Ragi Genome Sequence May Provide Insights Into Drought Tolerance And Nutraceutical Properties

Methods Used in This Research:

1. Genome size estimation of finger millet and wild species

2. Nucleic acid isolation

3. Paired-end, mate pair library preparation and sequencing

4. DNA-seq data pre-processing and de novo genome assembly

5. Gene prediction and functional annotation

6. Gene families, phylogenetic analysis and mining of transcription factors

   

   Phylogenetic relationship of six Poaceae species revealed based on single copy ortholog genes

7. Analysis of calcium transporter, disease resistant and C4 pathway genes

8. RNA-seq library preparation and data pre-processing

9. Transcriptome assembly, differential gene analysis and functional annotation

10. Validation of drought responsive genes through qRT-PCR

11. Simple and complex repeat prediction

12. Primer designing for SSRs and electronic PCR

13. Oligo synthesis and genotyping of finger millet accessions

Results

Experimental results from whole genome sequencing and assembling process of ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total estimated genome size. Genome analysis showed the presence of 85,243 genes and one-half of the genome is repetitive in nature.

• The finger millet genome was found to have higher colinearity with foxtail millet and rice as compared to other Poaceae species. Mining of simple sequence repeats (SSRs) yielded an abundance of SSRs within the finger millet genome.
• Functional annotation and mining of transcription factors revealed finger millet genome harbors a large number of drought tolerance related genes.
• Transcriptome analysis of low moisture stress and non-stress samples revealed the identification of several drought-induced candidate genes, which could be used in drought tolerance breeding.

4. DNA-seq data pre-processing and de novo genome assembly

Conclusions

This genome sequencing effort will strengthen plant breeders for allele discovery, genetic mapping, and identification of candidate genes for agronomically important traits. Availability of genomic resources of finger millet will enhance the novel breeding possibilities to address potential challenges of finger millet improvement.

Reference :https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3850-z