Skip to main content
SpringerLink
Log in

Constructing high-density genetic maps for polyploid sugarcane (Saccharum spp.) and identifying quantitative trait loci controlling brown rust resistance

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Sugarcane (Saccharum spp.) is an important economic crop for producing edible sugar and bioethanol. Brown rust has long been a major disease impacting sugarcane production worldwide. Resistance resource and markers linked to resistance are valuable tools for disease resistance improvement. An F1 segregating population derived from a cross between two hybrid sugarcane clones, brown rust-susceptible CP95-1039 and brown rust-resistant CP88-1762, were genotyped using genotyping by sequencing approach and also phenotyped in a replicated field trial. Single nucleotide polymorphism (SNP) and presence/absence markers were called with seven different pipelines to maximize reliable marker identification. High-density maps were constructed for both parental clones with a total map length of 4224.4 cM, and a marker density of one marker per 1.7 cM for CP95-1039, and a total map length of 4373.2 cM, and one marker per 2.0 cM for CP88-1762. Among the seven SNP callers, Tassel and Genome Analysis ToolKit performed better than other callers in single-dose SNP detection and contribution to genetic maps. Two major quantitative trait loci (QTL) controlling brown rust resistance were identified, which can explain 21 and 30% of the phenotypic variation, respectively. The genetic maps generated here will improve our understanding of sugarcane’s complex genome structure and discovery of underlying sequence variations controlling agronomic traits. The putative QTL controlling brown rust resistance can effectively be utilized in sugarcane breeding programs to expedite the selection process of brown rust resistance after validation.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Aitken KS, McNeil MD, Hermann S, Bundock PC, Kilian A, Heller-Uszynska K, Henry RJ, Li J (2014a) A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput diversity array technology (DArT) markers. BMC Genomics 15:1

    Article  Google Scholar 

  • Aitken KS, McNeil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J (2014b) Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane. BMC Plant Biol 14:190

    Article  PubMed  PubMed Central  Google Scholar 

  • Alwala S, Kimbeng CA, Veremis JC, Gravois KA (2008) Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers. Euphytica 164:37–51

    Article  CAS  Google Scholar 

  • Alwala S, Kimbeng C (2010) Molecular genetic linkage mapping in Saccharum: strategies, resource and achievements. In: Henry R, Kole C (eds) Genetics, genomics and breeding of sugarcane. Science Publishers, New Hampshire, pp 69–96

  • Balsalobre TWA, da Silva PG, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP (2017) GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 18:72

    Article  PubMed  PubMed Central  Google Scholar 

  • Bourke PM, Voorrips RE, Visser RG, Maliepaard C (2015) The double-reduction landscape in tetraploid potato as revealed by a high-density linkage map. Genetics 201:853–863

    Article  PubMed  PubMed Central  Google Scholar 

  • Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140

    Article  PubMed  PubMed Central  Google Scholar 

  • Costet L, Le Cunff L, Royaert S, Raboin L, Hervouet C, Toubi L, Telismart H, Garsmeur O, Rousselle Y, Pauquet J (2012) Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars. Theor Appl Genet 125:825–836

    Article  CAS  PubMed  Google Scholar 

  • Dahlquist E (2013) Biomass as energy source: resources, systems and applications. CRC Press, Taylor & Francis, London

  • Daugrois JH, Grivet L, Roques D, Hoarau JY, Lombard H, Glaszmann JC, d'Hont A (1996) A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’. Theor Appl Genet 92:1059–1064

    Article  CAS  PubMed  Google Scholar 

  • Deren CW (1995) Genetic base of US mainland sugarcane. Crop Sci 35:1195–1199

    Article  Google Scholar 

  • D'Hont A (2005) Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet Genome Res 109:27–33

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garrison E, Marth G (2012) Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907

  • Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9:e90346

    Article  PubMed  PubMed Central  Google Scholar 

  • Glynn NC, Laborde C, Davidson RW, Irey MS, Glaz B, D’Hont A, Comstock JC (2013) Utilization of a major brown rust resistance gene in sugarcane breeding. Mol Breed 31:323–331

    Article  CAS  Google Scholar 

  • Goldemberg J (2008) The Brazilian biofuels industry. Biotechnol Biofuels 1:6

    Article  PubMed  PubMed Central  Google Scholar 

  • Guimaraes CT, Sills GR, Sobral BW (1997) Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. Proc Natl Acad Sci U S A 94:14261–14266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hackett CA, Luo ZW (2003) TetraploidMap: construction of a linkage map in autotetraploid species. J Hered 94 (4):358–359

  • Harrell Jr FE (2013) Hmisc: Harrell miscellaneous. R package version 3.12-2. Computer software]. Available from http://cran.R-project.Org/web/packages/Hmisc

  • Heffelfinger C, Fragoso CA, Moreno MA, Overton JD, Mottinger JP, Zhao H, Tohme J, Dellaporta SL (2014) Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics 15:979

    Article  PubMed  PubMed Central  Google Scholar 

  • International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768

    Article  Google Scholar 

  • Islam MS, Thyssen GN, Jenkins JN, Fang DD (2015) Detection, validation, and application of genotyping-by-sequencing based single nucleotide polymorphisms in upland cotton. The plant genome 8(1). https://doi.org/10.3835/plantgenome2014.07.0034

  • Islam MS, Thyssen GN, Jenkins JN, Zeng L, Delhom CD, McCarty JC, Deng DD, Hinchliffe DJ, Jones DC, Fang DD (2016) A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC genomics 17:903.Hackett CA, Luo ZW (2003) tetraploid map: construction of a linkage map in autotetraploid species. J Hered 94:358–359

    Google Scholar 

  • Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugenics 12:172–175

    Article  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Li X, Wei Y, Acharya A, Jiang Q, Kang J, Brummer EC (2014) A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome. G3 (Bethesda) 4:1971–1979

    Article  CAS  Google Scholar 

  • Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9:e1003215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCord PH, Migneault AJ (2015) Genotyping sugarcane for the brown rust resistance locus Bru1 using unlabeled probe melting. Sugar Tech:1–6

  • McCouch SR (2008) Gene nomenclature system for rice. Rice 1:72–84

    Article  Google Scholar 

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ming R, Liu SC, Lin YR, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TF, Wu KK, Moore PH et al (1998) Detailed alignment of Saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663–1682

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mukherjee SK (1957) Origin and distribution of Saccharum. Bot Gaz 119:55–61

    Article  Google Scholar 

  • Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L et al (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:883

    Article  Google Scholar 

  • Palhares AC, Rodrigues-Morais TB, Van Sluys M, Domingues DS, Maccheroni W, Jordão H, Souza AP, Marconi TG, Mollinari M, Gazaffi R (2012) A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 13:1

    Article  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556

    Article  CAS  PubMed  Google Scholar 

  • Pinheiro J, Bates D, DebRoy S, Sarkar D, Team RC (2009) Nlme: linear and nonlinear mixed effects models. R package version 3:96

  • Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raboin L, Oliveira KM, Lecunff L, Telismart H, Roques D, Butterfield M, Hoarau J, D’Hont A (2006) Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene. Theor Appl Genet 112:1382–1391

    Article  CAS  PubMed  Google Scholar 

  • Rott PC, Girard J (2013) Impact of pathogen genetics on breeding for resistance to sugarcane diseases. Proc Int Soc Sugar Cane Technol 28:1–11

    Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    Article  CAS  PubMed  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14

    Article  CAS  Google Scholar 

  • Serang O, Mollinari M, Garcia AAF (2012) Efficient exact maximum a posteriori computation for Bayesian SNP genotyping in polyploids. PLoS One 7:e30906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shrivastava AK, Srivastava S (2016) Diversity of the germplasm of Saccharum species and related genera available for use in directed breeding programmes for sugarcane improvement. Curr Sci 111:475–482

    Article  Google Scholar 

  • Song J, Yang X, Resende MF Jr, Neves LG, Todd J, Zhang J, Comstock J, Wang J (2016) Natural allelic variations in highly polyploid Saccharum complex. Front Plant Sci 7:804

    PubMed  PubMed Central  Google Scholar 

  • Sood SG, Comstock JC, Glynn NC (2009) Leaf whorl inoculation method for screening sugarcane rust resistance. Plant Dis 93:1335–1340

    Article  Google Scholar 

  • Van Ooijen JW (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen

    Google Scholar 

  • Waclawovsky AJ, Sato PM, Lembke CG, Moore PH, Souza GM (2010) Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnol J 8:263–276

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J et al (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11:261

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang S, Basten CJ, Zeng ZB (2012) Windows QTL cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh

    Google Scholar 

  • Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD (1992) The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83:294–300

    Article  CAS  PubMed  Google Scholar 

  • Yang X, Song J, You Q, Paudel D, Zhang J, Wang J (2017) Mining sequence variations in representative polyploid sugarcane germplasm accessions. BMC Genomics 18:594

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Erik A. Hanson of the Agronomy Department, University of Florida, for editing this manuscript. We gratefully thank Kay McCorkle at Sugarcane Field Station, USDA, ARS, for technical support in the greenhouse and field. This research is financially supported by the Florida Sugar Cane League.

Author information

Authors and Affiliations

  1. Agronomy Department, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA

    Xiping Yang & Jianping Wang

  2. Sugarcane Field Station, USDA, ARS, Canal Point, FL, 33438, USA

    Sushma Sood, Md. Sariful Islam & Jack Comstock

  3. Syngenta Seeds, Vero Beach, FL, 32967, USA

    Neil Glynn

  4. Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China

    Jianping Wang

Authors
  1. Xiping Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sushma Sood
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Neil Glynn
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Md. Sariful Islam
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jack Comstock
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jianping Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jianping Wang.

Ethics declarations

Data availability

The GBS sequences are available from the NCBI sequence read archive (SRA) database with an accession number of SRP102185.

Electronic supplementary material

Figure S1

(DOC 714 kb)

Figure S2

(DOC 653 kb)

ESM 1

(XLSX 15 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, X., Sood, S., Glynn, N. et al. Constructing high-density genetic maps for polyploid sugarcane (Saccharum spp.) and identifying quantitative trait loci controlling brown rust resistance. Mol Breeding 37, 116 (2017). https://doi.org/10.1007/s11032-017-0716-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-017-0716-7

Keywords

Search

Navigation