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Transcriptomic Profiling of Pearl Millet for Salinity Stress Response

Pearl Millet

In an article which discussed the exploration of the ‘orphan crop’ pearl millet, Amibka Dudhate concluded that photosynthesis, plant hormone signal transduction, and mitogen-activated protein kinase signalling pathways are significantly activated on the advent of drought stress in pearl millet. Her colleague, Harshraj Shinde, expands on these findings.


Salinity stress severely limits crop production. Low precipitation, irrigation with saline water, a rising water table, and poor irrigation practices generally cause salinity stress. More than 6% of the world’s total land area is affected by soil salinity. The adverse effects of salinity on plants include ion toxicity, nutrient constraints, oxidative stress, and osmotic stress.

Research outcome

Pearl millet (Pennisetum glaucum (L) R. Br.) is a staple crop for more than 90 million poor farmers. It is known for its tolerance against drought, salinity, and high temperature. To understand the molecular mechanisms underlying its salinity tolerance, physiological analyses and a comparative transcriptome analysis between salinity tolerant (ICMB 01222) and salinity susceptible (ICMB 081) lines were conducted under control and salinity conditions.

Sequencing using the Illumina HiSeq 2500 system generated a total of 977 million reads, and these reads were assembled de novo into contigs corresponding to gene products. A total of 11,627 differentially expressed genes (DEGs) were identified in both lines. These DEGs are involved in various metabolic pathways such as plant hormone signal transduction, mitogen-activated protein kinase signaling pathways, and so on. Genes involved in ubiquitin-mediated proteolysis and phenylpropanoid biosynthesis pathways were upregulated in the tolerant line. In contrast, unigenes involved in glycolysis/gluconeogenesis and genes for ribosomes were downregulated in the susceptible line. Genes encoding SBPs (SQUAMOSA promoter binding proteins), which are plant-specific transcription factors, were differentially expressed only in the tolerant line. Functional unigenes and pathways that are identified can provide useful clues for improving salinity stress tolerance in pearl millet.

Physiological analysis showed that total soluble sugar content was higher in the salinity stressed tolerant pearl millet line than in the susceptible line under salinity stress. Sugar plays roles in the detoxification of Na+ ions under salinity stress, and also acts as an osmoprotectant. In our KEGG pathway analysis, sugar metabolism related pathways such as glycolysis/gluconeogenesis and starch and sucrose pathways were downregulated in the susceptible line and were upregulated in the tolerant line.

In many cases, activation of starch metabolism under abiotic stress is a common plant response, as it contributes to sugar accumulation and stress tolerance. Together the sugar metabolism related pathways and total soluble sugar are likely to contribute to salinity stress tolerance of pearl millet. The sodium content (Na+) of ICMB 01222 was lower than that of ICMB 081 during salinity stress. This result is consistent with the finding from the RNA-Seq that the genes encoding salt transporters such as NHXs (sodium hydrogen exchangers), Ca2+ATPases (calcium ATPases), CAXs (cation hydrogen exchangers) and ABC (ATP-binding cassettes) transporters are strongly expressed in ICMB 01222.


Our comparative transcriptomic analysis between the salinity tolerant and salinity susceptible pearl millet lines provides useful clues for understanding the salinity stress tolerance mechanism of this crop. We found that DEGs encoding transcription factors, ion transporters, and regulators of metabolic pathways are extremely useful in improving the pearl millet productivity under salinity stress condition.

The most conspicuous differences between the two lines are pathways related to sugar metabolism and total sugar accumulation pattern during the salinity stress. Identified DEGs and metabolic pathways with contrasting expression patterns between two contrasting lines are excellent targets for future functional studies to understand mechanism of salinity stress tolerance.  It is also possible to use the tolerant line, ICMB 01222 as a donor of useful genes to further improve the salinity-tolerance in pearl millet using either cross breeding or transgenic approach.

Note – Pearl millet lines used in this study were provided by International Crop Research Institute of Semi-Arid Tropics (ICRISAT), India.

Harshraj Shinde


Harshraj Shinde is a researcher at the Asian Natural Environmental Science Center (ANESC), University of Tokyo.


With tracks on Plant Genome Engineering, Phenotyping & Bioinformatics, the agenda for the 7th Plant Genomics and Gene Editing Congress: Europe is well worth a read. Download it here to find out more.

To view the accompanying poster presentation, please visit our resources page here

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