Development and utilisation of conserved-intron scanning marker in sugarcane
M. Suhail Khan A , Sonia Yadav A , Sangeeta Srivastava A , M. Swapna A , A. Chandra B and Ram K. Singh A C
+ Author Affiliations
- Author Affiliations
A Division of Crop Improvement, Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow 226002, Uttar Pradesh, India.
B Division of Physiology and Biochemistry, Indian Institute of Sugarcane Research, Rae Bareli Road, Lucknow 226002, Uttar Pradesh, India.
C Corresponding author. Email: ikrps@yahoo.com
Australian Journal of Botany 59(1) 38-45 https://doi.org/10.1071/BT10188
Submitted: 26 July 2010 Accepted: 9 December 2010 Published: 10 February 2011
Abstract
Genetic dissection of economic traits in sugarcane requires sufficiently informative molecular markers that are currently lacking in this highly valued crop. Through comparative analysis of publicly available expressed-sequence data of sugarcane, sorghum and barley, and the whole rice genome-sequence survey, novel functional markers based on conserved-intron scanning primers (CISP) were developed and evaluated in different accessions across various taxonomic ranks of sugarcane. Polymorphism was moderate (55.2%), whereas 94.7% of the markers developed amplified fragments in selected genotypes. Mean polymorphism information content value was 0.582 (range 0.320–0.715), which was comparable to that with genic microsatellite markers (0.52) but lower than that with EST-SSR (0.73). Genetic-similarity coefficient ranged from 0.39 to 0.95, indicating variable levels of divergence depending on the taxonomic rank assessed. Cluster analysis revealed that the genotypes grouped in accordance with the taxonomical classification of sugarcane, with a relatively good support from a Mantel’s test (r = 0.847) and a moderate bootstrap value (65–89%). The CISP markers reported in the present study have potential utility for genetic-diversity analysis and application in sugarcane-breeding programs.
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