Genetic diversity of the cultivated Salvia miltiorrhiza populations revealed by four intergenic spacers

Abstract

For better understanding the genetic diversity and phylogeny of the cultivated Salvia miltiorrhiza populations, four intergenic spacer sequences, ETS, psbA-trnH, trnL-trnF, and ycf1-rps15 of the 40 populations collected from China were Polymerase Chain Reaction (PCR) amplified, analyzed both individually and in combination. Haplotype diversity analysis showed that the cultivated S. miltiorrhiza populations had a very rich genetic diversity and an excellent capacity to resist environmental pressure. The best-fit nucleotide substitution models for ETS, psbA-trnH, trnL-trnF, ycf1-rps15, and their combined sequences were HKY+I, T92, T92, T92+G, and T92+G, respectively; the nucleotide conversion frequency in the combined sequences was lower than the transversion, and the relatively high nucleotide substitution frequencies suggests its high genetic variability. Neutral tests showed that the spacer sequences of the populations conform with the neutral evolution model, and there has been no current expansion events occurred. Phylogeny analyses based on both the individual and the combined sequences showed that the 40 populations were clustered in two clades with a very similar topological structure. The discrimination rate of the combined sequence marker is significantly increased to 52.5% (21 populations) over the highest 35% (13 populations) by the single marker of ETS, though still inadequate but a big step forward. Further exploration of more DNA markers is needed. This study for the first time revealed the rich genetic diversity and phylogeny of the currently cultivated S. miltiorrhiza populations in China and provides novel alternative molecular markers for the genetic identification and resources evaluation of the cultivated S. miltiorrhiza populations.

Genetic diversity of 1-deoxy-D-xylulose 5-phosphate synthase gene (SmDXS) among the cultivated Danshen (Salvia miltiorrhiza) populations

“…The highest rate of the discrimination 34.2% is by the spliced exon sequences of SmDXS, which is comparable to ETS (35%) (Feng et al, 2022a;Feng et al, 2022b), higher than by ITS (7.1%) (Liao et al, 2021, rbcL(15%) (Feng et al, 2021), SmHMGR (10.5%) trnL-trnF (10%), psbA-trnH (20%) and ycf1-rps15 (27.5%) (Feng et al, 2022a), but much lower than the four combined intergenic spacers (52.5%) (Feng et al, 2022a). It seems that single molecular marker, whether from DNA sequence markers or functional genes, nuclear or chloroplastic, is inadequate for population discrimination, while useful in some situations.…”

“…Zhou et al (2021) assessed the wild germplasm diversity of S. miltiorrhiza and its related species providing fundamental genetic background for cultivation and molecular breeding of this medicinally important species. The genetic diversity of cultivated Danshen populations by various markers, internal transcribed spacers (ITS) (Liao et al, 2021), chloroplast rubisco large subunit (rbcL) gene (Feng et al, 2021), and four combined intergenic spacers of nuclear rDNA(ETS) and the chloroplast (psbA-trnH, trnL-trnF, and ycf1-rps15) , have also been revealed. Recently functional genes, SmHMGR (Ren et al, 2022) and SmTAT (Li et al, 2022), for the biosynthesis of bioactive components of the cultivated Danshen have been employed to understand its genetic diversity and phylogeny, and encouraging new insights have been appearing.…”

Chloroplast DNA polymorphism and morphometric characteristics of Carpinus betulus in the Lithuania forests

“…The chloroplast intergenic spacer psbA-trnH is one of the most important variables in the genome of gymnosperm and angiosperm chloroplasts. It is also used for plant barcodes and widely used in population genetics for revealing phylogeographical patterns and population dynamics (Štorchová and Olson 2007;Hao et al 2010;Anabat et al 2020;Intharuksa et al 2020;Kholina et al 2020Kholina et al , 2022Feng et al 2022;Olsson et al 2022). Noncoding DNA changes more rapidly than coding DNA, and mutations accumulate in it because it is not affected by selection.…”