Molecular Characterization of Mid-late Maturing Sugarcane Clones by Using Microsatellite Markers

Pooja Kumari *

Department of Plant Breeding and Genetics, Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar-848125, India.

Balwant Kumar

Department of Plant Breeding and Genetics, Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar-848125, India.

D. N. Kamat

Department of Plant Breeding and Genetics, Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar-848125, India.

Rajvinder Singh

Department of Plant Breeding and Genetics, Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar-848125, India.

Digvijay Singh

Department of Plant Breeding and Genetics, Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar-848125, India and Narayan Institute of Agricultural Sciences, GNS University, Jamuhar, Sasaram, Bihar-821305, India.

Sandeep Kumar Suman

Department of Agricultural Biotechnology and Molecular Biology, Dr Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar-848125, India.

*Author to whom correspondence should be addressed.


Abstract

A total of 56 alleles were obtained, of which 41 shared and 15 unique allelic variants were generated as the amplified product by polymerase chain reaction using eleven primer pairs. The PIC values revealing allelic diversity and frequency among the genotypes varied from 0.36 in the case of NKS 57 to 0.90 in the case of NKS 1 with an average of 0.62. The similarity coefficients revealing genetic similarity with respect to the size of the amplified products generated from targeted regions of the genome varied from 0.518 to 0.857 for the pairwise combinations amongst the thirteen entries under evaluation. Two Clusters were obtained when the phenol line was drawn at twenty-five similarity units. Cluster I consist of ten genotypes. The tri-genotypic cluster II consists of three genotypes. When phenol level drew at fifty similarity unit clusters I and II were further divided into sub-clusters. It is concluded that using an SSR marker is a very reliable approach for identifying diverse genotype(s) where phenotypic similarity of the cultivars leads to difficulty while selecting parents for hybridization.

Keywords: Sugarcane, molecular, shared alleles, unique alleles, microsatellite marker, and similarity coefficient.


How to Cite

Kumari , P., Kumar , B., Kamat , D. N., Singh , R., Singh , D., & Suman , S. K. (2023). Molecular Characterization of Mid-late Maturing Sugarcane Clones by Using Microsatellite Markers. International Journal of Environment and Climate Change, 13(9), 1644–1654. https://doi.org/10.9734/ijecc/2023/v13i92395

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References

Sobral BW, Braga DP, LaHood ES, Keim P. Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. subtribe of the Andropogoneae Dumort. tribe. Theoretical and Applied Genetics. 1994 Feb;87: 843-53.

Daniels J, Roach BT. Taxonomy and evolution. InDevelopments in crop science. Elsevier. 1987;11:7-84.

Akhter S, Rauf S, Akhter B, Ghias M, Parveen N, Ibrar I, Ali Q. Microsatellite (SSR) markers a tool; for genetic diversity assessment among sugarcane accessions. Plant Cell Biotechnol Mol Biol. 2021;22: 1-7.

Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. 1987;19): 11-15.

Govindaraj P, Gowri R, Mohanraj K, Amalraj VA. SSR marker based molecular genetic diversity analysis among Saccharum spontaneum (L.) collected from North Western region of India. Sugar Tech. 2021;23:730-740.

Harvey M, Botha FC. Use of PCR-based methodologies for the determination of DNA diversity between Saccharum varieties. Euphytica. 1996;89:257-265.

Kanwar PG, Devarumath RM, Nerkar YS. Use of RAPD markers for assessment of genetic diversity in sugarcane cultivars. Indian Journal of Biotechnology. 2009;8: 67-71.

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

Daniels C, Daniels J. The geographical, historical, and cultural aspects of the origin of Indian and Chinese sugarcanes, S. barberi and S. sinense. International Journal of Sugar Cane Breeders’ Newsletter; 1975.

FAO. Statistical databases, Food and Agriculture Organization of the United Nations; 2017.

Available: http://www.fao.org/faostat/en/#data/home (accessed May 01, 2019)

Gupta A, Verma JP. Sustainable bio-ethanol production from agro-residues: A review. Renewable and sustainable energy reviews. 2015);41:550-567.

DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech. 13(2):129–136

Pinto LR, Oliveira KM, Marconi T, Garcia AAF, Ulian EC, Souza AP. Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breeding. 2006;125:378-384.

Powell W, Machray GC, Provan J. Polymorphism is revealed by simple sequence repeats. Trends in Plant Sciences. 1996);1:215-222.

Singh RB, Mahenderakar MD, Jugran AK, Singh RK, Srivastava RK. Assessing genetic diversity and population structure of sugarcane cultivars, progenitor species and genera using microsatellite (SSR) markers. Gene. 2020;753:144800.

Tazeb, Hyeileaellassie T, Tesfaye K. Molecular characterization of introduced sugarcane genotype in Ethiopia using IISR molecular marker. African Journal of Biotecnolog. 2017; 16(10):434-449.

Singh RK, Srivastava S, Singh SP, Sharma ML, Mohopatra T, Singh NK, Singh SB. Identification of new microsatellite DNA markers for sugar and related traits in sugarcane. Sugar Tech. 2008;10:327-33.

Srivastava S, Gupta PS, Srivastava BL. Molecular genetic diversity of sugarcane genotypes of subtropical India: SSCP-PCR analysis of simple sequence repeats. Proc. ISSCT. 2005;25:602-606.

Srivastava S, Jain R, Gupta PS, Singh J. Genetic stability of in vitro raised sugarcane plantlets by RAPD markers. Journal of Plant Cell Biotechnology and Molecular Biology. 2006;7(1&2):93-96.

Singh RB, Singh B, Singh RK. Evaluation of genetic diversity in Saccharum species clones and commercial varieties employing molecular (SSR) and physiological markers. Indian Journal of Plant Genetic Resources. 2018;31(1):17-26.

Pan Y. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech. 2006;8:246256.

Kalia RK, Rai M, Kalia K, Singh S, Dhawan RAK. Microsatellite markers: An overview of the recent progress in plants. Euphytica. 2011;177:309-334.

Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X. Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC genomics. 2011; 12(1):1-4.

Singh R, Kamat DN, Kumari P, Suman SK, Singh D. Molecular characterization of early maturing sugarcane clones using microsatellite markers. International Journal of Plant and Soil Science. 2022; 34(23):102-10.

Srivastava S, Gupta PS. Inter simple sequence repeat profile as a genetic marker system in sugarcane. Sugar Tech. 2008;10(1):48-52.

Cordeiro GM, Pan YB, Henry RJ. Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Journal of Plant Science. 2003;165:181-189.

Anderson 6A, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME. Optimizing parental selection for genetic linkage maps. Genome. 1993;36(1): 181-6.

Liu YQ, Yong B, Pan P. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech. 2011;13(2):129–136.

dos Santos JM, Duarte Filho LS, Soriano ML, da Silva PP, Nascimento VX, de Souza Barbosa GV, Todaro AR, Neto CE, Almeida C. Genetic diversity of the main progenitors of sugarcane from the RIDESA germplasm bank using SSR markers. Industrial Crops and Products. 2012; 40:145-50.

Smiullah S, Khan FA, Afzal A, Abdullah I, Ijaz U. Diversity analysis of sugarcane genotypes by microsatellite (SSR) markers. International Journal of Biotechnology and Molecular Biology. 2013;4(7):105-110.

Ahmed MS, Gardezi SDA. Molecular characterization of locally adopted sugarcane (Saccharum officinarum L.) varieties using microsatellite markers. Journal of Animal and Plant Science. 2017;27(1):164-174.

Sarath Padmanabhan TS, Hemaprabha G. Genetic diversity and population structure among 133 elite genotypes of sugarcane (Saccharum spp.) for use as parents in sugarcane varietal improvement. 3 Biotech. 2018;8(8):1-12

Ali A, Pan YB, Wang QN, Wang JD, Chen JL, Gao SJ. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers. Scientific reports. 2019; 9(1):1-10.

Cordeiro GM, Taylor GO, Henry RJ. Characterization of microsatellite marker from sugarcane (saccharum spp.) a high polyploidy species. Journal of Plant Science. 2000;55:161-168.

Weir BS. Genetic data analysis. Methods for discrete population genetic data. Sinauer Associates, Inc. Publishers; 1990.

Singh D, Kumar A, Kumar R, Kushwaha N, Mohanty TA, Kumari P. Genetic diversity analysis of QPM (Zea mays L.) inbreds using morphological characters. Journal of Pharmacognosy and Phytochemistry. 2020;9(1):1205-10.