Whole genome sequencing of spotted stem borer, Chilo partellus, reveals multiple genes encoding enzymes for detoxification of insecticides.

Spotted stem borer, Chilo partellus, is the most important constraint for increasing the production and productivity of maize and sorghum, the two major coarse cereals in Asia and Africa. The levels of resistance to this pest in the cultivated germplasm are low to moderate, and hence, farmers have to use insecticides for effective control of this pest. However, there is no information on the detoxification mechanisms in C. partellus, which is one of the constraints for deployment of appropriate insecticides to control this pest. The ability to detoxify insecticides varies across insect populations, and hence, we sequenced different populations of C. partellus to identify and understand detoxification mechanisms to devise appropriate strategies for deployment of different insecticides for controlling this pest. Larval samples were sequenced from three different cohorts of C. partellus using the Illumina HiSeq 2500 platform. The data were subjected to identify putative genes that are involved in detoxification on insecticides in our cohort insect species. These studies resulted in identification of 64 cytochrome P450 genes (CYP450s), and 36 glutathione S-transferases genes (GSTs) encoding metabolic detoxification enzymes, primarily responsible for xenobiotic metabolism in insects. A total of 183 circadian genes with > 80% homolog and 11 olfactory receptor genes that mediate chemical cues were found in the C. partellus genome. Also, target receptors related to insecticide action, 4 acetylcholinesterase (AChE), 14 γ-aminobutyric acid (GABA), and 15 nicotinic acetylcholine (nAChR) receptors were detected. This is the first report of whole genome sequencing of C. partellus useful for understanding mode of action of different insecticides, and mechanisms of detoxification and designing target-specific insecticides to develop appropriate strategies to control C. partellus for sustainable crop production.

Molecular mechanisms, genetic mapping, and genome editing for insect pest resistance in field crops.

KEY MESSAGE: Improving crop resistance against insect pests is crucial for ensuring future food security. Integrating genomics with modern breeding methods holds enormous potential in dissecting the genetic architecture of this complex trait and accelerating crop improvement. Insect resistance in crops has been a major research objective in several crop improvement programs. However, the use of conventional breeding methods to develop high-yielding cultivars with sustainable and durable insect pest resistance has been largely unsuccessful. The use of molecular markers for identification and deployment of insect resistance quantitative trait loci (QTLs) can fastrack traditional breeding methods. Till date, several QTLs for insect pest resistance have been identified in field-grown crops, and a few of them have been cloned by positional cloning approaches. Genome editing technologies, such as CRISPR/Cas9, are paving the way to tailor insect pest resistance loci for designing crops for the future. Here, we provide an overview of diverse defense mechanisms exerted by plants in response to insect pest attack, and review recent advances in genomics research and genetic improvements for insect pest resistance in major field crops. Finally, we discuss the scope for genomic breeding strategies to develop more durable insect pest resistant crops.

Development of Temporal Model for Forecasting of Helicoverpa armigera (Noctuidae: Lepidopetra) Using Arima and Artificial Neural Networks.

Helicoverpa armigera (Hübner) (Noctuidae: Lepidopetra) is a polyphagous pest of major crops grown in India. To prevent the damage caused by H. armigera farmers rely heavily on insecticides of diverse groups on a regular basis which is not a benign practice, environmentally and economically. To provide more efficient and accurate information on timely application of insecticides, this research was aimed to develop a forecast model to predict population dynamics of pod borer using Autoregressive Integrated Moving Average (ARIMA) and Artificial Neural Networks (ANN). The data used in this study were collected from the randomly installed sex pheromone traps at International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Patancheru, Hyderabad. Several ARIMA (p, d, q) (P, D, Q) and ANN models were developed using the historical trap catch data. ARIMA model (1,0,1), (1,0,2) with minimal BIC, RMSE, MAPE, MAE, and MASE values and higher R2 value (0.53) was selected as the best ARIMA fit model, and neural network (7-30-1) was found to be the best fit to predict the catches of male moths of pod borer from September 2021 to August 2023. A comparative analysis performed between the ARIMA and ANN, shows that the ANN based on feed forward neural networks is best suited for effective pest prediction. With the developed ARIMA model, it would be easier to predict H. armigera adult population dynamics round the year and timely intervention of control measures can be followed by appropriate decision-making schedule for insecticide application.

Development of a rapid process for purification of Bowman-Birk and Kunitz inhibitors from legume seeds, and evaluation of their biophysical, insecticidal, and antimicrobial properties.

Bowman-Birk inhibitor (BBI ~10 kDa) and Kunitz inhibitor (KI ~20 kDa) are serine protease/proteinase inhibitor(s) [PI(s)] ubiquitously found in several Leguminous plant species with insecticidal and therapeutic properties. Due to narrow molecular mass differences, the separation of these inhibitors from a single seed variety is tedious. The present study is aimed to develop a rapid protocol (<24 h) for purifying BBI and KI from legume seeds using mild trichloroacetic acid (TCA) extraction followed by trypsin-affinity chromatography. The mature seeds of Vigna radiata and Cajanus platycarpus are used as a model to purify BBI and KI using this protocol. The BBI and KI purified from the seeds of V. radiata are labeled as VrBBI & VrKI, and C. platycarpus are labeled as CpBBI & CpKI, respectively. These PIs are confirmed by immunodetection and MALDI-TOF studies and further characterized for their structural (CD & fluorescence spectroscopy) and functional properties (temperature & DTT stability). BBI(s) purified using the above process are effective in the management of castor semi-looper 'Achaea janata', while KI(s) are effective in the management of pod borer 'Helicoverpa armigera'. Besides, both BBI(s) and KI(s) have significant potential in controlling the growth of methicillin-sensitive 'Staphylococcus aureus', a gram-positive pathogenic bacterium.

Reaping the Potential of Wild Cajanus Species through Pre-Breeding for Improving Resistance to Pod Borer, Helicoverpa armigera, in Cultivated Pigeonpea (Cajanus cajan (L.) Millsp.).

Pod borer (Helicoverpa armigera) causes the highest yield losses in pigeonpea, followed by pod fly (Melanagromyza obtusa). High levels of resistance to pod borer are not available in the cultivated genepool. Several accessions of wild Cajanus species with strong resistance, and different resistance mechanisms (antixenosis and antibiosis) to pod borer have been identified. These accessions can be utilized to improve the pod borer resistance of cultivated pigeonpea. Using pod borer resistant Cajanus scarabaeoides and Cajanus acutifolius as pollen donors and popular pigeonpea varieties as recipients, pre-breeding populations were developed following simple- and complex-cross approaches. Preliminary evaluation of four backcross populations consisting of >2300 introgression lines (ILs) under un-sprayed field conditions resulted in identifying 156 ILs with low visual damage rating scores (5.0−6.0) and low pod borer damage (<50%). Precise re-screening of these ILs over different locations and years resulted in the identification of 21 ILs having improved resistance to pod borer. Because these ILs were derived from wild Cajanus species, they may contain different alleles for different resistance components to pod borer. Hence, these ILs are ready-to-use novel and diverse sources of pod borer resistance that can be utilized for improving the pod borer resistance of cultivated pigeonpea.

Biological and biochemical diversity in different biotypes of spotted stem borer, Chilo partellus (Swinhoe) in India.

Because of variation in incidence and severity of damage by Chilo partellus (Swinhoe) in different geographical regions, it is difficult to identify stable sources of resistance against this pest. Therefore, the present studies were undertaken on biological attributes (damage in resistant and susceptible genotypes, survival and development) and biochemical profiles (amino acids and lipophilic compound) of C. partellus populations from eight geographical regions to understand it's population structure in India. There was a significant variation in biological attributes and biochemical profiles of C. partellus populations from different geographical regions. Based on virulence and biological attributes, similarity index placed the C. partellus populations in five groups. Likewise, lipophilic and amino acid profiling also placed the C. partellus populations in five groups. However, the different clusters based on biological and biochemical attributes did not include populations from the same regions. Similarity index based on virulence, biological attributes, and amino acids and lipophilic profiles placed the C. partellus populations in six groups. The C. partellus populations from Hisar, Hyderabad, Parbhani and Coimbatore were distinct from each other, indicating that there are four biotypes of C. partellus in India. The results suggested that sorghum and maize genotypes need to be tested against these four populations to identify stable sources of resistance. However, there is a need for further studies to establish the restriction in gene flow through molecular approaches across geographical regions to establish the distinctiveness of different biotypes of C. partellus in India.

Genetic regulation of diapause and associated traits in Chilo partellus (Swinhoe).

Diapause is an endocrine controlled arrested metabolic state to delay development or reproduction under unfavorable conditions. To gain an understanding of importance of diapause for ecological adaptation, it is important to study regulation of diapause in insects. We examined genetics of diapause in Chilo partellus by crossing the hibernating (HD), aestivating (AD), post-hibernating (PHD), post-aestivating (PAD), and nondiapause (ND) strains. Reciprocal crosses were also made to gain full understanding of diapause regulation and the maternal effects, if any. Data were recorded on fecundity, egg hatching, larval survival, diapause induction and termination, adult emergence, and morphometrics of larvae, pupae and adults in the parents (P1, P2), F1 hybrids, and the reciprocal crosses. Genetic analysis showed that AD strain is general combiner, which also improved egg hatching, larval survival, diapause termination, adult emergence and proportion of females in the progenies. Incidence of diapause was highest in HD × AD, whereas termination was greatest in PHD × AD. However, ND strain and its reciprocal crosses with other strains did not exhibit any noticeable developmental response associated with diapause. Specific combining ability analysis suggested that where PHD and AD strains exist together there will be likely reduction in diapause incidence, increased survival with greater fitness and faster multiplication of their progenies resulting in outbreak of C. partellus. Degree of dominance estimates revealed that diapause, developmental and morphometric traits in C. partellus are governed by over dominance gene effects, and mainly depend on parental diapause history.

Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.).

Genetic enhancement for resistance against the pod borer, Helicoverpa armigera is crucial for enhancing production and productivity of chickpea. Here we provide some novel insights into the genetic architecture of natural variation in H. armigera resistance in chickpea, an important legume, which plays a major role in food and nutritional security. An interspecific recombinant inbred line (RIL) population developed from a cross between H. armigera susceptible accession ICC 4958 (Cicer arietinum) and resistant accession PI 489777 (Cicer reticulatum) was evaluated for H. armigera resistance component traits using detached leaf assay and under field conditions. A high-throughput AxiomCicerSNP array was utilized to construct a dense linkage map comprising of 3,873 loci and spanning a distance of 949.27 cM. Comprehensive analyses of extensive genotyping and phenotyping data identified nine main-effect QTLs and 955 epistatic QTLs explaining up to 42.49% and 38.05% phenotypic variance, respectively, for H. armigera resistance component traits. The main-effect QTLs identified in this RIL population were linked with previously described genes, known to modulate resistance against lepidopteran insects in crop plants. One QTL cluster harbouring main-effect QTLs for three H. armigera resistance component traits and explaining up to 42.49% of the phenotypic variance, was identified on CaLG03. This genomic region, after validation, may be useful to improve H. armigera resistance component traits in elite chickpea cultivars.