Dataset Information

Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].

ABSTRACT: The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (?48%) was prevalent when compared with dinucleotide repeats (?46%). Of the 28 342 microsatellites, 21 294 (?75%) primer pairs were successfully designed, and a total of 15 573 markers were physically mapped on 9 chromosomes of foxtail millet. About 159 markers were validated successfully in 8 accessions of Setaria sp. with ?67% polymorphic potential. The high percentage (89.3%) of cross-genera transferability across millet and non-millet species with higher transferability percentage in bioenergy grasses (?79%, Switchgrass and ?93%, Pearl millet) signifies their importance in studying the bioenergy grasses. In silico comparative mapping of 15 573 foxtail millet microsatellite markers against the mapping data of sorghum (16.9%), maize (14.5%) and rice (6.4%) indicated syntenic relationships among the chromosomes of foxtail millet and target species. The results, thus, demonstrate the immense applicability of developed microsatellite markers in germplasm characterization, phylogenetics, construction of genetic linkage map for gene/quantitative trait loci discovery, comparative mapping in foxtail millet, including other millets and bioenergy grass species.

SUBMITTER: Pandey G

PROVIDER: S-EPMC3628449 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].

Pandey Garima G Misra Gopal G Kumari Kajal K Gupta Sarika S Parida Swarup Kumar SK Chattopadhyay Debasis D Prasad Manoj M

DNA research : an international journal for rapid publication of reports on genes and genomes 20130203 2

The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (∼48%) was prevalent when compared with dinucleotide repeats (∼46%). Of the 28 342 microsatellites, 21 294 (∼75%) primer pairs were successfully designed ...[more]

PMID: 23382459

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Project description:RationaleCarbonised plant remains are analysed for reconstruction of past climates and agricultural regimes. Several recent studies have used C4 plants to address related questions, and correlations between modern C4 plant δ13 C values and rainfall have been found. The millets were important food crops in prehistoric Eurasia, yet little is known about causes of isotopic variation within millet species. Previous research has shown there to be significant isotopic variation between millet accessions. Here we compare isotope ratios from plants grown under different watering regimes. This allows for a consideration of whether or not Setaria italica is a good proxy for environmental reconstruction.MethodsWe compare stable isotope ratios of Setaria italica plants grown in a controlled environment chamber with different watering regimes. We compare the carbon isotope ratios of leaves and grains, and the nitrogen isotope ratios of grains, from 12 accessions of Setaria italica.ResultsWe find significant isotopic variability between watering regimes. Carbon isotope ratios are positively correlated with water availability, and on average vary by 1.9‰ and 1.7‰ for leaves and grains, respectively. Grain nitrogen isotope ratios also vary with watering regime; however, the highest isotope ratios are found with the 130-mL watering regime.ConclusionsThe carbon isotope ratios of Setaria italica are strongly correlated with water availability. However, the correlation is the opposite to that seen in studies of C3 plants. The difference in isotopic ratio due to watering regime is comparable with that seen between different accessions; thus distinguishing between changing varieties of Setaria italica and changing climate is problematic. In terms of grain nitrogen isotope ratios, the highest δ15 N values were not associated with the lowest watering regime. Again, δ15 N variation is comparable with that which would be expected from an aridity effect or a manuring effect, and thus distinguishing between these factors is probably problematic.

Dataset Information

Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].

Publications

Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)].

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