Chloroplast DNA analysis of Tunisian pistachio (Pistacia vera L.): Sequence variations of the intron trnL (UAA)

Abstract

The trnL (UAA) intron sequences of Pistacia vera ecotypes were employed to reconstruct the phylogeny and to elucidate molecular evolution. A single band of approximately 500pb length was amplified from each cultivars. Nucleotides sequences were aligned using the ClustalW package in the Bioedit program and analyzed with MEGA program version 4. The average of GC content was 35.8% to 39.6%. High values of A+T contents were detected in data sets and may explain the high proportions of transitions founded. Sequence alignment revealed the existence of 50 informative sites and 25 different haplotypes among the 39 cultivars studied yielding to a haplotype diversity of 0.8758 and a level of nucleotide diversity of 0.018. Furthermore, an average value of pairwise nucleotide of 8.641 differences was found, showing a relatively high diversity in the chloroplast intron. The neighbor joining dendrogram shows the presence of fairly high chloroplasts diversity, structured independently from the plant's sex but structured according to geographical origin. The trnL intron mismatch distribution is multimodal; characteristic of a stable population. This was also supported by non-significant values of all neutrality test parameters (Tajima's D and Fu and Li's). Although, the level of apparent diversity is considerable, we may conclude that non-coding regions of chloroplast genome provide a new and practical opportunity to evaluate genetic diversity and to discriminate pistachio cultivars. Revealed cytoplasmic DNA markers are reliable to elaborate a molecular data base to conduct management and breeding programs on local pistachio germplasm.