Abstract
The para rubber tree (Hevea brasiliensis) is a major producer of high-quality natural rubber, accounting for more than 98% of the total production worldwide. Conventional breeding through recurrent selection has been used to obtain high-yielding clones in the past several decades. Although traditional breeding based on phenotypic selection has been effective, it is very laborious and time-consuming. The use of molecular markers in the rubber tree began in the 1980s, with isozymes being the first set of genetic markers developed followed by restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and the more commonly adopted simple sequence repeat (SSR) markers. At the turn of the millennium, the first genetic linkage map for the rubber tree was constructed based on anonymous markers such as RFLP and AFLP. In the past decade, several linkage maps have been reported, most of which were based on SSR or microsatellite markers. More recently, researchers have shifted from SSR markers to direct analyses of sequence variations such as single nucleotide polymorphisms (SNPs). Even though SNPs are generally less polymorphic than multi-allelic SSRs, their ubiquity in eukaryotic genomes makes them valuable for clone identification and marker-trait association analyses. Rapid advances in next-generation sequencing technologies have facilitated initial efforts in large-scale SNP discovery for genetic map construction in the rubber tree, leading to the first reports of SNP-based linkage maps in 2015. Since then, several high-density maps have been generated in order to identify markers and QTLs associated with traits of interest such as growth and latex yield. As the cost of SNP genotyping becomes more affordable, breeders can take full advantage of marker-assisted selection to expedite the development of elite rubber tree clones with multiple desirable agronomic traits.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
An Z, Zhao Y, Zhang X, Huang X, Hu 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 and Products 132:440–448. https://doi.org/10.1016/j.indcrop.2019.03.002
Baulkwill WJ, Webster CC (1989) Rubber. Longman Scientific and Technical, Burnt Mill, Harlow, Essex, England and Wiley, Wiley, New York
Besse P, Lebrun P, Seguin M, Lanaud C (1993) DNA fingerprints in Hevea brasiliensis (rubber tree) using human minisatellite probes. Heredity 70:237–244
Besse P, Seguin M, Lebrun P, Chevallier MH, Nicolas D, Lanaud C (1994) Genetic diversity among wild and cultivated populations of Hevea brasiliensis assessed by nuclear RFLP analysis. Theor Appl Genet 88:199–207
Bindu-Roy C, Nazeer MA, Saha T (2004) Identification of simple sequence repeats in rubber (Hevea brasiliensis). Curr Sci 87:807–811
Breseghello F, Sorrells ME (2006) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330. https://doi.org/10.2135/cropsci2005.09-0305
Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11, 569. https://doi.org/10.1186/1471-2164-11-569
Chanroj V, Rattanawong R, Phumichai T, Tangphatsornruang S, Ukoskit K (2017) Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone. Genomics 109:475–484
Chevallier MH (1988) Genetic variability of Hevea brasiliensis germplasm using isozyme markers. J Nat Rubber Res 3:42–53
Conson ARO, Taniguti CH, Amadeu RR, Andreotti IA, De Souza LM, Dos Santos LHB, Rosa JRBF, Mantello CC, Da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, 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. https://doi.org/10.3389/fpls.2018.01255
Cros D, Mbo-Nkoulou L, Bell JM, Oum J, Masson A, Soumahoro M, Tran DM, Achour Z, Le Guen V, Clement-Demange A (2019) Within-family genomic selection in rubber tree (Hevea brasiliensis) increases genetic gain for rubber production. Ind Crops Prod 138:111464
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 133:419–426. https://doi.org/10.1111/pbr.12158
De Souza LM, Dos Santos LHB, Rosa JRBF, Da Silva CC, Mantello CC, Conson ARO, Scaloppi EJ, Fialho JDF, De Moraes MLT, Gonçalves PDS, Margarido GRA, Garcia AAF, Le Guen V, De Souza AP (2018) Linkage disequilibrium and population structure in wild and cultivated populations of rubber tree (Hevea brasiliensis). Front Plant Sci 9. 10.3389/fpls.2018.00815
De Souza LM, Le Guen V, Cerqueira-Silva CBM, Silva CC, Mantello CC, Conson ARO, Vianna JPG, Zucchi MI, Scaloppi Junior EJ, Fialho JDF, De Moraes MLT, Gonçalves PDS, Souza APD (2015) Genetic diversity strategy for the management and use of rubber genetic resources: more than 1,000 wild and cultivated accessions in a 100-genotype core collection. PLoS ONE 10:e0134607. https://doi.org/10.1371/journal.pone.0134607
De Souza LM, Toledo-Silva G, Cardoso-Silva CB, Da Silva CC, Andreotti IAA, Conson ARO, Mantello CC, Le Guen V, Souza AP (2016). Development of single nucleotide polymorphism markers in the large and complex rubber tree genome using next-generation sequence data. Mol Breed 36:115
Dean W (1987) Brazil and the struggle for rubber. Cambridge University Press, UK
Dijkman MJ (1951) Hevea. Thirty years of research in the far east. Chronica Botanica. Waltham, Mass
Edwards D, Batley J, Cogan NOI, Forster JW, Chagne D (2007) Single nucleotide polymorphism discovery. In: Association mapping in plants. Springer, NY, pp 53–76
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. https://doi.org/10.1371/journal.pone.0019379
Ersoz ES, Yu J, Buckler ES (2007) Applications of linkage disequilibrium and association mapping in crop plants. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement: Vol. 1: Genomics approaches and platforms. Springer Netherlands, Dordrecht, pp 97–119
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
Feng SP, Li WG, Wang JY and Wu YT (2010) Construction of genetic linkage map for rubber tree (Hevea brasiliensis) based on SSR markers. Yi Chuan 32:857–863
Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, Velasco R, Troggio M, Myles S (2014) Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3 (Bethesda) 4, 1681–1687. https://doi.org/10.1534/g3.114.011023
Huang YF, Poland JA, Wight CP, Jackson EW, Tinker NA (2014) Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS ONE 9:e102448. https://doi.org/10.1371/journal.pone.0102448
Labate JA, Baldo A (2005) Tomato SNP discovery by EST mining and resequencing. Mol Breed 16:343–349. https://doi.org/10.1007/s11032-005-1911-5
Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756
Lau NS, Makita Y, Kawashima M, Taylor TD, Kondo S, Othman AS, Shu-Chien AC, Matsui M (2016) The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Sci Rep 6:28594. https://doi.org/10.1038/srep28594
Le Guen V, Doare F, Weber C, Seguin M (2009) Genetic structure of Amazonian populations of Hevea brasiliensis is shaped by hydrographical network and isolation by distance. Tree Genetics and Genomes 5:673–683
Le Guen V, Garcia D, Doaré F, Mattos CR, Condina V, Couturier C, Chambon A, Weber C, Espéout S, 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 Genomes 7:877–889. https://doi.org/10.1007/s11295-011-0381-7
Le Guen V, Gay C, Xiong TC, Souza LM, Rodier-Goud M, Seguin M (2010) Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis). Plant Breed 130:294–296
Leconte A, Lebrun P, Nicolas D, Seguin M (1994) Electrophoresis application to Hevea clone identification. Plant Res Dev 1:28–36
Lekawipat N, Teerawatanasuk K, Rodier-Goud M, Seguin M, Vanavichit A, Toojinda T, Tragoonrung S (2003) Genetic diversity analysis of wild germplasm and cultivated clones of Hevea brasiliensis Muell. Arg. by using microsatellite markers. J Rubber Res 6:36–47
Leonforte A, Sudheesh S, Cogan N, Salisbury P, Nicolas M, Materne M, Forster J, Kaur S (2013) SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.). BMC Plant Biol 13:1–14. https://doi.org/10.1186/1471-2229-13-161
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 100:975–984
Li AQ, Zhao CZ, Wang XJ, Liu ZJ, Zhang LF, Song GQ, Yin J, Li CS, Xia H, Bi YP (2010) Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos. Electron J Biotechn 13:6–7
Mantello CC, Cardoso-Silva CB, Da Silva CC, De Souza LM, Scaloppi Junior EJ, De Souza Gonçalves P, Vicentini R, 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:e102665. https://doi.org/10.1371/journal.pone.0102665
Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202. https://doi.org/10.1105/tpc.109.068437
Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genom 9:312. https://doi.org/10.1186/1471-2164-9-312
Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genom 11:180. https://doi.org/10.1186/1471-2164-11-180
Penner GA, Bush A, Wise R, Kim W, Domier L, Kasha K, Laroche A, Scoles G, Molnar SJ, Fedak G (1993) Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. PCR Methods Appl 2:341–345
Pootakham W, Chanprasert J, Jomchai N, Sangsrakru D, Yoocha T, Therawattanasuk K, Tangphatsornruang S (2011) Single nucleotide polymorphism marker development in the rubber tree, Hevea brasiliensis (Euphorbiaceae). Am J Bot 98:e337–e338
Pootakham W, Jomchai N, Ruang-Areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S (2015a) Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 105:288–295. https://doi.org/10.1016/j.ygeno.2015.02.002
Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S (2015b) Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). Front Plant Sci 6:367. https://doi.org/10.3389/fpls.2015.00367
Pootakham W, Shearman JR, Ruang-Areerate P, Sonthirod C, Sangsrakru D, Jomchai N, Yoocha T, Triwitayakorn K, Tragoonrung S, Tangphatsornruang S (2014) Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz). PLoS ONE 9:e116028. https://doi.org/10.1371/journal.pone.0116028
Pootakham W, Sonthirod C, Naktang C, Ruang-Areerate P, Yoocha T, Sangsrakru D, Theerawattanasuk K, Rattanawong R, Lekawipat N, Tangphatsornruang S (2017) De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species. Sci Rep 7:41457. https://doi.org/10.1038/srep41457
Pootakham W, Uthaipaisanwong P, Sangsrakru D, Yoocha T, Tragoonrung S, Tangphatsornruang S (2013) Development and characterization of single-nucleotide polymorphism markers from 454 transcriptome sequences in oil palm (Elaeis guineensis). Plant Breed 132:711–717
Priyadarshan PM (2003) Breeding Hevea brasiliensis for environmental constraints. In: Advances in agronomy. Academic Press, pp 351–400
Priyadarshan PM (2017) Refinements to Hevea rubber breeding. Tree Genet Genomes 13:20
Priyadarshan PM, Gonçalves PS, Omokhafe KO (2009) Breeding Hevea rubber. In: Jain SM, Priyadarshan PM (eds) Breeding plantation tree crops: tropical species. Springer New York, New York, NY, pp 469–522
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100
Rahman AYA, Usharraj A, Misra B, Thottathil G, Jayasekaran K, Feng Y, Hou S, Ong SY, Ng FL, Lee LS, Tan HS, Sakaff MKLM, Teh BS, Khoo B, Badai SS, Aziz NA, Yuryev A, Knudsen B, Dionne-Laporte A, Mchunu N, Yu Q, Langston B, Freitas TA, Young A, Chen R, Wang L, Najimudin N, Saito J, Alam M (2013) Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genom 14:75
Rosa JRBF, Mantello CC, Garcia D, De Souza LM, Da Silva CC, Gazaffi R, Da Silva CC, Toledo-Silva G, Cubry P, Garcia AAF, De Souza AP, Le Guen V (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. https://doi.org/10.1186/s12870-018-1450-y
Saba Rahim M, Sharma H, Parveen A, Roy JK (2018) Trait mapping approaches through association analysis in plants. In: Varshney RK, Pandey MK, Chitikineni A (eds) Plant genetics and molecular biology. Springer International Publishing, Cham, pp 83–108
Salgado LR, Koop DM, Pinheiro DG, Rivallan R, Le Guen V, Nicolás MF, De Almeida LGP, Rocha VR, Magalhães M, Gerber AL, Figueira A, Cascardo JCDM, De Vasconcelos AR, Silva WA, Coutinho LL, Garcia D (2014) De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genom 15:236. https://doi.org/10.1186/1471-2164-15-236
Schafleitner R, Tincopa LR, Palomino O, Rossel G, Robles RF, Alagon R, Rivera C, Quispe C, Rojas L, Pacheco JA, Solis J, Cerna D, Young Kim J, Hou J, Simon R (2010) A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genom 11:604. https://doi.org/10.1186/1471-2164-11-604
Seguin M, Besse P, Lebrun P, Chevallier M (1995) Hevea germplasm characterization using isozymes and RFLP markers. SPB Academic Publishing, Amsterdam
Seguin M, Gay C, Xiong TC, Rodier-Goud M (2001) Microsatellite markers for genome analysis of rubber tree (Hevea spp.). In: Jérôme S-B (ed) Biotechnology and rubber tree. Proceedings of IRRDB symposium. IRRDB, CIRAD-CP-HEVEA: IRRDB, CIRAD-CP-HEVEA
Shearman JR, Sangsrakru D, Jomchai N, Ruang-Areerate P, Sonthirod C, Naktang C, Theerawattanasuk K, Tragoonrung S, Tangphatsornruang S (2015) SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome. PLoS ONE 10:e0121961. https://doi.org/10.1371/journal.pone.0121961
Souza LM, Francisco FR, Gonçalves PS, Scaloppi Junior EJ, Le Guen V, Fritsche-Neto R, Souza AP (2019) Genomic selection in rubber tree breeding: a comparison of models and methods for dealing with G × E. bioRxiv, 603662. https://doi.org/10.1101/603662
Souza LM, Gazaffi R, Mantello CC, Silva CC, Garcia D, Le Guen V, Cardoso SEA, Garcia AaF, Souza, AP (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, e61238. https://doi.org/10.1371/journal.pone.0061238
Souza LM, Mantello CC, Suzuki F, Gazaffi R, Garcia D, Le Guen V, Garcia AAF, Souza AP (2011) Development of a genetic linkage map of rubber tree (Hevea braziliensis) based on microsatellite markers. BMC Proc 5:39
Souza LM, Mantello CC, Santos MO, De Souza Gonçalves P, Souza AP (2009) Microsatellites from rubber tree (Hevea brasiliensis) for genetic diversity analysis and cross-amplification in six Hevea wild species. Conserv Genet Resour 1:75. https://doi.org/10.1007/s12686-009-9018-7
Tan H (1987) Strategies in rubber tree breeding. In: Abbot AJ, Atkin RK (eds) Improving vegetatively propagated crops. Academic Press, London, pp 28–54
Tang C, Yang M, Fang Y, Luo Y, Gao S, Xiao X, An Z, Zhou B, Zhang B, Tan X, Yeang H-Y, Qin Y, Yang J, Lin Q, Mei H, Montoro P, Long X, Qi J, Hua Y, He Z, Sun M, Li W, Zeng X, Cheng H, Liu Y, Yang J, Tian W, Zhuang N, Zeng R, Li D, He P, Li Z, Zou Z, Li S, Li C, Wang J, Wei D, Lai C-Q, Luo W, Yu J, Hu S, Huang H (2016) The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2:16073. https://doi.org/10.1038/nplants.2016.73
Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P (2009) Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol 9:137
Tragoonrung S, Kanazin V, Hayes PM, Blake TK (1992) Sequence-tagged-site-facilitated PCR for barley genome mapping. Theor Appl Genet 84:1002–1008
Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Chanprasert J, Ngamphiw C, Jomchai N, Therawattanasuk K, Tangphatsornruang S (2011) Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res 18. https://doi.org/10.1093/dnares/dsr034
Varghese YA, Knaak C, Sethuraj MR, Ecke W (1997) Evaluation of random amplified polymorphic DNA (RAPD) markers in Hevea brasiliensis. Plant Breed 116:47–52. https://doi.org/10.1111/j.1439-0523.1997.tb00973.x
Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genom 11:726. https://doi.org/10.1186/1471-2164-11-726
Ward J, Bhangoo J, Fernandez-Fernandez F, Moore P, Swanson J, Viola R, Velasco R, Bassil N, Weber C, Sargent D (2013) Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genom 14:2
Weir BS (1979) Inferences about linkage disequilibrium. Biometrics 35:235–254. https://doi.org/10.2307/2529947
Xia Z, Liu K, Zhang S, Yu W, Zou M, He L, Wang W (2018) An ultra-high density map allowed for mapping QTL and candidate genes controlling dry latex yield in rubber tree. Ind Crops Prod 120:351–356
Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W, Zhang X (2013) Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biol 13:141
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Pootakham, W., Shearman, J.R., Tangphatsornruang, S. (2020). Development of Molecular Markers in Hevea brasiliensis for Marker-Assisted Breeding. In: Matsui, M., Chow, KS. (eds) The Rubber Tree Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-42258-5_5
Download citation
DOI: https://doi.org/10.1007/978-3-030-42258-5_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-42257-8
Online ISBN: 978-3-030-42258-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)