Genetic diversity and phylogenetic relationships in the rye genus Secale L. (rye) based on Secale cereale microsatellite markers

Abstract

The genetic diversity and phylogenetic relationships in the genus Secale L. (rye) was evaluated using 24 Secale cereale microsatellite (SCM) markers. The average polymorphism information content (PIC) value of each microsatellite locus in 30 Secale accessions evaluated was higher than that in 47 cultivated ryes (Secale cereale ssp. cereale). The mean genetic similarity (GS) index in Secale was lower than that in cultivated rye. The highest within-species GS index was observed for S. sylvestre and the lowest for S. strictum, whereas the highest between-species GS index was found between S. cereale and S. vavilovii and the lowest between S. sylvestre and S. cereale. There was no obvious difference in GS levels in the cultivated rye accessions from Asia, Europe, North America or South America. Cluster analysis indicated that all the Secale accessions could be distinguished by the 24 microsatellite loci. We also found that the S. sylvestre accessions were obviously divergent from the accessions of other species and that the S. vavilovii accessions were closely related to the S. cereale accessions. Our results also showed that S. strictum was heterogeneous and showed great within-species differences. The microsatellite-derived dendrogram faithfully reflected the phylogenetic relationships between Secale species but did not indicate a possible domestication process of the cultivated rye based on the geographical sources of the accessions.

Molecular diversity and genetic relationships in Secale

“…S. vavilovii was closely related to the cultivated rye (figure 2a). This species showed strong link to S. cereale subspecies which is in agreement with various other works (Cuadrado and Jouve 2002;De-Bustos and Jouve 2002;Chikmawati et al 2005;Shang et al 2006;Fu et al 2010;Zhou et al 2010;Ren et al 2011;Achrem et al 2014). Moreover, some authors suggested that the species S. strictum is the common ancestor of S. vavilovii and S. cereale species (Cuadrado and Jouve 2002;De Bustos and Jouve 2002;Zhou et al 2010;Achrem et al 2014).…”

“…The subspecies ancestrale and segetale have been grouped using other molecular markers (De Bustos and Jouve 2002;Chikmawati et al 2005;Shang et al 2006;Fu et al 2010;Ren et al 2011). The subspecies segetale was generally the farthest in the group (Chikmawati et al 2005;Shang et al 2006;Achrem et al 2014).…”

“…Vavilov 1926;Stutz 1972), cytogenetic (Khush 1962;Cuadrado and Jouve 2002;Zhou et al 2010), chemotaxonomic (Dedio et al 1969), biochemical, like isozymes (Vences et al 1987;Matos et al 2001); and molecular methods such as amplified fragment length polymorphism (AFLP) (Chikmawati et al 2005(Chikmawati et al , 2012, ISSR (Matos et al 2001;Ren et al 2011), random amplified polymorphic DNA (RAPD) (Matos et al 2001;Ma et al 2004), restriction fragment length polymorphism (RFLP) (Loarce et al 1996), simple sequence repeat (SSR) (Shang et al 2006;Jenabi et al 2011) and ribosomal DNA studies (De Bustos and Jouve 2002).…”

Assessment of genetic relationships among Secale taxa by using ISSR and IRAP markers and the chromosomal distribution of the AAC microsatellite sequence

“…afghanicum, providing support for the classification proposed by Hammer (1990), who recognized these 2 taxa as subspecies. Very similar conclusions can be drawn from SSR-based studies (Shang et al, 2006), ISSR-based studies (Ren et al, 2011), and the analysis of ITS rDNA regions (Bustos & Jouve, 2002). The physical localization of AAC clusters in Secale cereale was identical to Secale cereale subsp.…”

“…The differences should be considered in 2 ways: first, the amplification of microsatellites could appear at different chromosomal sites in 2 diverging species, and, second, events of differential deletions in evolving species could follow microsatellite amplifications in a common ancestor (Cuadrado & Jouve, 2002;Achrem & Rogalska, 2006). The distinctness of Secale sylvestre was also confirmed by molecular studies of chloroplast DNA (Murai et al, 1989;Petersen & Doebley, 1993), repetitive sequences (Cuadrado and Jouve, 2002;Shang et al, 2006;Zhou et al, 2010), 18S-5.8S-26S rDNA (De Bustos & Jouve, 2002), and AFLP-based analysis of genetic diversity (Chikmawati et al, 2005).…”