Assessment of molecular diversity and genetic relationship and structure of Iranian sugarcane germplasm using microsatellite markers

Document Type : Research Paper

Authors

1 Ph.D Student, Department of Agronomy & Plant Breeding, Agricultural College of Aburaihan, University of Tehran, Tehran, Iran.

2 Assistant Professor, Department of Agronomy& Plant Breeding, Agricultural College of Aburaihan, University of Tehran, Tehran, Iran.

3 Assistant Professor, Agriculture Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.

4 Assistant Professor, Department of Biotechnology, Cane Development and Sidelong Industrial Research and Education Institute, Khuzestan, Ahvaz, Iran.

5 Associate Professor, Department of Agronomy& Plant Breeding, Agricultural College of Aburaihan, University of Tehran, Tehran, Iran.

6 Laboratory Technician, Agriculture Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

Abstract

Considering the potential of sugarcane in terms of energy and sugar production the study of genetic diversity is the best way to use available genetic germplasm for breeding programs in this plant. Thirty microsatellite primer pairs were used to screen 160 varieties. In total 169 alleles were recorded with an average of 5.6 alleles per locus. The number of effective alleles per locus was ranged from 1.06 (locus AP-SSR03) to 1.921 (locus SMC119CG) with an average of 1.508. The PIC value was variable ranging from 0.06 (for AP-SSR03) to 0.5 (for SMC851MS). The principal coordinate analysis (PCoA) revealed six groups, so that the first three axes explained 15.20% of cumulative variation altogether. Clustering analysis was done using Neihbour-Joining algorithm and population structure analysis was performed using Bayesian method. The best number of sub-populations was identified as six. The grouping of genotypes in the sub-populations was not in consistent with their geographic origins. The grouping obtained from Bayesian method, phylogenetic relatedness analysis results and principal coordinates analysis grouping showed good agreement with each other. Analysis of molecular variance revealed that variation within subgroups was significantly higher than that of among subgroups. So it will be better to do selection within populations in order to select suitable parents in sugarcane breeding programs. The knowledge obtained in this study would be useful for breeding programs to improve the conservation and management of this valuable genetic resource to meet the demand of sugarcane cultivation for sugar and bioenergy production.

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References

Aitken KS, Jackson PA, Mcintyre CL (2005) A combination of AFLP and SSR markers provides extensive map coverage and identification of homo (eo) logous linkage groups in a sugarcane cultivar. Theor. Appl. Gene. 110: 789–801.
 Alwala S, Suman A, Arro JA, et al (2006) Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Sci. 46: 448–455.
Andru S, Pan Y-B, Thongthawee S, Burner DM, Kimbeng CA  (2011) Genetic analysis of the sugarcane (Saccharum spp .) cultivar “LCP 85-384”. I. Linkage mapping using AFLP, SSR, and TRAP markers. Theor. Appl. Genet. 123: 77–93.
Aragón C, Carvalho LC, González J, Escalona M, Amanicio S (2009) Sugarcane (Saccharum sp. Hybrid) propagated in headspace renovating systems shows autotrophic characteristics and develops improved anti-oxidative response. Trop. Plant. Biol. 2: 38–50.
Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196: 80–83.
Besse P, Mcintyre CL, Berding N (1997) Characterisation of Erianthus sect . Ripidium and Saccharum germplasm (Andropogoneae - Saccharinae ) using RFLP markers. Euphytica. 93:283–292.
Chen PH, Pan Y-B, Chen RK, et al (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.
Cordeiro GM, Casu R, Mcintyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant. Sci. 160: 1115-1123.
Cordeiro GM, Taylor GO, Henry RJ (2000) Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species. Plant. Sci. 155: 161–168.
D’Hont A, Grivet L, Feldmann P, Glaszman JC, Rao S, Beding N (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol. Gen. Genet. 250: 405–413.
D Hont A lique, Paulet F, Glaszmann JC (2002) Oligoclonal interspecific origin of “North Indian” and “Chinese” sugarcanes. Chromosome. Res. 10:253–262.
Daniels J, Roach B (1987) Taxonomy and evolution. In: Sugarcane improvement through breeding. Elsevier, pp 7–84.
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Mol. Ecol. 14:2611–2620.
Hameed U, Pan Y-B, Muhammad K, Afghan S, Igbal J (2012) Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot. Genet. Mol. Res. 11:1195–1204.
Haq S, Jain R, Sharma M, Kachhwaha S, Kothari SL (2014) Identification and Characterization of Microsatellites in Expressed Sequence Tags and Their Cross Transferability in Different Plants. Int. J. Genom. 1–12.
Henry RJ, Kole C (2010) Genetics, genomics and breeding of sugarcane. CRC Press, Taylor & Francis Group.
Huckett BI, Botha FC (1995) Stability and potential use of RAPD markers in a sugarcane genealogy. Euphytica. 86: 117–125.
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor .Appl. Genet. 103: 455–461.
Lima MLA, Garcia AAF, Oliveira KM, Matsuoka S, Arizono H, DeSouza CL, DeSouza AP (2002) Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane (Saccharum spp.) Theor. Appl. Genet. 104: 30–38.
Liu P, Que Y, Pan Y-B (2011) Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech. 13:129–136.
Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants: Salient statistical tools. Crop Sci. 43: 1235–1248.
Nair NV, Selvi A, Sreenivasan TV, Pushpalatha KN (2002) Molecular diversity in Indian sugarcane cultivars as revealed by randomly amplified DNA polymorphisms. Euphytica. 127:219–225.
Nayak SN, Song J, Villa A, Villa  A, Pathak B, Ayala-Silva T, Yang J, Todd J, Glynn NC, Kuhn DN, Glaz  B, Gilbert RA, Comstock JC, Wang  J (2014) Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS ONE. 9:e110856.
Pan Y-B, Cordeiro GM, Richard Jr EP, Henry R (2003) Molecular genotyping of sugarcane clones with microsatellite DNA markers. Maydica. 48:319–329.
Pandey A, Mishra RK, Mishra S, Singh YP, Pathak S (2011) Assessment of Genetic Diversity among Sugarcane Cultivars (Saccharum officinarum L.) using Simple Sequence Repeats Markers. J. Biol. Sci. 11:105–111.
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research — an update. Bioinformatics 28: 2537–2539.
Perrier X., Flori A, Bonnot F (2003) Data analysis methods. In: Genetic diversity of cultivated tropical plants. Enfield Science Publishers, Montpellier, pp 43–76.
Pocovi MI, Mariotti JA (2015) A bayesian approach to inferring the genetic population structure of sugarcane accessions from INTA (Argentina). Chil. J. Agr. Rese.75: 152–159.
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant. Mol. Biol. 15: 8–15.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics. 156:945–959.
Rae AL, Jackson MA, Nguyen CH, Bonnett GD (2009) Functional specialization of vacuoles in sugarcane leaf and stem. Trop. Plant. Biol. 2: 13–22.
Roach B, Daniels J (1987) A review of the origin and improvement of sugarcane. In: Copersucar international sugarcane breeding. Workshop. pp 1–31.
Shanthi RM, Kumar R, Nimmakayala P, Reddy O (2013) Genic SSRS From Saccharum officinarum in Wrky and stress transcription factors to use them as markers in Sugarcane. J. Sugarcane. Res. 3:118–129.
Sharma MD, Dobhal U, Singh P, Kumar S, Gaur AK, Singh SP, Jeena AS, Koshy EP, Kumar S (2014) Assessment of genetic diversity among sugarcane cultivars using novel microsatellite markers. Afr. J. Biotechnol. 13: 1444–1451.
Singh RK, Mishra SK, Singh SP, Mishra N, Sharma ML (2010) Evaluation of microsatellite markers for genetic diversity analysis among sugarcane species and commercial hybrids. Aust. J. Crop. Sci. 4:116–125.
Tew T, Cobill R (2008) Genetic improvement of sugarcane (Saccharum spp.) as an energy crop. In: Genetic improvement of bioenergy crops. Springer. p 273–294.
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: Features and applications. Trends. Biotechnol. 23: 48–55.
Virupakshi S, Naik GR (2008) ISSR analysis of chloroplast and mitochondrial genome can indicate the diversity in sugarcane genotypes for red rot resistance. Sugar Tech. 10: 65–70.
Weir B (1989) Sampling properties of gene diversity. In: Plant population genetics breeding and genetic resources. Sinauer Associates, Sunderland, Massachusetts., pp 23–42
Yeh F, Boyle T (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg. J. Bot. 129:157–163.
You Q, Xu L, Zheng Y, Que Y (2013) Genetic diversity analysis of sugarcane parents in Chinese breeding programmes using gSSR markers. The Scientific World J. 1–11.

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