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Shedding light on response of Triticum aestivum cv. Kharchia Local roots to long-term salinity stress through transcriptome profiling

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Abstract

Among the various abiotic stresses, salinity is one of the major limitations for production and productivity of wheat. Kharchia Local is the most salt-tolerant wheat cultivar developed from farmers’ selection on salt affected areas of India. Here, to investigate the molecular response of Kharchia Local under salinity stress, transcriptome sequencing of root tissue samples at the anthesis stage was performed. Illumina sequencing generated a total of 82.84 million clean reads and were assembled into 1,18,200 unigenes. A set of 10,805 unigenes were differentially expressed in response to salinity stress. Around 8232 unigene-derived SSRs were mined from these DEGs that can be used as functional molecular markers. Expression pattern of salinity stress-responsive unigenes was validated using real time PCR and results were found to be consistent with that of transcriptome profiling. Functional annotation of DEGs against GO, KEGG, COG and BLASTX using nr protein database was performed. This revealed the upregulation of genes involved in various biological processes including ROS homeostasis, ion transport, signal transduction, ABA biosynthesis and osmoregulation. Genes encoding expansin, xyloglucan endotransglucosylase/hydrolase, dehydrins and peroxidases that take part in enhancement of root growth were found to be upregulated under salinity. This could be the reason for better root growth of Kharchia Local under long-term salinity stress as compared to its susceptible counterpart. The present investigation provides primary information on transcriptome profiling of Kharchia Local roots under long-term salinity stress at the anthesis stage. In conclusion, the data generated in this study provide useful insights in understanding the molecular mechanism of salinity stress tolerance and will also serve as a valuable genomic reservoir for functional characterization of salinity responsive genes to develop tolerant genotypes.

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Acknowledgements

This work was financially supported by ICAR-National Institute for Plant Biotechnology, New Delhi, India.

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Authors and Affiliations

  1. ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Mahesh M. Mahajan

  2. Vilasrao Deshmukh College of Agricultural Biotechnology, Latur, 413512, India

    Mahesh M. Mahajan

  3. Biotechnology and Climate Change Laboratory, ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India

    Mahesh M. Mahajan, Etika Goyal, Amit K. Singh, Kishor Gaikwad & Kumar Kanika

  4. North Carolina State University, Raleigh, NC, 27606, USA

    Etika Goyal

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Contributions

MMM, KK, and KG, conceived, designed and coordinated the experiment. MMM and EG were associated with wet lab work and carried out experiment. MMM, EG and AKS involved in in silico data analysis. MMM, EG, AKS, KG and KK were involved in result interpretation and integration besides associated with finalising the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Kumar Kanika.

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Electronic supplementary material

Electronic supplementary material 1—Figure S1: Enrichment of GO terms under molecular function category (JPEG 121 kb)

Electronic supplementary material 2—Figure S2: Enrichment of GO terms under biological processes category (JPEG 790 kb)

Electronic supplementary material 3—Figure S3: Enrichment of GO terms under cellular component category (JPEG 394 kb)

10725_2019_565_MOESM4_ESM.jpg

Electronic supplementary material 4—Figure S4: Classification of unigenes according to COG database. The most abundantclasses were R- general function prediction only followed by P- inorganic ion transport &metabolism and E- amino acid transport & metabolism (JPG 115 kb)

10725_2019_565_MOESM5_ESM.jpg

Electronic supplementary material 5—Figure S5: Distribution of unigenes into TF families. Out of 47 transcription factor families C2H2, WD40-like, AP2-EREBP, CCHC(Zn) and MYB-HB-like were found to be most abundant (JPG 63 kb)

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Mahajan, M.M., Goyal, E., Singh, A.K. et al. Shedding light on response of Triticum aestivum cv. Kharchia Local roots to long-term salinity stress through transcriptome profiling. Plant Growth Regul 90, 369–381 (2020). https://doi.org/10.1007/s10725-019-00565-4

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