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Analysis of SSH library of rice variety Aganni reveals candidate gall midge resistance genes

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Abstract

The Asian rice gall midge, Orseolia oryzae, is a serious insect pest causing extensive yield loss. Interaction between the gall midge and rice genotypes is known to be on a gene-for-gene basis. Here, we report molecular basis of HR− (hypersensitive reaction—negative) type of resistance in Aganni (an indica rice variety possessing gall midge resistance gene Gm8) through the construction and analysis of a suppressive subtraction hybridization (SSH) cDNA library. In all, 2,800 positive clones were sequenced and analyzed. The high-quality ESTs were assembled into 448 non-redundant gene sequences. Homology search with the NCBI databases, using BlastX and BlastN, revealed that 73% of the clones showed homology to genes with known function and majority of ESTs belonged to the gene ontology category ‘biological process’. Validation of 27 putative candidate gall midge resistance genes through real-time PCR, following gall midge infestation, in contrasting parents and their derived pre-NILs (near isogenic lines) revealed induction of specific genes related to defense and metabolism. Interestingly, four genes, belonging to families of leucine-rich repeat (LRR), heat shock protein (HSP), pathogenesis related protein (PR), and NAC domain-containing protein, implicated in conferring HR+ type of resistance, were found to be up-regulated in Aganni. Two of the reactive oxygen intermediates (ROI)–scavenging-enzyme-coding genes Cytosolic Ascorbate Peroxidase1, 2 (OsAPx1 and OsAPx2) were found up-regulated in Aganni in incompatible interaction possibly suppressing HR. We suggest that Aganni has a deviant form of inducible, salicylic acid (SA)-mediated resistance but without HR.

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Acknowledgments

We thank the Project Director, ICAR-IIRR, formerly, Directorate of Rice Research, Hyderabad and the Director, International Centre for Genetic Engineering and Biotechnology, New Delhi, for the facilities and encouragement. This work was partly supported by a research grant (F. no. BT/AB/FG-2 (PH-II)/2009) to JSB and (F. no. BT/AB/FG-2 (PH-II)(4B)/2009) to SN from the Department of Biotechnology (DBT), Government of India.

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Author notes

  1. Y. Tunginba Singh

    Present address: Department of Botany, Mizoram University, Tanhril, Aizawl, Mizoram, 796004, India

  2. J. S. Bentur

    Present address: Agri Biotech Foundation, Rajendranagar, Hyderabad, 500030, India

Authors and Affiliations

  1. Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India

    Dhanasekar Divya & J. S. Bentur

  2. International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India

    Y. Tunginba Singh & Suresh Nair

  3. Agri Biotech Foundation, Rajendranagar, Hyderabad, 500030, India

    Dhanasekar Divya

Authors
  1. Dhanasekar Divya
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  2. Y. Tunginba Singh
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  3. Suresh Nair
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  4. J. S. Bentur
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Corresponding authors

Correspondence to Suresh Nair or J. S. Bentur.

Additional information

Dhanasekar Divya and Y. Tunginba Singh contributed equally to this work.

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S1

Functional classification of ESTs, from Aganni, Suraksha and TN1 SSH libraries, into the three principal Gene Ontology (GO) categories: a biological process, b molecular function, and c cellular component. Values represent the number of ESTs found under each sub-category under the three main GO categories. Color bars represent ESTs from green bar—Aganni, red bar—Suraksha, and blue bar—TN1 library, respectively. (GIF 4 kb)

(GIF 4 kb)

(GIF 3 kb)

High resolution image (TIF 2333 kb)

High resolution image (TIF 2339 kb)

High resolution image (TIF 2299 kb)

S2

Relative expression profiles of 8 ESTs induced (≤2-fold) when compared with the respective uninfested control a at 24 hai and b at 120 hai. Error bars represent Mean ± S.D. Light bars represent Aganni-GMB1 and dark bars 74R-GMB1 incompatible interaction, respectively. (GIF 3 kb)

(GIF 3 kb)

High resolution image (TIF 2287 kb)

High resolution image (TIF 2285 kb)

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Divya, D., Singh, Y.T., Nair, S. et al. Analysis of SSH library of rice variety Aganni reveals candidate gall midge resistance genes. Funct Integr Genomics 16, 153–169 (2016). https://doi.org/10.1007/s10142-016-0474-3

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  • DOI: https://doi.org/10.1007/s10142-016-0474-3

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