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

• Published in: Plant breeding Vol. 132; no. 6; pp. 736 - 747
• Main Authors: Devarumath, Rachayya M., Kalwade, Sachin B., Bundock, Peter, Eliott, Frances G., Henry, Robert
• Format: Journal Article
• Language: English
• Published: Berlin Blackwell Publishing Ltd 01-12-2013; Wiley Subscription Services, Inc
• Subjects: Erianthus; genetic diversity; Narenga; polymorphism; Saccharum; Saccharum spontaneum; single-nucleotide polymorphism markers; sugarcane genotypes; target region amplification polymorphism marker
• ISSN: 0179-9541; 1439-0523
• DOI: 10.1111/pbr.12092

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.