Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium
ABSTRACT 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
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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. Keywords Allium cepa L. – A. roylei –Genetic diversity–Molecular markers–Onion–SSR–Wild speciesGenetic Resources and Crop Evolution 01/2011; 58(5):741-752. · 1.59 Impact Factor
- Gastroenterology 01/2011; 140(5). · 12.82 Impact Factor
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ABSTRACT: Improved understanding of genetic diversity in onion and shallot (Allium cepa L.) is required to inform breeding and genetic resource conservation, and to enable development of association genetics and seed quality assurance methods. To develop quantitative estimates of diversity we estimated within- and among-population heterozygosity in a set of onion populations using genomic simple sequence repeat (SSR) markers developed by genomic skim sequencing. Primer sets (166) designed to flank SSR motifs identified were evaluated in a diverse set of lines, with 80 (48 %) being polymorphic. The 20 most robust single copy markers were scored in 12 individuals from 24 populations representing short-day to long-day adapted material from diverse environments. The average genetic diversity estimate (H e) per population was 0.3 (SD 0.08) and the average per marker was 0.49 (SD 0.2). The onion populations assessed in this survey were distinct with moderate to large population differentiation but also had high within-population variation (F st = 0.26). There was evidence of inbreeding (F is = 0.22) with observed heterozygosities lower than the expected. This marker resource will be applicable for DNA fingerprinting, measuring levels of inbreeding in breeding lines, assessing population structure for association mapping and expanding linkage maps that are principally based on expressed sequence tag-based markers. A Galaxy workflow was developed to facilitate bulk SSR marker design from next-generation sequence data. This study provides one of the first quantitative views of population genetic variation in onion and a practical toolset for further genetics.Molecular Breeding 01/2012; 30(3). · 3.25 Impact Factor