tangphatsornruang S. 2011. Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res. 18:471-482.