Classification and identification of bunching onion (Allium fistulosum) varieties based on SSR markers

Abstract

We investigated the correspondence between classifications based on simple sequence repeat (SSR) markers and on morphological traits for 30 bunching onion (Allium fistulosum L.) varieties. We also examined applicability of an assignment test for variety identification in bunching onion. Cluster analysis based on the allele frequency data at 29 SSR loci classified most of the varieties except for 'Iwatsuki-2' into the predicted variety groups, 'Kaga', 'Senju' or 'Kujo', which were categorized based on morphological traits. Although 'Iwatsuki-2' has been regarded as a member of 'Kaga' group, molecular data suggested the variety belonging to 'Kujo' rather than 'Kaga'. In the assignment test at the individual level, 89.1% of the individuals were assigned to their original variety. When the assignment was conducted based on groups each consisting of four individuals, the percentage of correct assignments was considerably improved (99.3%). These results suggested that the assignment test approach will be useful for variety identification in allogamous bunching onions, which have large within-variety genetic diversity. On the other hand, it was also suggested that sampling of true source varieties will be fundamental to avoid misjudgment.

Development of genomic and EST-SSR markers in radish (Raphanus sativus L.)

“…In spite of such the conservative nature of ESTs, some of the EST-derived SSRs were failed in stable amplification. This could be because some primer sites may have been designed across splicing sites or because of chimerical origins of the cDNA clones in the database, as discussed by Tsukazaki et al (2010) . Although polymorphism of EST-SSRs is generally lower than that of genomic SSRs ( Blair et al 2006 ) because of the conservative nature of exon sequences, no obvious difference was found in polymorphism rate between the genomic and EST-SSRs as long as comparison of the present two radish lines.…”

Exploring genetic diversity and quality traits in a collection of onion (Allium cepa L) landraces from north-west Spain

“…Genetic diversity assessment on the basis of molecular markers should be preferred compared to morphological traits because of their neutral behavior, independency on the environment, their easy access, assay and exchange of data between laboratories (JOSHI et al, 1999). Molecular characterization constitutes the first essential step towards the successful exploitation of the potentially new genetic variability, as it allows us to gain knowledge on the genetic relationship among lines, the level of fixation or heterozygosity and the development of genetic profiles for variety identification and protection of breeders and grower´s rights (TSUKAZAKI et al, 2010, KHAR et al, 2011. Genetic background studies in onion have used different types of molecular markers to characterize the variability inside germplasm collections (TANIKAWA et al, 2002, JAKSE et al, 2005, ARAKI et al, 2010.…”

The Preference of Thrips tabaci for Allium cepa, Allium fistulosum, and Allium roylei

“…There are many local and commercial cultivars of A. fistulosum with distinctive differences in morphological and other traits that are adapted to a variety of climatic conditions. The wide variety of A. fistulosum phenotypes that exist around the world [58] suggests that some of them will likely develop traits that will promote resistance or tolerance to T. tabaci; thus, further research in this direction appears to be justified.…”