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Genes tagging and molecular diversity of red rot susceptible/tolerant sugarcane hybrids using c-DNA and unigene derived markers

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Abstract

Sugarcane is an important international commodity as a valuable agricultural crop especially in tropical and subtropical countries. Two bulked DNA used to screen polymorphic primers from commercial hybrids (varieties) with moderately resistant and highly susceptible to red rot disease. Among 145 simple sequence repeat and unigene primers screened, 37 (25%) were found to be highly robust and polymorphic with Polymorphism Information Content values ranging from 0.50 to 1.00 with the mean value of 0.82. Among these microsatellites, twenty one were used in the study of genetic relationships and marker identification in sugarcane varieties for red rot resistance. A total of 105 polymorphic DNA bands were identified, with their fragment size ranging from 54 to 1,280 bp. Jaccard’s similarity coefficient value recorded between closely related hybrids was 0.986 while lowest coefficient value of 0.341 was detected with distantly related hybrids. The average similarity coefficient among these hybrids was 0.663. Cluster analysis resulted in a dendrogram with two major clusters separating the moderately resistant varieties from highly susceptible varieties. Three group specific fragments amplified by unigene Saccharum microsatellite primers viz; two markers UGSM316850 and UGSM31660 were closely associated with moderately resistant varieties by appearing bands in this region but the bands were absent in highly susceptible varieties. Similarly UGSM316400 marker was tightly linked with highly susceptible varieties by amplifying uniformly in sugarcane varieties showing highly susceptible reaction to red rot but it was absent in moderately resistant varietal groups. Validation of red rot resistance/susceptibility associated markers on a group of different mapping populations for red rot resistant/susceptible traits is in progress.

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Abbreviations

RFLP:

Restriction fragment length polymorphism

RAPD:

Random amplified polymorphic DNA

AFLP:

Amplified fragment length polymorphism

SSR:

Simple sequence repeats

TRAP:

Target region amplification polymorphism

SRAP:

Sequence-related amplified polymorphism

RGA:

Resistance gene analog

BSA:

Bulk segregation analysis

EST:

Expressed sequence tag

UGSM:

Unigene Saccharum microsatellite

SEGMS:

Sugarcane enriched genomic microsatellite

cDNA:

Complementary deoxyribonucleic acid

CTAB:

Cetyl trimethyl ammonium bromide

R:

Resistant

MR:

Moderately resistant

MS:

Moderately susceptible

S:

Susceptible

HS:

Highly susceptible

PCR:

Polymerase chain reaction

TBE:

Tri-Borate EDTA

QTL:

Quantitative trail locus

PIC:

Polymorphic information content

UPGMA:

Unweighted pair group method with arithmetic mean

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Acknowledgments

The authors gratefully thanks to Dr. N.K. Singh and Dr. T. Mohapatra for providing primer sequences generated under DBT funded project. Research work has been financially supported by Cane Development and Sugar Industry, Uttar Pradesh government, India.

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  1. Centre for Sugarcane Biotechnology, Sugarcane Research Institute, U.P. Council of Sugarcane Research, Shahjahanpur, 242 001, Uttar Pradesh, India

    R. K. Singh, R. B. Singh, S. P. Singh & M. L. Sharma

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Singh, R.K., Singh, R.B., Singh, S.P. et al. 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 (2012). https://doi.org/10.1007/s11274-011-0974-1

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