EST and EST-SSR marker resources for Iris

Abstract

Background: Limited DNA sequence and DNA marker resources have been developed for Iris (Iridaceae), a monocot genus of 200-300 species in the Asparagales, several of which are horticulturally important. We mined an I. brevicaulis-I. fulva EST database for simple sequence repeats (SSRs) and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications in Iris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database) and the cross-species utility and polymorphisms of I. brevicaulis-I. fulva EST-SSR markers among wild collected ecotypes and horticulturally important cultivars.

Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

“…Similar abundance of GA dinucletide repeats, has been observed in many other plant species in the recent past (Tang et al 2009;Roorkiwal and Sharma 2011;Victoria et al 2011). This repeat class is known to play an active role in gene regulation in both animal and plant species (Trivedi 2004).…”

“…Among microsatellites, dinucleotides were most frequent repeats (63.46 %) followed by trinucleotide repeats (31.35 %) while a very small share of 5.19 % was altogether contributed by tetra-, penta-and hexa-nucleotide repeats (Supplementary table 1). Similar abundance of dinucleotide repeats over trinucleotide repeats, was reported in other plant species (Tang et al 2009;Roorkiwal and Sharma 2011). One of the possible reasons behind such abundance could be that shorter repeating units allow more number of possible slippage events per unit length of DNA.…”

Genomic collinearity and the genetic architecture of floral differences between the homoploid hybrid species Iris nelsonii and one of its progenitors, Iris hexagona

“…A total of 282 microsatellite primers (developed by Tang et al (2009) for I. fulva and I. brevicaulis map production) were screened for utility in the I. nelsonii  I. hexagona F 2 mapping population. Of those, 137 markers were both polymorphic and reliably scored in the mapping population.…”

“…The marker names reported here are the same as those reported for linkage maps previously constructed using I. brevicaulis  I. fulva reciprocal backcross populations (Tang et al, 2010). PCR reactions (modified from Tang et al, 2009) were performed in 10 ml reaction volumes that included 1x PCR buffer, 2.5 mM MgCl 2 , 0.3 mM of each deoxyribonucleotide triphosphate, 4 pmol fluorescently labeled forward primer (either 6-FAM/HEX/TAMRA dye), 4 pmol reverse primer, 0.5 units GoTaq Flexi DNA Polymerase (Promega Corporation, Madison, WI, USA), and B10 ng of genomic DNA. Loci were amplified using touchdown PCR (Don et al, 1991) (Tang et al, 2009).…”

“…PCR reactions (modified from Tang et al, 2009) were performed in 10 ml reaction volumes that included 1x PCR buffer, 2.5 mM MgCl 2 , 0.3 mM of each deoxyribonucleotide triphosphate, 4 pmol fluorescently labeled forward primer (either 6-FAM/HEX/TAMRA dye), 4 pmol reverse primer, 0.5 units GoTaq Flexi DNA Polymerase (Promega Corporation, Madison, WI, USA), and B10 ng of genomic DNA. Loci were amplified using touchdown PCR (Don et al, 1991) (Tang et al, 2009). Fragments were multiplexed when possible (when fluorescent labels and/or allele sizes allowed for multiplexing) and run on an ABI 3700xl capillary sequencer (Applied Biosystems, Foster City, CA, USA) at the Georgia Genomics Facility and scored by eye in Peakscanner v.1.0 (Applied Biosystems) and GeneMarker v.1.8 (Softgenetics LLC, State College, PA, USA).…”