Skip to main content

Advertisement

SpringerLink
Log in

Molecular Identification and Genetic Diversity Analysis of Chinese Sugarcane (Saccharum spp. Hybrids) Varieties using SSR Markers

  • Published:
Tropical Plant Biology Aims and scope Submit manuscript

Abstract

Sugarcane (Saccharum spp. hybrids) is an important sugar and renewable bio-energy crop with a high aneu-polyploidy and complex genome. The complex characteristics of sugarcane genome enhance the difficulty of selecting elite varieties in sugarcane breeding program. The objectives of this study were to establish the molecular identities (ID) of 91 nationally or provincially released Chinese sugarcane varieties and to evaluate the extent of genetic diversity among these varieties using SSR DNA markers and two fingerprinting systems, i.e., capillary electrophoresis (CE) and polyacrylamide gel electrophoresis (PAGE). A total of 151 SSR alleles together with 20 new alleles were detected by CE and 117 SSR alleles were detected by PAGE. Primer pairs SMC336BS, SMC31CUQ, and SMC597CS amplified more than eight alleles detectable by either CE or PAGE. Polymorphism information content (PIC) values of the SSR markers varied from 0.71-0.98 with an average of 0.90 for CE, or from 0.55-0.95 with an average of 0.84 for PAGE. UPGMA method classified the 91 varieties based on the CE data into four major groups with pair-wise similarity coefficients ranging from 58% to 95%. The genetic similarity estimates within and between the four groups varied from 0.31 to 0.87, with a mean of 0.49. Our results illustrated that the 21 SSR primer pairs in combination with CE or PAGE detection system could be a very useful working tool for molecular identification of sugarcane varieties, genetic diversity assessment, and parental selection in sugarcane breeding.

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
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631

    Article  CAS  PubMed  Google Scholar 

  • Arif IA, Bakir MA, Khan HA, Al Farhan AH, Al Homaidan AA, Bahkali AH, Sadoon MA, Shobrak M (2010) A brief review of molecular techniques to assess plant diversity. Int J Mol Sci 11:2079–2096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Casu RE, Manners JM, Bonnett GD, Jackson PA, McIntyre CL, Dunne R, Chapman SC, Rae AL, Grof CPL (2005) Genomics approaches for identification of genes determining important traits in sugarcane. Field Crop Res 92:137–147

    Article  Google Scholar 

  • Chen PH, Pan YB, Chen RK, Xu LP, Chen YQ (2009) SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries. Sugar Tech 11:347–354

    Article  CAS  Google Scholar 

  • Cordeiro GM, Taylor GO, Henry RJ (2000) Characterization of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species. Plant Sci 155:161–168

    Article  CAS  PubMed  Google Scholar 

  • Cordeiro GM, Pan YB, Henry RJ (2003) Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Sci 165:181–189

    Article  CAS  Google Scholar 

  • D’Hont A, Grivet L, Feldmann P, Rao P, Berding N, Glaszmann JC (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet 250:405–413

    PubMed  Google Scholar 

  • da Silva JAG (2001) Preliminary analysis of microsatellite markers derived from sugarcane expressed sequence tags (ESTs). Genet Mol Biol 24:155–159

    Article  Google Scholar 

  • Dos Santos JM, Duarte Filho LSC, Soriano ML, da Silva PP, Nascimento VX, de Souza Barbosa GV, Todaro AR, Ramalho Neto CE, Almeida C (2012) Genetic diversity of the main progenitors of sugarcane from the RIDESA germplasm bank using SSR markers. Ind Crop Prod 40:145–150

    Article  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Fu YH, Pan YB, Lei CY, Grisham MP, Yang CL, Meng QY (2016) Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm from the Karst Region of Guizhou, China. Am J Plant Sci 7:2209–2220

    Article  Google Scholar 

  • Grivet L, Arruda P (2001) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5:122–127

    Article  Google Scholar 

  • Haq SU, Kumar P, Singh RK, Verma KS, Bhatt R, Sharma M, Kachhwaha S, Kothari SL (2016) Assessment of functional EST-SSR markers (sugarcane) in cross-species transferability, genetic diversity among poaceae plants, and bulk segregation analysis. Genet Res Int 2016:1–16

    Article  Google Scholar 

  • Heinz DJ, Tew TL (1987) Hybridization procedures. In: Heinz DJ (ed) Sugarcane Improvement through Breeding. Elsevier, Amsterdam, pp 313–342

    Chapter  Google Scholar 

  • Jaccard P (1908) Nouvelles recherché sur la distribution florale. Bull Soc Vaudoise Sci Nat 44:223–270

    Google Scholar 

  • James BT, Chen C, Rudolph A, Swaminathan K, Murray JE, Na JK, Spence AK, Smith B, Hudson ME, Moose SP, Ming R (2012) Development of microsatellite markers in autopolyploid sugarcane and comparative analysis of conserved microsatellites in sorghum and sugarcane. Mol Breeding 30:661–669

    Article  Google Scholar 

  • Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  • Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J (2013) Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 33:111–125

    Article  PubMed  Google Scholar 

  • Liu XL, Ma L, Chen XK, Ying XM, Cai Q, Liu JY, Wu CW (2010) Establishment of DNA fingerprint ID in sugarcane cultivars in Yunnan, China. Acta Agron Sin 36:202–210

    CAS  Google Scholar 

  • Liu XL, Li XJ, Xu CH, Lin XQ, Deng ZH (2016) Genetic diversity of populations of Saccharum spontaneum with different ploidy levels using SSR molecular markers. Sugar Tech 18:365–372

    Article  CAS  Google Scholar 

  • Oliveira K, Pinto L, Marconi T, Margarido G, Pastina M, Teixeira L, Figueira A, Ulian E, Garcia A, Souza A (2007) Functional integrated genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Mol Breeding 20:189–208

    Article  CAS  Google Scholar 

  • Oliveira KM, Pinto LR, Marconi TG, Mollinari M, Ulian EC, Chabregas SM, Falco MC, Burnquist W, Garcia AAF, Souza AP (2009) Characterization of new polymorphic functional markers for sugarcane. Genome 52:191–209

    Article  CAS  PubMed  Google Scholar 

  • Pan YB (2010) Data basing molecular identities of sugarcane (Saccharum spp.) clones constructed with microsatellite (SSR) DNA markers. Am J Plant Sci 1:87–94

    Article  CAS  Google Scholar 

  • Pan YB, Cordeiro GM, Richard EP, Henry RJ (2003a) Molecular genotyping of sugarcane clones with microsatellite DNA markers. Maydica 48:319–329

    Google Scholar 

  • Pan YB, Miller JD, Schnell RJ, Richard J (2003b) Application of microsatellite and RAPD fingerprints in the Florida sugarcane variety program. Sugar Cane Int (3/4):19–28

  • Pan YB, Tew TL, Schnell RJ, Viator RP, Richard EP, Grisham MP, White WH (2006) Microsatellite DNA marker-assisted selection of Saccharum spontaneum cytoplasm-derived germplasm. Sugar Tech 8:23–29

    Article  CAS  Google Scholar 

  • Pan YB, Scheffler B, Richard EP (2007) High-throughput genotyping of commercial sugarcane clones with microsatellite (SSR) DNA markers. Sugar Tech 9:176–181

    Google Scholar 

  • Perera MF, Arias ME, Costilla D, Luque AC, García MB, Díaz Romero C, Racedo J, Ostengo S, Filippone MP, Cuenya MI, Castagnaro AP (2012) Genetic diversity assessment and genotype identification in sugarcane based on DNA markers and morphological traits. Euphytica 185:491–510

    Article  Google Scholar 

  • Pinto LR, Oliveira KM, Marconi T, Garcia AAF, Ulian EC, De Souza AP (2006) Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breed 125:378–384

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–221

    Article  Google Scholar 

  • Qi YW, Pan YB, Lao FY, Zhang CM, Fan LN, He HY, Liu RA, Wang QN, Liu SM, Liu FY, Li QW, Deng HH (2012) Genetic structure and diversity of parental cultivars involved in China mainland sugarcane breeding programs as inferred from DNA microsatellites. J Integr Agr 11:1794–1803

    Article  CAS  Google Scholar 

  • Rohlf FJ (2000) NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter Software, New York

  • Singh RK, Jena SN, Khan S, Yadav S, Banarjee N, Raghuvanshi S, Bhardwaj V, Dattamajumder SK, Kapur R, Solomon S, Swapna M, Srivastava S, Tyagi AK (2013) Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene 524:309–329

    Article  CAS  PubMed  Google Scholar 

  • Ukoskit K, Thipmongkolcharoen P, Chatwachirawong P (2012) Novel expressed sequence tag- simple sequencere peats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane (Saccharum spp.) breeding lines. Afr J Biotechnol 11:1337–1363

    CAS  Google Scholar 

  • Varshney RK, Garner A, Sorells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55

    Article  CAS  PubMed  Google Scholar 

  • You Q, Pan YB, Xu LP, Gao SW, Wang QN, Su YC, Yang YQ, Wu QB, Zhou DG, Que YX (2016) Genetic diversity analysis of sugarcane germplasm based on fluorescence-labeled simple sequence repeat markers and a capillary electrophoresis-based genotyping platform. Sugar Tech 18:380–390

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by an Earmark Fund from the China Agriculture Research System (CARS-170106 and CARS-170302) and the Major Science and Technology Project of Fujian Province, China (No. 2015NZ0002-2). We sincerely thank the Chinese sugarcane breeders in Guangxi Academy of Agricultural Science (Dr. Yang Rongzhong), Ganzhou sugarcane research Institute (Dr. Qi Yong-wen and Wang Qinnan), Yunnan Academy of Agricultural Science (Prof. Wu Caiwen), Guizhou Institute of Subtropical Crops (Dr. Lu Jiaju), and Fujian Academy of Agricultural Science (Prof. Pan Shimin) for suppling with the smpales of varieties.

Author information

Authors and Affiliations

  1. National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    Ahmad Ali, Wang Jin-Da, Deng Zu-Hu, Chen Ru-Kai & Gao San-Ji

  2. USDA-ARS, Sugarcane Research Unit, Houma, LA, 70360, USA

    Pan Yong-Bao

  3. College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    Chen Zhi-Wei

Authors
  1. Ahmad Ali
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wang Jin-Da
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pan Yong-Bao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Deng Zu-Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chen Zhi-Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chen Ru-Kai
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Gao San-Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

San-Ji Gao conceived the project and designed this work. Ali Ahmad and Jin-Da Wang performed the experiments, analyzed the data, and drafted the manuscript. Yong-Bao Pan performed interpretation of data and critical revision of the manuscript. Zu-Hu Deng, Zhi-Wei Chen and Ru-Kai Chen participated in revising the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Chen Ru-Kai or Gao San-Ji.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by: Sithichoke Tangphatsornruang

Electronic Supplementary Material

ESM 1

(DOCX 43 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ali, A., Jin-Da, W., Yong-Bao, P. et al. Molecular Identification and Genetic Diversity Analysis of Chinese Sugarcane (Saccharum spp. Hybrids) Varieties using SSR Markers. Tropical Plant Biol. 10, 194–203 (2017). https://doi.org/10.1007/s12042-017-9195-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12042-017-9195-6

Keywords

Search

Navigation