A search for markers of sugarcane evolution

Abstract

To determine the phylogenetic relationship between sugarcane cultivars and other members of the Saccharinae subtribe, we identified the fast evolving ITS1-5.8S-ITS2 (ITS = internal transcribed spacer; 5.8S = 5.8S ribosomal DNA) region of the sugarcane genome in the Sugarcane Expressed Sequence Tag (SUCEST) genome project database. Parsimony analysis utilizing this region and homologs belonging to the 23 closely related Andropogoneae currently deposited in the GenBank database has shown sugarcane as the sister group of Saccharum sinense. However, because there are few parsimony-informative characters and high homoplasy in the ITS1-5.8S-ITS2 region we were not able to determine with confidence the phylogenetic relationship between sugarcane and some of the remaining members of Saccharine subtribe. To find alternatives for the phylogenetic reconstruction of sugarcane evolutionary history, we selected 17 markers (nuclear, chloroplastic or mitochondrial) from the SUCEST database of which apha-tubulin, ribosomal protein L16 (rpl16) and DNA-directed RNA polymerase beta chain (rpoC2) were found to have a low incidence of polymorphism and comparable, or even faster, rates of evolution than the ITS1-5.8S-ITS2 region. We suggest that these markers should be considered as preferential choices for phylogenetic studies of Saccharinae subtribe.

Molecular identification of endangered Korean lady’s slipper orchids (Cypripedium, Orchidaceae) and related taxa

“…The atpF-H region is a DNA bar-coding marker used for molecular identification and phylogenetic study of low-taxonomic-level plant species, although it does not function independently (Hollingsworth et al 2008;Dong et al 2012;Gitsopoulos et al 2013). Since Cummings et al (1994 reported that rpoC2, a gene coding beta-2-subunit of RNA polymerase, has an extra coding sequence restricted to grass (Poaceae), this gene has been used in molecular phylogenetic studies of the grass family (Duvall et al 2001(Duvall et al , 2013Bacci Jr. et al 2001;Petersen et al 2004).…”

A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum

“…Based on previous studies on nrDNA-ITS in sugarcane germplasms, the tetra-primer ARMS PCR technique can be used to analyze genetic diversity and phylogenetic relationships in interspecific and intergenus samples [ 9 , 10 , 19 ]. However, studies exploring the identification and use of SNPs as molecular markers in Saccharum breeding have not been performed.…”