Abstract
Genetic diversity among 55 different sugarcane (Saccharum) cultivars varying in their response for red rot disease (Colletotrichum falcatum) was studied using Resistance Gene Analog Polymorphism (RGAP) markers. A total of 28 primers were used in the present study to screen 30 moderately resistant, five resistant, seven moderately susceptible, nine susceptible and four highly susceptible cultivars resulted in the generation of 87 distinct fragments with 91.9% polymorphism. Polymorphism Information Content (PIC) and Resolving Power (RP) were also calculated and the values were found to be 16.28 and 52.36 respectively. On analyzing the dendrogram, a clear distinctive grouping was observed between red rot resistant and red rot susceptible cultivars. This study, therefore clearly revealed that Resistant Gene Analog (RGA) markers showed greater genetic diversity and hence, constitute a rich source for analyzing the genetic diversity and phylogenetic relationships. The genotypes belonging to different clusters can be crossbreed to gain high variability of good combinations of characters.
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Afghan S, Iqbal J, Pan YB, Mohammad K (2012) SSR markers for DNA fingerprinting and diversity analysis of sugarcane cultivars resistant and susceptible to red rot. Pak–US Science and Technology Co-operative Research Project
Ali W, Muhammad K, Nadeem MS, Inamullah Ahmad H, Iqbal J (2013) Use of RAPD markers to characterize commercially grown rust resistant cultivars of sugarcane. Int J Biosci 3:115–121
Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J 7:347–354
Chen XM, Line RF, Leung H (1998) Genome scanning for resistance-gene analogs in rice, barley and wheat by high resolution electrophoresis. Theor Appl Genet 9:345–355
da Costa MLM, Amorim LLB, Onofre AVC, de Melo LJOT, de Oliveira MBM, de Carvalho R, Benko-Iseppon AM (2011) Assessment of genetic diversity in contrasting sugarcane varieties using inter-simple sequence repeat (ISSR) markers. Am J Plant Sci 2:425–432
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Duttamajumder SK (2008) Red rot of sugarcane. Indian Institute of Sugarcane Research, Lucknow
Faigon-Soverna A, Harmon FG, Storani L, Karayekov E, Staneloni RJ, Gassmann W, Mas P, Casal JJ, Kay SA, Yanovsky MJ (2006) A constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development. Plant Cell 18:2919–2928
Hameed U, Pan YB, Muhammad K, Afghan S, Iqbal 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
Hogarth DM, Berding N (2005) Breeding for a better industry: conventional breeding. Proceedings of ISSCT XXV Jubilee Congress, Guatemala
Jayashree J, Selvi A, Nair NV (2010) Characterization of resistance gene analog polymorphisms in sugarcane cultivars with varying levels of red rot resistance. Electron J Plant Breed 1:1191–1199
Martin GB, Bogdanove AJ, Sessa G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol 54:23–61
Muhammad K, Afghan S, Pan YB, Iqbal J (2013) Genetic variability among the brown rust resistant and susceptible genotypes of sugarcane by RAPD technique. Pak J Bot 45:163–168
Mumtaz AS, Nayab DE, Iqbal MJ, Shinwari ZK (2011) Probing genetic diversity to characterize red rot resistance in sugarcane. Pak J Bot 43:2513–2517
Nimchuk Z, Eulgem T, Holt BF, Dangl JL (2003) Recognition and response in the plant immune system. Annu Rev Genet 37:579–609
Parida SK, Sanjay KK, Sunita K, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338
Prevost A, Wilkinson MJ (1999) A new system for comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112
Shahid MTH, Khan FA, Saeed A, Fareed I (2011) Variability of red rot-resistant somaclones of sugarcane genotype S97US297 assessed by RAPD and SSR. Genet Mol Res 10:1831–1849
Shahid MTH, Khan FA, Saeed A, Aslam M, Rasul F (2012) Development of somaclones in sugarcane genotype BF-162 and assessment of variability by random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers in selected red rot resistant somaclones. Afr J Biotechnol 11:3502–3513
Sharma R, Tamta S (2015) A review on Red rot: the “Cancer” of sugarcane. J Plant Pathol Microbiol S 1:003
Sharma R, Tamta S (2017) Red rot resistant gene characterization using RGAP markers among sugarcane cultivars resistant and susceptible to the red rot disease. 3 Biotech 7:306
Singh RK, Khan MS, Singh R, Pandey DK, Kumar S, Lal S (2011a) Analysis of genetic differentiation and phylogenetic relationships among sugarcane genotypes differing in response to red rot. Sugar Tech 13:137–144
Singh RK, Singh RB, Singh SP, Sharma ML (2011b) Genes tagging and molecular diversity of red rot susceptible/tolerant sugarcane hybrids using c-DNA and unigene derived markers. World J Microbiol Biotechnol 28:1669–1679
Singh RK, Singh RB, Singh SP, Sharma ML (2011c) Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes. Euphytica 182:335–354
Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Michell SE, Kresovick S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparison with data from RFLPs and pedigrees. Theor Appl Genet 95:163–173
Weir B (1990) Genetic data analysis: methods for discrete population genetic data. Sinauer Associates, Sunderland
Williams JGK, Kubelik AR, Kenneth JL, Rafalski AJ, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Yadav RL (2006) Research vision to manage red-rot disease of sugarcane in India. Sugar Tech 8:99–100
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The authors are thankful to the Head, Department of Biotechnology, Kumaun University, Nainital, India for providing lab facilities.
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Sharma, R., Tamta, S. Genetic variation in sugarcane cultivars for red rot resistance revealed by resistant gene analog polymorphism markers. Vegetos 33, 92–99 (2020). https://doi.org/10.1007/s42535-019-00086-5
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DOI: https://doi.org/10.1007/s42535-019-00086-5