Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane
- 144 Downloads
Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to morphological/agronomical traits.
KeywordsDedrogram EST Genetic diversity Polymorphism information content SSR
The authors are grateful to the Indian Council of Agricultural Research and the Sugarcane Breeding Institute, Coimbatore for the funding and infrastructure.
Dr. P. Govindaraj designed the research, instrumental in conception of the work, provided a critical review of the article and valuable suggestions in the interpretation of data. Mr. S. Parthiban performed the lab and field experiments, analyzed the results and drafted the manuscript. Mr. S. Senthilkumar helped in field and lab experiments.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interests.
- Ahmed MS, Gardezi SDA (2017) Molecular characterization of locally adopted sugarcane (Saccharum officinarum L.) varieties using microsatellite markers. The J Anim. Plant Sci 27(1):164–174Google Scholar
- Casu R, Dimmock C, Thomas M, Bower N, Knight D, Grof C (2001) Genetic and expression profiling in sugarcane. Proc Int Soc Sugarcane Technol 24:626–627Google Scholar
- Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
- Govindaraj P, Balasundaram N, Sharma TR, Bansal KC, Koundal KR, Singh NK (2005) Development of new STMS markers for sugarcane. Sugarcane Breeding Institute, Coimbatore, TamilNadu, India. http://www.nrcpb.org/content/development-new-stms-markers-sugarcane. Accessed 25 July, 2009
- Govindaraj P, Sindhu P, Appunu C, Parthiban S, Senthilkumar S (2013) Genetic diversity analysis among interspecific and intergeneric hybrids of Saccharum spp. using STMS markers. Res Crops 14(3):915–920Google Scholar
- Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Aken SV, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 16:761–768CrossRefGoogle Scholar
- Raboin LM, Oliveira KM, Lecunff L, Telismart H, Roques D, Butterfield M, Hoarau JY, 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 TAG. Theor Appl Genet 112:1382–1391CrossRefGoogle Scholar
- Roach BT (1972) Nobilization sugarcane. Proc Int Soc Sugarcane Technol 14:206–216Google Scholar
- Saravanakumar K, Govindaraj P, Appunu C, Senthilkumar S, Kumar Ravinder (2014) Analysis of genetic diversity in high biomass producing sugarcane hybrids (Saccharum spp. complex) using RAPD and STMS markers. Indian J Biotechnol 13:214–220Google Scholar
- Singh RK, Jena SN, Khan S, Yadav S, Banarjee N, Raghuvanshi D, 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 524:309–329CrossRefGoogle Scholar
- Singh RB, Singh B, Singh RK (2015) Development of microsatellite (SSRs) markers and evaluation of genetic variability within sugarcane commercial varieties (Saccharum spp. hybrids). Int J Adv Res 3(12):700–708Google 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(4):380–390CrossRefGoogle Scholar