Interspecific polymorphism at non-coding regions of chloroplast, mitochondrial DNA and rRNA IGS region in Elymus species

Abstract

Several published universal primers for amplification of non-coding regions of chloroplast, mitochondrial and ribosomal (rRNA) IGS region were tested whether they can amplify respective regions in Elymus species. PCR-RFLP analysis of the chloroplast, mitochondral DNA, and rRNA IGS region of the genus Elymus was used to determine if the method could be employed to detect inter-specific variation in this genus. Published universal primers for amplification of trnK [tRNA-Lys (UUU) exon 1]-trnK [tRNA-Lys (UUU) exon2], and mitochondrial nad1 exon B-nadl exon C intron successfully amplified the respective regions in Elymus species. However, the primers for amplification of chloroplast trnD-trnT intron and rRNA IGS failed to amplify the respective region in Elymus species. New primer pairs were designed and successfully amplified the cpDNA trnD-trnT intron and rRNA IGS region in Elymus species. The amplification products were digested with seven restriction enzymes. The results showed that the investigated regions of chloroplast and mitochondrial genomes are variable in most of the tested taxa and contain multiple variable regions. These regions should serve as useful molecular markers in phylogenetic studies of closely related species, at least at the interspecific level in Elymus. It is likely that further studies, including larger sample sizes, more regions of these genomes and/or more powerful methods for the detection of cpDNA and mt DNA variation will reveal additional variation for this genus. Highly inter- and intra-specific polymorphisms for rRNA IGS region were detected, suggesting the IGS will be a useful molecular marker for population studies of Elymus species.

The conservation of mitochondrial genome sequence in Leucadendron (Proteaceae)

“…Sizes of selected fragments of the 100 bp ladder (Promega) are indicated. example, among 13 Elymus species analysed, polymorphisms were detected within 1600 bp of mtDNA sequence space with two of seven primer-enzyme combinations tested (Sun 2002). The complete inability to detect site variation or indels among seven Leucadendron species with 62 primer pair-enzyme combinations indicates the extreme conservation of mtDNA sequence in this genus.…”

“…This contrasts strongly to the situation found in other plants. For example, PCR-RFLP analysis of mtDNA intronic regions has been used successfully to detect interspecific polymorphisms in Actinidia (Testolin and Cipriani 1997), Elymus (Sun 2002), Musa (Nwakanma et al 2003), Vasconcellea (Van Droogenbroeck et al 2004) and Houttuynia (Wei et al 2005), and even intraspecific polymorphisms in Quercus robur (Dumolin-Lapegue et al 1995), Actinidia deliciosa (Testolin and Cipriani 1997), Picea abies (Grivet et al 1999), Solanum tuberosum (Bastia et al 2001), Eucalyptus globulus (Vaillancourt et al 2004) and Buchloe dactyloides (Gulsen et al 2005). In a study of eight genotypes of Eucalyptus globulus, a mtDNA polymorphism was detected within 7960 bp of sequence space after screening only 36 primer pair-enzyme combinations (Vaillancourt et al 2004).…”

Phylogenetic analysis of Elymus (Poaceae) in western China

“…This indicated that either Hordeum is the maternal genome donor to Elymus species or that there was gene flow from Hordeum to Elymus species. Previous studies showed that the female parent of North American tetraploid Elymus species (StH-genome) originated from North American Pseudoroegneria species (Mason-Gamer and Orme, 2002;Sun, 2002), indicating that the female parent of Elymus species from North America and Asia have different origins. Interestingly, E. nutans (KF905218, StHYgenome) and H. brevisubutatum (AY740790, H-genome) species were from Asia, while Elymus species in the former group were from Asia, and Hordeum species were from North America and Asia.…”

Are Epichloë endophytes specific to Elymus grass hosts?

“…cylindricus, StHY (Mason-Gamer et al, 2010;Mason-Gamer, 2013). The chloroplast genome typically represents the maternal parent in angiosperms, and previous studies have found that North American Pseudoroegneria species (St genome) are the maternal donor to North American Elymus species (Mason-Gamer and Orme, 2002;Sun, 2002Sun, , 2014. We found that the maternal parent of Chinese E. tangutorum (KF905207) and E. dahuricus var.…”