Genetic diversity and phylogeny of pearl millets [Pennisetum glaucum (L.) R. Br.] based on chloroplast trnL-F region

Local varieties of pearl millets in Saudi Arabia are heat- and drought-tolerant and are grown under various environments. Here, we evaluated the diversity of six local varieties based on sequencing and analysis of the trnL-F region of their chloroplast DNA that includes the genes of tRNA^Leu and tRNA^Phe and the intergenic spacer between them, trnL-F. The obtained sequences were 1171–1172 bp in length, including the complete sequences of the tRNA^Leu, trnL-F and tRNA^Phe regions. Three variable nucleotide sites were observed in the sequences of the Indian variety, whereas for each of the three varieties, Tihamah, Jazan, and Sayah, a single variable site was observed. The varieties, Yemeni and Baydhan, were identical for the entire analyzed sequence. The secondary structure of tRNA^Leu intron of Indian variety was distinct from the other five varieties, while Tihamah and Jazan were distinct in the secondary structure of trnL-F spacer. Additionally, Indian was distinct in the secondary structure of tRNA^Leu whereas Sayah and Jazan were distinct in the secondary structure of tRNA^Phe. Phylogenetic analysis with NCBI-retrieved accessions of the Pennisetum glaucum revealed close relationships between the investigated varieties with an exception of the Indian, which clustered separately from the other five varieties. The nucleotide polymorphism analysis revealed higher nucleotide diversity in the spacer between tRNA^Leu and tRNA^Phe than in the tRNA^Leu intron across the six local varieties. This study provides insights into the genetic diversity within local pearl millets, which is important for the conservation of the local varieties that exhibit exceptional adaptation to the harsh climate conditions in the Arabian Peninsula.