Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Abstract

Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

Identification of orchardgrass (Dactylis glomerata L.) cultivars by using simple sequence repeat markers

“…To overcome these limitations, a number of molecular markers in orchardgrass have been employed for genetic diversity assessments, genetic mapping, and quantitative trait loci (QTL) analysis, because these traits are not influenced by variable environmental conditions with similar phenotype or plant phenology (Belaj et al, 2002). These markers include sequence-related amplified polymorphism (SRAP) (Zeng et al, 2008;Xie et al, 2011), random amplified polymorphic DNA (RAPD) (Kolliker et al, 1999;Tuna et al, 2004), amplified fragment length polymorphism (AFLP) (Peng et al, 2008), inter-simple sequence repeat (ISSR) (Zeng et al, 2006), and simple sequence repeats (SSR) (Xie et al, 2010;Bushman et al, 2011).…”

“…SSR markers have been widely used in genetic diversity analyses (Wang et al, 2009;Bushman et al, 2011;Erfani et al, 2012;Zhang et al, 2012a). In the current study, a total of 29 SSR primer pairs were used to estimate the genetic diversity of a collection of orchardgrass cultivars.…”

“…The main species of D. glomerata L. is referred to as orchardgrass or cocksfoot (Lindner and Garcia, 1997;Bushman et al, 2011), and is an economically important and extensively used cool-season perennial forage grass in China, along with many other countries that have temperate and cold climates (Sanada et al, 2010). Because of its high yield, good nutrition, adaptability, and shade tolerance, orchardgrass is widely used for grazing and hay production worldwide (Xie et al, 2012).…”

“…Therefore, the ability to rapidly and reliably identify a cultivar is becoming increasingly important. Bushman et al (2011) assessed the molecular diversity of 3 cultivars and several subspecies of orchardgrass. In addition, another study assessed the isozymes of orchardgrass populations in Europe (Lumaret, 1982).…”

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

“…This plant is commonly used for forage and hay production worldwide because of its remarkable local adaptation, good tolerance to shadow (and thus is also known as orchardgrass), high yield, and high sugar content (Horn et al, 1988;Bushman et al, 2011;Xie et al, 2012). It plays an important role as forage material in North America, Europe (Casler et al, 2000), and Oceania, as well as in grassland animal husbandry and ecological construction of southern subtropical mountains of China.…”