Diversity comparison and phylogenetic relationships of cocksfoot (Dactylis glomerata L.) germplasm as revealed by SSR markers

Abstract

. 2010. Diversity comparison and phylogenetic relationships of cocksfoot (Dactylis glomerata L.) germplasm as revealed by SSR markers. Can. J. Plant Sci. 90: 13Á21. Phylogenetic relationships among and within 16 accessions collected from China, Russia, Kazakhstan, India and Japan were investigated using SSR markers. The 21 SSR primer pairs generated a total of 143 polymorphic alleles, with an average of 6.8 alleles per locus, and a range of 3Á13 alleles. The average genetic diversity, as measured by the polymorphic information content (PIC), was 0.33. The average polymorphic rate (P) for this species was 90.7%, suggesting a high degree of genetic diversity. Analysis of molecular variation (AMOVA) revealed larger genetic variation within accessions (65.75%) and geographical regions (75.58%) rather than between them, while among ploidy level variance contributed only 2.62%. A high degree of genetic diversity within tetraploid group was detected based on the polymorphic rate (P 094.23%) and shannon's information index of diversity (I00.4300) when compared with diploid group (P 091.25%, I 00.3922). The values of the genetic identity (GI) among accessions ranged from 0.7320 to 0.9691 and were used to produce a dendrogram using the UPGMA approach. The 16 accessions were grouped into two major clusters (GI00.876); specifically, all tetraploid (2n 04x028) accessions originating from different regions were grouped into the same cluster, whereas the diploid (2n 02x014) accessions were grouped into the two major clusters. The dendrogram was concordant with the morphological variability, agronomic traits and karyotype. Generally, the results of this study indicate that cocksfoot germplasm contains high molecular variation within accession and geographical region. The implications of these results for conservation of the species were discussed. Les 21 paires d'amorces SSR ont donne´143 alle`les polymorphes, avec une moyenne de 6,8 alle`les par locus et une fourchette de 3 a`13 alle`les. La diversite´ge´ne´tique moyenne e´tablie d'apre`s l'importance de l'information polymorphe est de 0,33. Le taux moyen de polymorphisme pour l'espe`ce est de 90,7%, ce qui laisse croire a`une grande diversite´ge´ne´tique. L'analyse de la variation mole´culaire (AMOVA) re´ve`le que la variation ge´ne´tique est plus grande au sein des obtentions (65,75%) et a`l'inte´rieur des re´gions (75,58%) qu'entre elles, mais la variance des ploı¨dies n'explique que 2,62% de cette variation. Le taux de polymorphisme (P 094,23%) et l'indice Shannon de diversite´(I 00,4300) re´ve`lent une grande diversite´ge´ne´tique pour les groupes te´traploı¨des, comparativement aux groupes diploı¨des (P 091,25%, I 00,3922). L'identite´ge´ne´tique (GI) des obtentions varie de 0,7320 a`0,9691; on s'en est servi pour produire un dendrogramme par la me´thode UPGMA. Les 16 obtentions ont e´te´re´unies en deux grandes grappes (GI00,876), plus pre´cise´ment, les obtentions te´traploı¨des (2n04 x028) venant des diverses re´gions se sont toutes retrouve´es dans une grappe, alors ...

Genetic diversity and structure of natural Dactylis glomerata L. populations revealed by morphological and microsatellite-based (SSR/ISSR) markers

“…The results indicated that all 3 locations had relatively high level of genetic variation for polymorphic rates (P = 100%) based on both SSR and ISSR markers. Polymorphism in the present study was higher compared to previous reports on SSR variation (P = 84.63) (Xie et al, 2010), ISSR variation (P = 86.3) (Xie et al, 2010), and AFLP variation (P = 84%) (Peng et al, 2008).…”

“…Genetic variability mainly existed within rather than among the tested locations, as shown by AMOVA, based on both SSRs and ISSRs. Similarly, analysis of molecular variation (AMOVA) based on SSRs revealed larger genetic variation within accessions (65.75%) and geographical regions (75.58%), rather than between them, in the analysis of 16 D. glomerata accessions collected from China, Russia, Kazakhstan, India, and Japan (Xie et al, 2010). In addition, Kölliker et al (1999) obtained 85% variability within 3 cultivars of D. glomerata.…”

“…ISSR analysis has been used to assess the genetic diversity of a large number of plant species, including Lolium spp (Dinelli et al, 2004) and Cynodon dactylon (Wang et al, 2013). Both SSRs and ISSRs are powerful and useful tools for genetic studies and have been used in several plant species; however, at present, reports remain P. Madesis et al limited about their use in studies of D. glomerata populations (Litrico et al, 2009;Xie et al, 2010Xie et al, , 2012.…”

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

“…Heterologous marker transferability also decreases as species diverge (Thiel et al 2003;Zhang et al 2005;Litrico et al 2009), and are accompanied by higher likelihood of homoplasy and polymorphism due to mutations that exist among the species (Thiel et al 2003;Saha et al 2004;Zhang et al 2006). Recently, genomic library-derived SSR markers were used to describe relationships among some Asian germplasm (Xie et al 2010). Genomic SSR markers also tend to have lower transferability and amplification success than EST-derived SSR markers across diverse germplasm (Varshney et al 2005;Xie et al 2010).…”

“…Recently, genomic library-derived SSR markers were used to describe relationships among some Asian germplasm (Xie et al 2010). Genomic SSR markers also tend to have lower transferability and amplification success than EST-derived SSR markers across diverse germplasm (Varshney et al 2005;Xie et al 2010). In contrast to these approaches, EST-derived markers developed from within a target species can circumvent these constraints and provide sufficient polymorphism.…”