Transcriptome Wide Identification and Validation of Calcium Sensor Gene Family in the Developing Spikes of Finger Millet Genotypes for Elucidating Its Role in Grain Calcium Accumulation

Singh, Uma Maheshwar; Chandra, Muktesh; Shankhdhar, S. C.; Kumar, Anil

doi:10.1371/journal.pone.0103963

Cited by 59 publications

(23 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Research illuminating the finger millet transcriptome is beginning to appear. As the crop is valued for its high calcium content, studies have characterized calcium sensing and accumulation mechanisms across genotypes differing in their grain calcium content with the use of transcriptome high-throughput sequencing (Kumar et al, 2014b ; Singh et al, 2014 ). A similar transcriptome analysis has been conducted on salinity responsiveness (Rahman et al, 2014 ).…”

Section: Diversity Of the Small Milletsmentioning

confidence: 99%

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

2015

View full text Add to dashboard Cite

Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed “orphan cereals.” Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.

show abstract

Section: Diversity Of the Small Milletsmentioning

confidence: 99%

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

2015

View full text Add to dashboard Cite

show abstract

“…Through systems biology approach, 82 unique calcium sensor genes identified from finger millet transcriptome data have been categorized into eight calcium sensor gene families viz., CaM and CaMLs, CBLs, CIPKs, PEPRKs, CRKs, CDPKs, CaMKs, and CCaMK. Out of 82 genes, 12 were found to be different from the rice orthologs (Singh et al, 2014; Kumar et al, 2015b). Nineteen Ca 2+ transporter genes identified from developing seed transcriptome data of finger millet showed 33–90% variation in amino acid sequence compared to rice Ca 2+ transporter (Kumar et al, 2015c).…”

Section: Omics Revolution Through Hi-throughput Technologiesmentioning

confidence: 99%

“…Nineteen Ca 2+ transporter genes identified from developing seed transcriptome data of finger millet showed 33–90% variation in amino acid sequence compared to rice Ca 2+ transporter (Kumar et al, 2015c). High level of correlation between the expression of “EcCAX3” a calcium exchanger gene and the amount of calcium accumulated in spikes could be utilized in a future biofortification program (Singh et al, 2014; Singh U. M. et al, 2015). Further attempts have also been made to identify and characterize the calcium binding proteins (CaBPs) in grain filling stages of finger millet using proteomics, bioinformatics and molecular approaches.…”

Section: Omics Revolution Through Hi-throughput Technologiesmentioning

confidence: 99%

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

et al. 2016

Self Cite

View full text Add to dashboard Cite

The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2–4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet.

show abstract

“…Finger millet containing about 5–30 times higher Ca than wheat and rice serves as a model system to understand seed calcium accumulation. Singh et al (2014) undertook transcriptomics approach to characterize calcium sensor gene family from the developing spikes of finger millet using Illumina paired-end sequencing methods. This study included characterization, identification, classification, phylogeny, and pathway analysis of calcium sensor genes of two genotypes, GP-1(low calcium) and GP-45 (high calcium).…”

Section: Micronutrientsmentioning

confidence: 99%

Biofortification in Millets: A Sustainable Approach for Nutritional Security

Alphonse¹,

Ravindhran²

2017

Front. Plant Sci.

113

View full text Add to dashboard Cite

Nutritional insecurity is a major threat to the world’s population that is highly dependent on cereals-based diet, deficient in micronutrients. Next to cereals, millets are the primary sources of energy in the semi-arid tropics and drought-prone regions of Asia and Africa. Millets are nutritionally superior as their grains contain high amount of proteins, essential amino acids, minerals, and vitamins. Biofortification of staple crops is proved to be an economically feasible approach to combat micronutrient malnutrition. HarvestPlus group realized the importance of millet biofortification and released conventionally bred high iron pearl millet in India to tackle iron deficiency. Molecular basis of waxy starch has been identified in foxtail millet, proso millet, and barnyard millet to facilitate their use in infant foods. With close genetic-relatedness to cereals, comparative genomics has helped in deciphering quantitative trait loci and genes linked to protein quality in finger millet. Recently, transgenic expression of zinc transporters resulted in the development of high grain zinc while transcriptomics revealed various calcium sensor genes involved in uptake, translocation, and accumulation of calcium in finger millet. Biofortification in millets is still limited by the presence of antinutrients like phytic acid, polyphenols, and tannins. RNA interference and genome editing tools [zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)] needs to be employed to reduce these antinutrients. In this review paper, we discuss the strategies to accelerate biofortification in millets by summarizing the opportunities and challenges to increase the bioavailability of macro and micronutrients.

show abstract

Transcriptome Wide Identification and Validation of Calcium Sensor Gene Family in the Developing Spikes of Finger Millet Genotypes for Elucidating Its Role in Grain Calcium Accumulation

Cited by 59 publications

References 41 publications

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics—An Important Nutri-Cereal of Future

Biofortification in Millets: A Sustainable Approach for Nutritional Security

Contact Info

Product

Resources

About