Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

Abstract

Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.