Independent target region amplification polymorphism and single-nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes

Devarumath, Rachayya M., Kalwade, Sachin B., Bundock, Peter, Eliott, Frances G. and Henry, Robert (2013) Independent target region amplification polymorphism and single-nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes. Plant Breeding, 132 6: 736-747. doi:10.1111/pbr.12092


Author Devarumath, Rachayya M.
Kalwade, Sachin B.
Bundock, Peter
Eliott, Frances G.
Henry, Robert
Title Independent target region amplification polymorphism and single-nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes
Journal name Plant Breeding   Check publisher's open access policy
ISSN 0179-9541
1439-0523
Publication date 2013-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1111/pbr.12092
Volume 132
Issue 6
Start page 736
End page 747
Total pages 12
Place of publication Berlin, Germany
Publisher Wiley-Blackwell Verlag GmbH
Language eng
Subject 1311 Genetics
1110 Nursing
1102 Cardiovascular Medicine and Haematology
Abstract The independent target region amplification polymorphism (TRAP) and single-nucleotide polymorphism (SNP) markers were used for genetic evaluation of different selected 47 sugarcane genotypes. A total of 23 pairs of TRAP markers generated 925 alleles, of which 74% alleles were polymorphic. Polymorphism was generally high (>50%), ranging from 54 to 98%. The polymorphism information content (PIC) values 0.20 varied among the primer combination ranging from 0.17 in SAI + Arbi 2 to 0.31 in GL 2+ Arbi 1 with an average of 0.24. However, the Pearson correlation between PIC and power of discrimination (PD) was found to be less significant. Single-nucleotide polymorphisms were used first time for the assessment of genetic diversity among different species of Saccharum and cultivated sugarcane varieties. The SNPs were detected from 454 sequencing. A total of 245 SNP markers were assayed across the 47 genotypes, and 167 SNPs were found to be polymorphic. The PIC values ranged from 0.04 to 0.38 with an average of 0.21, and their respective PD varied from 0.58 to 0.04 with an average value of 0.31. The obtained results relatively significant were compared with the other marker systems through genetic similarity and the clusters formed in different unweighted pair group method with arithmetic mean clustering dendrogram. The clustering analysis established genetic relationship in the order of Erianthus > Sclerostachya > Narenga > Saccharum spontaneum > S. robustum > S. barberi > S. officinarum/cultivars. These results ratify TRAP and SNP marker systems for assessing genetic diversity studies, and more diversified Erianthus spp. can contribute substantially towards sugarcane varietal improvement through breeding with Saccharum spp. or hybrid cultivars.
Keyword Genetic diversity
Polymorphism
Single-nucleotide polymorphism markers
Sugarcane genotypes
Target region amplification polymorphism marker
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2014 Collection
 
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