Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium. Euphytica

Tottori University The United Graduate School of Agricultural Sciences Tottori 680-8553 Japan
Euphytica (Impact Factor: 1.39). 06/2009; 173(3):321-328. DOI: 10.1007/s10681-009-0087-1


The potential of microsatellite markers for use in genetic studies has been evaluated in Allium cultivated species (Allium cepa, A. fistulosum) and its allied species (A. altaicum, A. galanthum, A. roylei, A. vavilovii). A total of 77 polymerase chain reaction (PCR) primer pairs were employed, 76 of which amplified a single product or several
products in either of the species. The 29 AMS primer pairs derived from A. cepa and 46 microsatellites primer pairs from A. fistulosum revealed a lot of polymorphic amplicons between seven Allium species. Some of the microsatellite markers were effective not only for identifying an intraspecific F1 hybrid between shallot and bulb onion but also for applying to segregation analyses in its F2 population. All of the microsatellite markers can be used for interspecific taxonomic analyses among two cultivated and four
wild species of sections Cepa and Phyllodolon in Allium. Generally, our data support the results obtained from recently performed analyses using molecular and morphological markers.
However, the phylogeny of A. roylei, a threatened species with several favorable genes, was still ambiguous due to its different positions in each dendrogram
generated from the two primer sets originated from A. cepa and A. fistulosum.

KeywordsAllium-Microsatellite markers-DNA polymorphism

Download full-text


Available from: Hikaru Tsukazaki, Mar 22, 2015
  • Source
    • "Lee et al. (2011) tested the transferability of 50 SSR markers of A. sativum in five Allium species, obtaining the highest transferability (73%) in A. ampeloprasum L. var porrum and the lowest (47.6%) in A. altaicum. Araki et al. (2010) using 29 SSRs, derived from bulb onions, found a transferability rate ranging from 73.3% to 93.3% in six Allium species. Tsukazaki et al. (2008) "
    [Show abstract] [Hide abstract]
    ABSTRACT: Onion (Allium cepa L.) is one of the most valuable vegetables in the world. However, despite its global culinary and economic significance, the knowledge about onion genetic diversity and resources is limited. The Vegetable Germplasm Bank of Zaragoza (BGHZ) (Spain) holds an important A. cepa L. collection, where most of the Spanish onion variability is represented. Since the genetic diversity of Spanish onion germplasm is an unexploited resource for onion breeding, a total of 85 Spanish onion landraces (A. cepa L.) and 6 related Allium outgroups from the BGHZ collection were studied by means of SSR markers. The results showed that 12 out of the 18 SSR markers amplified were useful and polymorphic to distinguish all the studied onion accessions, allowing the detection of 47 alleles, with an average of 3.9 alleles per SSR, ranging from 2 to 7. Within related Allium species, the total number of detected alleles was 45, with an average of 3.7 alleles per SSR, ranging from 1 to 10. Specific alleles were obtained both in the Spanish onion landraces and in related Allium species, with cross transferability rates ranging from 25.0% to 91.7% in the six Allium species assayed. The resulting UPGMA dendrogram grouped the 91 Allium accessions according to their taxonomical classification, producing 6 main clusters, with all the Spanish onion landraces included in one cluster at a genetic distance of 0.69. These results revealed an interesting reservoir of genetic variability, useful for onion breeding, and confirmed the need to preserve these irreplaceable genetic resources.
    Full-text · Article · May 2014 · Scientia Horticulturae
  • Source
    • "The grouping revealed by the cluster analysis and principal coordinate analysis was similar to previous subgroupings of the Allium genus in that it distinguished the Rhizirideum and Allium subgenera (Hanelt et al., 1992; Ohri et al., 1998). In the Cepa section of the Rhizirideum subgenera, A. fistulosum and A. altaicum were each other's closest relatives and formed distinctive groups among the Allium species (Araki et al., 2010; Fischer and Bachmann, 2000; Khar et al., 2010). A. fistulosum likely originated from an A. altaicum progenitor based on the characteristics of nuclear and chloroplast DNA (Friesen et al., 1999) and supported by SSR profiles (Fischer and Bachmann, 2000). "
    [Show abstract] [Hide abstract]
    ABSTRACT: For genetic analysis of the genus Allium, which is composed of diverse species, we acquired 50 transferable and polymorphic microsatellite markers from A. sativum and tested them for transferability in five Allium species. Among the 50 simple sequence repeat (SSR) loci, the dinucleotide motif was the most prevalent, with a ratio of 50% (25/50), and (GT)n was more frequent than (GA)n within the dinucleotide motif. The average number of amplified alleles ranged from 1.452 to 1.910 and the accessions of A. tuberosum had a maximum of 4.8 alleles per accession with the GB-AS-104 SSR marker. Whereas A. porrum belonging to the Allium section revealed 73.0% transferability, A. altaicum and A. fistulosum appertaining to different sections showed low transferability, with a ratio of 47.6% and 48.0%, respectively. The phylogenetic results for these SSR markers did not deviate from previous classifications of the genus Allium. As the rate of successful amplification of SSR markers generally correlates with genetic distance, these SSR markers are potentially useful in the analysis of genetic relationships between or within Allium species.Highlights► We tested 50 SSR markers from A. sativum for transferability in 5 Allium species. ► A. porrum belonging to the Allium section revealed 73.0% transferability. ► A. altaicum and A. fistulosum (other sections) showed the lowest transferability. ► These will be useful in the study of genetic relationships between Allium species.
    Full-text · Article · May 2011 · Scientia Horticulturae
  • [Show abstract] [Hide abstract]
    ABSTRACT: This paper deals with the diversity assessment of tropical Indian onion and cross amplification of genomic and EST-SSR markers in distantly related native wild species. Out of 60 SSRs, 10% genomic SSRs were able to amplify as compared to EST-SSR where 53.3% primers were able to reveal amplicons. Clustering revealed five groups and indigenous short day onion formed separate cluster from the exotic short day and long day onions. A. roylei accessions exhibited a dissimilarity index of 35.5% between themselves whereas ‘Pran’ and A. × proliferum grouped together at a genetic distance of 0.4. A. fistulosum accessions formed a tight cluster and distantly related wild species A. carolinianum, A. chinense and A. hookeri formed neutral nodes. Present results are important to aid in analyzing the diversity present in short day onion and its utilization in breeding programs. Further, this is the first time that three accessions of A. roylei Stearn were used and rare alleles amplified in wild species will aid in detecting population structure and molecular marker aided selection for interspecific hybrid development.
    No preview · Article · Jun 2011 · Genetic Resources and Crop Evolution
Show more