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Use of RAPD markers to characterize commercially grown rust resistant cultivars of sugarcane

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Research Paper 01/02/2013
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Use of RAPD markers to characterize commercially grown rust resistant cultivars of sugarcane

Wajid Ali1, Khushi Muhammad, Muahammad Shahid Nadeem, Inamullah, Habib Ahmad, Javed Iqbal
Int. J. Biosci.3( 2), 115-121, February 2013.
Certificate: IJB 2013 [Generate Certificate]
Key: Puccinia melanaocephalaRAPDRustSCARSugarcane

Abstract

The brown leaf rust caused by Puccinia melanaocephala (Syd. & P. Syd.) is a major cause of reduction in sugar production and withdrawal of sugarcane cultivars from growing fields. In The present study, the eight commercially grown sugarcane cultivar was characterized under natural inoculation and divided into two discrete groups i.e. four rust resistant and four rust susceptible. The extracted genomic DNA was subjected against RAPD (Random Amplified Polymorphic DNA) markers. After screening of decamers, 7 were picked for further analysis on the basis of polymorphism, which is the most important application of DNA markers. These decamers generated 21 trackable loci with the range of 400-2500 bp and 100% polymorphic loci were recorded genomic DNA of eight sugarcane cultivars. From 7 primers, 3 generated 5 specific loci in 4 sugarcane cultivars, which is a potential use of RAPD-PCR for identifying Saccharum spp. hybrids and clones. Primer G-06 generated only one locus 1200 bp in the rust susceptible cultivar NSG-59 while J-05 had produced two loci i.e. 400 bp and 1100 bp in rust resistant cultivars NSG-555 and CP-77-400 respectively. Primer L-18 generated 700 bp and 1400 bp loci in rust susceptible cultivar CoJS-84. The homology tree was constructed using DNAMAN software based on binary data set. During cluster analysis, we found two major groups of cultivars with different minor groups. This study will be useful to characterize rust resistance in sugarcane and could be extended for the development of SCAR (Sequence Characterized Amplified Region) marker, which is specific, reliable and reproducible marker.

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Aitken K, 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. Theoretical and Applied Genetics 110, 789– 801.

Alvi AK, Iqbal J, Shah AH, Pan Y-B. 2008. DNA based genetic variation for red rot resistance in sugarcane. Pakistan Journal of Botany 40, 1419-1425. Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau JY. 2004. Targeted mapping of a sugarcane rust resistance gene Bru1 using bulked segregant analysis and AFLP markers. Theoretical and Applied Genetics 108, 759–764.

Barnes JM, Botha FC. 1998. Progress towards identifying a marker for rust resistance in sugarcane variety NCo376. Proceedings Congress of the South African Sugar Technologists Association 72, 149-152.

Casu R, 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 Crops Research 92(2-3), 137-147, http://dx.doi.org/10.1016/j.fcr.2005.01.029

Comstock JC, Tew TL, Ferreira SA. 1982. Sugarcane rust in Hawaii. Plant Disease 66, 1193-1194.

Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus 12, 13-15.

Fernandez F, Peteire B, Pino B, Cornide MT, Lednard H. 1999. Determination of genomic diversity in sugarcane varieties by RAPD markers. Theoretical and Applied Genetics 87, 697-704.

Franco J, Crossa JM, Ribaut J,. Betran ML, Warburton M, Khairallah. 2001. A method for combining molecular markers and phenotypic attributes for classifying plant genotypes. Theoretical and Applied Genetics 103, 944–952.

Grivet L, Arruda P. 2002. Sugarcane genomics: depicting the complex genome of an important tropical crop. Current Opinion in Plant Biology 5, 122–127, http://dx.doi.org/10.1016/S1369-5266(02)00234-0

Hameed U, Muhammad K, Pan Y-B, Afghan S, Iqbal J. 2012. Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot. Genetics and Molecular Research 11(2), 1195-1204.

Hoy JW, Hollier CA. 2009. Effect of Brown Rust on Yield of Sugarcane in Louisiana. Plant Disease 93, 1171-1174, http://dx.doi.org/10.1094/PDIS-93-11-1171

Hutchinson PB, Daniels J. 1972. A rating scale for sugarcane characteristics. International Society of Sugar Cane Technologists 14, 128–131.

Kawar PG, Devarumath PM, Nerkar Y. 2009. Use RAPD marker for assement of genetic diversity in sugarcane cultivars. International Journal of Biotechnology 8, 67-71.

Khan FA, Khan A, Azhar FM, Rauf S. 2009. Genetic diversity of Saccharum officinarum accessions in Pakistan as revealed by random amplified polymorphic DNA. Genetics and Molecular Research 8, 1376-1382.

Le Cunff L, Garsmeur O, Raboin LM, Pauquet J, Telismart H, Selvi A, Grivet L, Philippe R, Begum D, Deu M. 2008. Diploid ⁄ polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n _ 12x _ 115). Genetics 180, 649–660, http://dx.doi.org/10.1534/genetics.108.091355

Mariotti, JA. 2002. Selection for sugar cane yield and quality components in subtropical climates. Sugar Cane International 2/3, 22–26.

Muhammad K, Pan Y-B, Grisham MP, Iqbal J. 2010. Identification of RAPD marker associated with brown rust resistance in sugarcane [Abstract]. International Society of Sugar Cane Technologists 30, 154.

Mumtaz S, Khan IA, Ali S, Zeb B, Iqbal A, Shah Z, Swati ZA. 2009. Development of RAPD based markers for wheat rust resistance gene cluster (Lr37-Sr38 Yr17) derived from Triticum ventricosum L. African Journal of Biotechnology 8, 1188–1192.

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.

Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.

Pan Y-B, Burner DM, Legendre BL, Grisham MP, White WH. 2004. An assessment of the genetic diversity within a collection of Saccharum spontaneum L. with RAPD-PCR. Genetic Resources and Crop Evolution 51(8), 895-903, http://dx.doi.org/10.1007/s10722-005-1933-1

Park SO, Coyne DP, Steadman JR, Skroch PW. 2003. Mapping of the Ur-7 gene for specific resistance to rust in common bean. Crop Science 43: 1470–1476. 164.

Ribaut, J-M, Hu X, Hoisington D, Gonzalez-De-Leon D. 1997. Use of STSs and SSRs as rapid and reliable preselection tools in marker-assisted selection backcross scheme. Plant Molecular Biology Reporter 15, 156–164.

Ryan CC, Egan BT. 1989. Diseases of Sugarcane: Major Diseases. Amsterdam, the Netherlands: Elsevier 189–210.

Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425.

Selvi A, Nair NV, Balasundaram N, Mohapatra T. 2003. Assessment of diversity and phylogtenetic relationships in the Saccharum complex using molecular markers. Sugarcane Breeding Institute, Coimbatore 641007, Tamilnadu, India (Abstract. I.S.S.T., IVTH Molecular Biology Workshop, Montpellier, France). Shan, X., T.K., Blake and L.E.

Srivastava MK, Li C, Li Y. 2012. Development of sequence characterized amplified region (SCAR) marker for identifying drought tolerant sugarcane genotypes. Australian Journal of Crop Science 6(4), 763-767.

Taylor PWJ, Croft BJ, Ryan CC. 1986. Studies into the effect of sugarcane rust (Puccinia melanocephala) on yield. Proceeding International of Society Sugar Cane Technologist 19, 411-419.

Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531-6535.

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