Sequence Characteristics and Phylogenetic Implications of the nrDNA Internal Transcribed Spacers (ITS) in Protospecies and Landraces of Sugarcane (Saccharum officinarum L.)

Abstract

Internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA) cistrons were studied in 19 protospecies and 11 landraces of Saccharum spp. The purpose of the present study was to investigate genetic variability and genetic divergence among the 30 genotypes of Saccharum officinarum L. for exploitation of potential parent resources in sugarcane breeding. ITS region analysis revealed the length of the ITS sequences from 589 to 590 bp, G+C content from 64.01 to 65.03 % (ITS1: 207 bp, G+C: 62.8–65.22 %; ITS2: 218–219 bp, G+C: 69.27–70.78 %; and 5.8S: 164 bp, G+C: 57.32–57.93 %). The ITS1 and ITS2 regions showed variable sequence lengths and G+C content. The 5.8S region was found to be more conserved (99.39 %). ITS1 recorded highest percentage of variation sites (90.48 %), high number of transitions and transversions. The neighbor-joining (NJ) method was used to assess the phylogenetic relationship based on the combined nucleotide sequence data of ITS1, 5.8S and ITS2, and the 30 accessions were divided into two clades. Clade I included all the 11 S. spontaneum accessions, and clade II consisted of S. officinarum, S. barberi, S. sinense, S. robustum and endemic species. Eleven accessions of S. spontaneum were clustered into several subclasses, indicating that the genetic diversity of S. spontaneum genotypes is abundant. Six landraces namely Hongpi S17, Tuojianghong, Loethers, Guzhizhe, Mango, Guilin Zhuzhe in the present study were closely related to S. spontaneum species, which may be used as available resources. This study validates the utility of rDNA-ITS region as a reliable indicator of phylogenetic relationships, especially ITS1 as probable DNA barcode at higher levels and can serve as an additional approach for studying genetic diversity in sugarcane and related relatives. The analysis on ITS sequences could provide a reference for exploitation of potential parent resources in sugarcane breeding.