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INDIAN SCIENTISTS DECODED THE DRAFT GENOME OF RICE YELLOW STEM BORER

By Priyankar Mondal

Climate change, global warming, depleting resources are the major concerns to agriculture. These events have a major impact on the distribution and severity of crop pests. It is estimated that up to 40 percent of crop yield losses are due to pest damage (FAO). The use of chemical control methods for insect pest control has a long-term effect on human and animal health. There is a need for greener interventions for managing insect pests in major food crops like rice which is the staple food crop in several countries across the globe.


Rice Yellow Stem Borer (YSB), Scirpophaga incertulas is one of the most destructive and cosmopolitan pests of rice occurring round the year that accounts for 5-10% annual losses which may reach up to 50-60% in individual fields depending upon variety, management practices, and geoclimatic conditions. The YSB, as monophagous pest has developed a dynamic interaction with its host plant and no consistent genetic source of resistance is available till now. The YSB has dynamic host interaction and can destroy rice at any stage of the plant from seedling stage to maturity. The larvae feed upon tillers and causes dead hearts or drying of the central growing shoot, during vegetative phase and causes white ear heads at reproductive phase. The genome information needs to be generated for economically relevance insect pest for designing next-generation pest resistant rice. Howbeit, such information is not available for many rice pests and in this context, it became necessary to unveil the genome of YSB. The development of such genomic data is crucial for understanding evolutionary, defence and behavioral characteristics that can be used further for developing alternative pest management strategies.

To solve the problem a group of Indian scientists from ICAR-Indian Institute of Rice Research, Hyderabad took a lead along with other institutes- ICAR-National Institute of Plant Biotechnology, New Delhi and Osmania University, Hyderabad. This collaboration has come forward to mine the genes responsible for the “difficult to manage” attributes of this notorious pest and look for additional genes to use as targets for genetic manipulation, development of resistant varieties and new specific insecticidal molecules.


This is the first endeavour to draft the complete genome of the female S. incertulas and the team recovered a median genome size of 308 Mb which is 1 time more than that of Drosphila melanogaster (180 Mb), slightly smaller than the genome size of Spodoptera frugiperda (371 Mb) and almost one third the genome of Nilaparvata lugens. The genome consists of 46,057 protein coding genes having an average gene length of 427 bp and GC content of 36.7%. They also found that only 1% of the YSB genome consists of transposons or jumping genes which are fundamental to the evolution of insect genomes by translocating genomic sequences or shuffling of exons and thus creating mostly deleterious mutations. Interestingly, Transposons take up 50% of human genomes and some of which play causal role in disease development and cancer-inducing mutations. The transposon content in YSB is significantly lesser than other rice pests such as N. lugens (38.9%), S. frugiperda (20.28%) and S. furcifera (39.7%). Transcription factors which regulate the expression of genes at spatial and temporal scale and controls the development and phenology of an insect were particularly found in higher proportion in the genome of YSB when compared to honey bee, red flour beetle, jewel wasp and fruitfly which might explain YSB’s activity round the year and concomitant development with different phenological stages of Rice. The genes vitellogenin (Vg) and Vitellogenin Receptor (VgR) which regulate nutrient uptake during embryonic development of insects and also targeted in S. furcifera and N. lugens for controlling these pests were identified in the YSB for the very first time and this opens a new window for management of YSB.


YSB and rice dynamic interaction (by Kattupalli et al. 2021))

(Details for the figure: Ops-Opsins, LW Ops- Long wavelength, UV Ops- Ultra violet, B Ops- Blue, RDH – Retinol Dehydrogenase, RALDH- Retinal Dehydrogenase; OR- Odorant Receptors, OBP Odorant Binding Proteins, PBP- Pheromone Binding Proteins, IR- Ionotropic Receptors, MGR- Metabotropic Glutamate Receptors, CSP- Chemosensory proteins; GR- Gustatory Receptors; AMPN- AminopeptidaseN, AMY- Amylase, SP- Serine Proteases, Try- Trypsin, Chy- Chymotrypsin, Cat- Cathepsin; JH- Juvenile Hormone, MH- Molting Hormone, Vit- Vitellogenin, Ecdy- Ecdysteroid, EcR- Ecdysone receptor, EcIP- Ecdysone-induced protein, Met- Methoprene- tolerant, KLFs-Krüppel like factor, cycle (CYC), clock (CLK), cryptochrome (CRY1 and CRY2), period (PER), timeless protein (TIM), takeout gene, Cwo- Clockwork orange; OS-oral secretion, AP- alkaline phosphatase, β-glu- β-glucosidase; Apy- Apyrases, Glv- Gloverin, Att- Attacin; Allen shephard- Gravitaxis, Anox- Anoxia up-regulated; Abd- Abdominal-A/B, Antp- Antennapedia, Ato- Atonal, Da: Daughterless, SOX-SRY-related HMG-box genes, FOX-forkhead box)


The unique gene repertoire for visual perception and chemosensation explains the highly monophagous nature of YSB. The team identified higher number of Opsins (the genes coding for light sensitive proteins facilitating visual acuity and circadian rhythms) when compared to other cosmopolitan pests such as mosquitoes, red flour beetle and fruitflies which might facilitate the precise host finding behaviour of YSB among a mosaic landscape of different grasses. They also identified 140 chemosensory genes including some specific odorant receptors, odorant binding proteins, gustatory receptors, ionotropic receptors and chemosensory proteins which were in concurrence with previous reports in genome of Nilaparvata lugens, another monophagous pest of Rice. The Serine proteases were also found to be distinct as compared to other insects which also explains its readiness to break the resistance barriers in different rice cultivars.


The researchers also found several insecticidal targets such as nicotinic acetylcholine receptor (nAChR), γ-aminobutyric acid receptor (GABA), glutamate-gated chloride channel (GluCl) and voltage-gated sodium channel (VGSC), acetylcholinesterase (AchE), acetylCoA carboxylase (ACCase), cys-loop ligand-gated ion channel (cysLGIC) superfamily and ryanodine receptor (RyR). According to them the specificity of GABA receptors CysLGIC receptors and of YSB can be explored further to develop new insecticide molecules. Additionally, the identification of these receptors will help a lot in insecticide resistance and resurgence studies.


The repertoire of immunity genes which deactivates the chemical defenses of host plants, fights against invading pathogens and parasitoids and form a crucial basis for developing and deploying pest management tactics were also identified as very wide and also specific in YSB. Several Pattern Recognition Receptors (PRRs) and the presence of five Polyphenoloxidase (PPO) genes explains the pest’s ability to handle toxic plant phenolics. The aberrant plant growth and development in rice due to infestation of YSB can be attributed to the employment of apyrase enzymes by the pest which hydrolyze plant ATP and reduces its availability to plant. The virus resistance genes and presence of immunoregulators serpins and serine protease homologs explains the difficulty of managing YSB through biocontrol approaches. The team also identified several effector genes including the venom related genes in the YSB genome which plays important roles in plant defensive chemistry and counter adaptation by YSB. They also decoded the complete RNAi (RNA silencing) machinery in YSB which might be critical targets to develop management strategies through novel chemicals and genetic manipulation of both YSB and rice cultivars. In addition to this, the group also identified several behaviour regulating genes such as cacophony, alan shepard, anoxia upregulated etc. which provides a deep insight to their ecological and behavioural adaptations.


The researchers also identified 21,696 SSR markers (microsatellites) which can be effectively utilized to understand YSB diversity across different ecological and geographical regimes.


The first draft genome of female YSB will surely help to decipher the mysterious molecular mechanisms involved in interaction with its host plant -rice, climatic factors, natural enemies and insecticides. This information can further be explored by scientists in academia and industry to develop novel and better management strategies for management of the notorious S. incertulas infesting rice across all the ecosystems and significantly lowering its productivity all over the world.


For further details, please refer to

https://www.mdpi.com/2075-4450/12/6/563

Priyankar Mondal is one of the Student Associate Editor of IE and working as a Researcher Scholar at Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India. You can contact him @ Email: priyankar.ento@gmail.com

Disclaimer: The contents, style, language, plagiarism, references, mention of any products if any, etc., are the sole responsibility of the authors.

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