Decoding of Finger Millet Genome: A Milestone of Millet Genomics

Abstract

Whole genome sequencing is an important milestone of the genomics-assisted molecular biology studies. Sequencing the whole genome of plants unravels the complex molecular structure of these complex organisms. In this respect, whole genome sequencing of important small millet that is finger millet was subsequently released by 2 independent groups. This commentary outlines the major applications of these reports, which also provided some opinion about this.

Whole genome and transcriptome sequences of finger millet provide novel perspectives to develop drought tolerance and nutraceutical properties in millets. ¹ The modern sequencing technologies and the transcriptome analysis offer more possibilities to analyze complex genomes.^2,3 To date, only little attention has been paid on genome sequencing and crop improvement programs, and as a result, this millet has been categorized as an orphan crop for modern genetics studies. ⁴ The presence of duplicated genes derived from genome duplication, size, and complex nature slowed down the progress in genome sequencing of finger millet. ¹ The genome size of wild species varied from 580 Mb (Erythrolamprus Jaegeri) to 1217 Mb (Eleusine coracana ssp. africana), and the genome size of cultivated finger millet (ML-365) was estimated to be 1453 Mb. The whole genome sequencing of ML-365 was yielded 1196 Mb covering ~82% of total estimated genome size. ¹ As finger millet is an allotetraploid and has a large genome size, the genome duplication events are very high where the assembly and its functional annotation have been a major challenge in genomics. ⁵ Totally, 85 243 genes have been predicted from whole genome sequences, which are found to be involved in different molecular, biological, and cellular processes of finger millet. ¹ In general, the millets, including finger millet, are considered highly tolerant to drought and rich in nutrients when compared with other cereals. Notably, finger millet possesses 10-fold higher seed calcium than any other cereal. However, the lack of whole genome information hindered advance genetic studies in this crop. ⁶ The recent release of draft genomes may aid to develop high-resolution studies, namely, forward and reverse genetics, functional genomics, and proteomics studies (Figure 1), which may help to unravel the drought tolerance and nutrient fortification mechanisms in finger millet.

Figure 1.

Importance of other omics technologies in crop improvement.

The comparative genomics and transgenic research will help to transfer key genes of drought tolerance and nutrient fortification into other millets and non-millet cereals. The number of genes identified from this study ¹ is also higher compared with those identified by Hatakeyama et al. ⁵ Pathway prediction analysis using KEGG Automatic Annotation Server revealed that the finger millet genes are also predicted to be involved in carbohydrate and amino acid metabolism. This drought-hardy crop can grow well even in low moisture and hot environmental conditions, because it has an effective carbon assimilating mechanism through C4 pathway. ⁷ High-resolution pathway analysis coupled with computational biology on finger millet genome sequence will help to understand key traits like drought tolerance and grain nutrient filling, which can be transferred to other cereals.

Genome collinearity analysis revealed that there was a high synteny between genomes of finger millet and rice followed by foxtail millet, and the least synteny was witnessed between finger millet and maize. ¹ Comparative analyses between genomes of grasses belonging to the subfamilies such as Ehrhartoideae, Panicoideae, and Pooideae have shown high conservation of collinearity despite some 60 million years of independent evolution of the major grass lineages.^7,8 Genomes of finger millet, rice, and foxtail millet have found to show high synteny, which might be due to the fact that these three species shared some genes that are common among these crops. ⁹ Comparative maps of finger millet and rice demonstrated that other than the rearrangements that are necessary to account for the difference in the chromosome number between these 2 genomes, the finger millet genome has remained highly conserved as its divergence from a common ancestor with rice some 60 million years ago. ¹⁰ Changes in photosynthetic pathway are clustered in similar time period, suggesting that global climatic forces in addition to temperature may have facilitated transitions between C3 and C4. Assembling the sequence data (phyB and ndhF) of 97 grasses also provide estimates for dates of critical nodes of the grass phylogeny, including the divergence of maize from rice. ¹¹ The whole genome sequence of finger millet has nearly 50% of repetitive DNA, which includes retro elements, unclassified repeats, and DNA transposons. In the search for simple sequence repeats (SSR), 114 083 SSRs were found throughout the genome; among these, most predominant are di-nucleotide followed by tri-nucleotide repeats. ¹ Development of high-throughput markers that are highly linked with important traits will provide the marker–trait associations. As finger millet has the huge collection of germplasms as both cultivated and wild type with broad genetic diversity, these markers will be useful for association of mapping-based allele discovery for novel variants.^12,13

Genes that code proteins of several important functions, namely, plant transcription factors, drought responsive genes, resistance genes for various diseases, calcium transport, and accumulation-related genes, were identified by homology-based analysis. ¹ Drought tolerance is regulated by various genes, including transcription factors that allow plants to withstand harsh conditions. ¹⁴ Moreover, the identification of genes and its function is necessary for dissecting and engineering the regulatory network for enhanced productivity, selection of quantitative trait loci (QTL), and crop breeding. In the recent past, only a limited number of studies were performed on the characterization of finger millet genes involved in important agronomical traits. For example, heterologous expression of finger millet NAC1 gene in tobacco found to confer drought and salinity tolerance. ¹⁵ Mohanta and Bae ¹⁶ reported that finger millet PIN1a is involved in the development of lateral root and root hairs. The four phosphate transporter1 (PHT1) genes, EcPHT1 1, 1;2, 1;3, and 1;4 involved in the acquisition of phosphorus from soil solution, were characterized ¹⁷ and the EcCIPK24 proved as a calcium transporter. ¹⁸ Even though, compared with the other millets, namely, foxtail millet and pearl millet, the attention paid for finger millet genomics is very less. The new genomic resources produced by Hittalmani et al ¹ will undoubtedly help to conduct more comprehensive functional genomics studies on nutrient transport in finger millet. For example, each crop plant, including foxtail millet, found to possess more than 10 PHT1 family phosphate transporters, ¹⁹ but only 4 genes were identified due to lack of whole genome information. With the release of draft genome, additional PHT1 genes may be identified and characterized in near future. The draft genome of finger millet, as Hittalmani et al have already outlined, is an excellent opening for identifying and validating the functional genes and understanding the genetic base of the finger millet. Especially, calcium and other nutrient transport and regulatory genes can be validated for future researches like identification of genes involved in the grain filling. Overall, the whole genome sequencing of finger millet by Hittalmani et al ¹ will be a great resource to accelerate the food security and nutrient fortification in the least developed nations of Asia and Africa.