Dataset Information

Finger Millet [Eleusine coracana (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence.

ABSTRACT: The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, finger millet (Eleusine coracana (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of finger millet, disposing it as one of the lastly sequenced genomes in cereals. The genomic information available for this crop is very little when compared to other major cereals like rice, maize and barley. As a result, only a limited number of genetic and genomic studies has been undertaken for the improvement of this crop. Finger millet is known especially for its superior calcium content, but the high-throughput studies are yet to be performed to understand the mechanisms behind calcium transport and grain filling. The WGS of finger millet is expected to help to understand this and other important molecular mechanisms in finger millet, which may be harnessed for the nutrient fortification of other cereals. In this review, we discuss various efforts made so far on the improvement of finger millet including genetic improvement, transcriptome analysis, mapping of quantitative trait loci (QTLs) for traits, etc. We also discuss the pitfalls of modern genetic studies and provide insights for accelerating the finger millet improvement with the interventions of WGS in near future. Advanced genetic and genomic studies aided by WGS may help to improve the finger millet, which will be helpful to strengthen the nutritional security in addition to food security in the developing countries of Asia and Africa.

SUBMITTER: Antony Ceasar S

PROVIDER: S-EPMC6064933 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Finger Millet [<i>Eleusine coracana</i> (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence.

Antony Ceasar S S Maharajan T T Ajeesh Krishna T P TP Ramakrishnan M M Victor Roch G G Satish Lakkakula L Ignacimuthu Savarimuthu S

Frontiers in plant science 20180723

The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, finger millet (<i>Eleusine coracana</i> (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of finger millet, disposing it as one of the lastly sequenced genomes in cereals. The ...[more]

PMID: 30083176

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Project description:Drought is one of the most significant abiotic stresses that affects the growth and productivity of crops worldwide. Finger millet [Eleusine coracana (L.) Gaertn.] is a C4 crop with high nutritional value and drought tolerance. However, the drought stress tolerance genetic mechanism of finger millet is largely unknown. In this study, transcriptomic (RNA-seq) and proteomic (iTRAQ) technologies were combined to investigate the finger millet samples treated with drought at different stages to determine drought response mechanism. A total of 80,602 differentially expressed genes (DEGs) and 3,009 differentially expressed proteins (DEPs) were identified in the transcriptomic and proteomic levels, respectively. An integrated analysis, which combined transcriptome and proteome data, revealed the presence of 1,305 DEPs were matched with the corresponding DEGs (named associated DEGs-DEPs) when comparing the control to samples which were treated with 19 days of drought (N1-N2 comparison group), 1,093 DEGs-DEPs between control and samples which underwent rehydration treatment for 36 hours (N1-N3 comparison group) and 607 DEGs-DEPs between samples which were treated with drought for 19 days and samples which underwent rehydration treatment for 36 hours (N2-N3 comparison group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 80 DEGs-DEPs in the N1-N2 comparison group, 49 DEGs-DEPs in the N1-N3 comparison group, and 59 DEGs-DEPs in the N2-N3 comparison group, which were associated with drought stress. The DEGs-DEPs which were drought tolerance-related were enriched in hydrolase activity, glycosyl bond formation, oxidoreductase activity, carbohydrate binding and biosynthesis of unsaturated fatty acids. Co-expression network analysis revealed two candidate DEGs-DEPs which were found to be centrally involved in drought stress response. These results suggested that the coordination of the DEGs-DEPs was essential to the enhanced drought tolerance response in the finger millet.

Project description:Finger millet, an orphan crop, possesses immense potential in mitigating climate change and could offer threefold security in terms of food, fodder, and nutrition. It is mostly cultivated as a subsistence crop in the marginal areas of plains and hills. Considering the changes in climate inclusive of recurrent weather vagaries witnessed every year, it is crucial to select stable, high-yielding, area-specific, finger millet cultivars. Sixty finger millet varieties released across the country were evaluated over six consecutive rainy seasons from 2011 to 2016 at the Agricultural Research Station, Vizianagaram. The genotype × environment interaction (GEI) was found to be significant in the combined ANOVA. Furthermore, the Additive Main effects and Multiplicative Interaction (AMMI) analysis asserted that genotypes and the GEI effects accounted for approximately 89% of the total variation. Strong positive associations were observed in an estimated set of eleven stability parameters which were chosen to identify stable genotypes. Furthermore, Non-parametric and Parametric Simultaneous Selection indices (NP-SSI and P-SSI) were calculated utilizing AMMI-based stability parameter (ASTAB), modified AMMI stability value (MASV), and Modified AMMI Stability Index (MASI) to identify stable high yielders. Both methods had inherent difficulties in ranking genotypes for SSI. To overcome this, the initial culling [i.e., SSI with culling strategy (C-SSI)] of genotypes was introduced for stability. In the C-SSI method, the top ten genotypes were above-average yielders, while those with below-average yield were observed in NP-SSI and P-SSI methods. Similarly, the estimation of best linear unbiased prediction (BLUP)-based simultaneous selections, such as harmonic mean of genotypic values (HMGV), relative performance of genotypic values (RPGV), and harmonic mean of relative performance of genotypic values (HMRPGV), revealed that none of the top ten entries had below-average yield. The study has proven that C-SSI and BLUP-based methods were equally worthy in the selection of high-yielding genotypes with stable performance. However, the C-SSI approach could be the best method to ensure that genotypes with a considerable amount of stability are selected. The multi-year trial SSI revealed that entries Indaf-9, Sri Chaitanya, PR-202, and A-404; and VL324 and VL146 were ascertained to be the most stable high-yielding genotypes among medium-to-late and early maturity groups, respectively.

Dataset Information

Finger Millet [Eleusine coracana (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence.

Publications

Finger Millet [<i>Eleusine coracana</i> (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence.

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