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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. Abstract 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.

Background Rice breeders stand at the forefront for application and advancement in breeding and genome based marker system for more realistic and applicable strategies in order to create opportunities for sustainable utilization of genetically diverse rice resources. In Kashmir rice cultivation is under diverse environmental conditions that is encountered by selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent enough to provide good yields, whereby drawing the attention of the breeder. Therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. Methods and Results This study is a pioneering effort where agro-morphological and SSR markers has been employed to assess the genetic diversity and genetic structure of advanced rice breeding lines and local collections from northern Himalayan region of India along with screening for disease resistance. In the present investigation, a total of 15markers (12 polymorphic SSR markers and three gene specific markers) were used for agro-morphological characterization and genetic differentiation of 48 rice genotypes (40 advanced breeding lines and eight cultivated varieties). The genotypes were evaluated under two environments; Khudwani (E1) and Wadura (E2) during Kharif 2020. Results based on agro-morphological and cooking quality traits revealed that 48 genotypes got grouped into seven clusters with KS11 and KS7 at the extremes. The cluster I was the largest comprising of 13 genotypes followed by cluster III (11 genotypes), cluster II and cluster IV had 9 genotypes each. ANOVA also revealed significant mean squares for the genotypes under study with respect to all the traits in two environments (E1and E2). From principal component analysis (PCA) only six principal components (PCs) exhibited more than 1.00 Eigen value and explained 71.44 % cumulative variability among the traits studied. The result from the calculation of SSR molecular marker was further verified with clustering analysis, genetic diversity parameters, AMOVA, phenotypic characterization and validation based on gene specific marker analysis. The cluster analysis revealed wide genetic variability among the 48 genotypes with Cluster III comprises of 19 genotypes, Cluster I with 17 genotypes, whereas cluster II comprised of 12 genotypes. The genetic profiles detected 53 alleles from these 15 loci, with PIC values of 0.494 per locus. Based on AMOVA, variation was distributed within population 99% and among populations no significant genetic differentiation was observed. The average number of effective alleles (Ne) was 1.38 with higher effective alleles in Population-1 (1.52) than Population-2 (1.24). Based on phenotypic characterization, most of genotypes along with two resistant checks (DHMAS and Shalimar Rice-1) displayed resistant reaction, followed by 16 genotypes showing moderately resistant while two landraces viz., Mushk Budji and Red Rice proved highly susceptible. Out of 48, three and nine genotypes were positive for gene Pikm with respect to marker Ckm-2 and dominant marker Pikh-STS, respectively. Moreover, this low level differentiation among sub-species could provide an opportunity to identify the gene combination well-adapted by natural selection. Conclusion The pattern of clustering based on SSR markers provided information about shared genetic characters among rice genotypes in order to eliminate duplications between rice genotypes. Such a genetic differentiation within genotypes provides an insight towards selective pressure and evolution adaptation to local conditions and could be utilized for introgression of resistant gene for higher yield potential, and development of rice varieties with better plant types as per the preferences of rice consumers.

Sea buckthorn (Hippophae) is in the focus of interest mainly for its positive effects on health of both human and animal organisms. Due to the similarities in vegetative morphology, Hippophae species are often misidentified. Therefore, current study was focused on ITS based sequence characterization of sea buckthorn species and comparative biochemical evaluation for its antioxidant properties. DNA was extracted from leaf samples. Primer pairs K-Lab-SeaBukRhm-ITS1F1- K-Lab-SeaBukRhm-ITS1R1 and K-LabSeaBukTib- ITSF1- K-LabSeaBukTib-ITSR1 were used for PCR amplification. The purified PCR products were outsourced for sequencing. Phylogenetic tree was constructed based on neighbor-joining (NJ) method. Moreover, comparison of antioxidant potential of leaves of two sea buckthorn species (Hippophae rhamnoides and Hippophae tibetana) collected from different regions of Ladakh viz., Stakna, Nubra, DRDO Leh and Zanskar was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis (3- ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS), and Total antioxidant capacity (TAC) by phosphomolybdenum assays. The present investigation led to the differentiation of two sea buckthorn species viz., H. rhamnoides and H. tibetana based on Internal Transcribed Spacer (ITS) region. Moreover, significant variation was observed in antioxidant potential of leaf extracts collected from different regions. Primary ITS sequence analysis was found to be powerful tool for identification and genetic diversity studies in sea buckthorn. Leaves of sea buckthorn have pronounced antioxidant properties and can be used in food, neutraceuticals and pharmaceutical industries etc. The current study will pave the way to discover small bioactive molecules responsible for antioxidant and anticancer properties in sea buckthorn.

In order to meet the dietary requirements of the rising human population with diminishing water resources, there is the need to adopt techniques that optimize crop yield under reduced water conditi...

Two soybean QDRL were identified with additive interaction to P. sansomeana isolate MPS17-22. Further analyses uncovered four interaction patterns between the two QDRL and seven additional P. sansomeana isolates. Phytophthora sansomeana is a recently recognized species that contributes to root rot in soybean. Previous studies indicated that P. sansomeana is widely distributed among soybean growing regions and has a much wider host range than P. sojae, a well-known pathogen of soybean. Unlike P. sojae, no known disease resistance genes have been documented that can effectively control P. sansomeana. Therefore, it is important to identify resistance that can be quickly integrated into future soybean varieties. E13901 is an improved soybean line that confers partial resistance to P. sansomeana. A mapping population of 228 F4:5 families was developed from a cross between E13901 and a susceptible improved soybean variety E13390. Using a composite interval mapping method, two quantitative disease resistance loci (QDRL) were identified on Chromosomes 5 (designated qPsan5.1) and 16 (designated qPsan16.1), respectively. qPsan5.1 was mapped at 54.71 cM between Gm05_32565157_T_C and Gm05_32327497_T_C. qPsan5.1 was contributed by E13390 and explained about 6% of the disease resistance variation. qPsan16.1 was located at 39.01 cM between Gm16_35700223_G_T and Gm16_35933600/ Gm16_35816475. qPsan16.1 was from E13901 and could explain 5.5% of partial disease resistance. Further analysis indicated an additive interaction of qPsan5.1 and qPsan16.1 against P. sansomeana isolate MPS17-22. Marker assisted resistance spectrum analysis and progeny tests verified the two QDRL and their interaction patterns with other P. sansomeana isolates. Both QDRL can be quickly integrated into soybean varieties using marker assisted selection.

Horsegram (Macrotyloma uniflorum (Lam.) Verdc.) is a drought hardy food and fodder legume of Indo-African continents with diverse germplasm sources demonstrating alternating mechanisms depicting contrasting adaptations to different climatic zones. Tissue specific expression of genes contributes substantially to location specific adaptations. Regulatory networks of such adaptive genes are elucidated for downstream translational research. MicroRNAs are small endogenous regulatory RNAs which alters the gene expression profiles at a particular time and type of tissue. Identification of such small regulatory RNAs in low moisture stress hardy crops can help in cross species transfer and validation confirming stress tolerance ability. This study outlined prediction of conserved miRNAs from transcriptome shotgun assembled sequences and EST sequences of horsegram. We could validate eight out of 15 of the identified miRNAs to demonstrate their role in deficit moisture stress tolerance mechanism of horsegram variety Paiyur1 with their target networks. The putative mumiRs were related to other food legumes indicating the presence of gene regulatory networks. Differential miRNA expression among drought specific tissues indicted the probable energy conservation mechanism. Targets were identified for functional characterization and regulatory network was constructed to find out the probable pathways of post-transcriptional regulation. The functional network revealed mechanism of biotic and abiotic stress tolerance, energy conservation and photoperiod responsiveness.

Pythium root rot is an important seedling disease of soybean [Glycine max (L.) Merr.], a crop grown worldwide for protein and oil content. Pythium irregulare and P. sylvaticum are two of the most prevalent and aggressive Pythium species in soybean producing regions in the North Central U.S. A few studies have been conducted to identify soybean resistance against the two pathogens. In this study, a mapping population (derived from E13390 x E13901) with 228 F4:5 recombinant inbred lines were screened against P. irregulare isolate MISO 11 − 6 and P. sylvaticum isolate C-MISO2-2-30 for QDRL mapping. Correlation analysis indicated significant positive correlations between soybean responses to the two pathogens, and a pleiotropic QDRL (qPirr16.1) was identified. Further investigation found that the qPirr16.1 imparts dominant resistance against P. irregulare, but recessive resistance against P. sylvaticum. In addition, two QDRL, qPsyl15.1, and qPsyl18.1 were identified for partial resistance to P. sylvaticum. Further analysis revealed epistatic interactions between qPirr16.1 and qPsyl15.1 for RRW and DRX, whereas qPsyl18.1 contributed resistance to RSE. Marker assisted resistance spectrum analysis using F6:7 progeny lines verified the resistance of qPirr16.1 against four additional P. irregulare isolates. Intriguingly, although the epistatic interaction of qPirr16.1 and qPsyl15.1 can be confirmed using two additional isolates of P. sylvaticum, the interaction appears to be suppressed for the other two P. sylvaticum isolates. An ‘epistatic gene-for-gene’ model was proposed to explain the isolate-specific epistatic interactions. The integration of the QDRL into elite soybean lines has been initiated containing all the desirable alleles.

Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study entails the agro-morphological, cooking quality and molecular characterization of 51 genotypes / advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles per locus and an average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing and also the analysis was useful to generate information on indica - japonica classification of our germplasm.

Phytoremediation is the most simple and powerful approach for reducing heavy metals from polluted soils. Cleanup in most polluted environments is necessary to protect the area and minimize the introduction of harmful components into the food chain. Phytoremediation is a clean and cost-effective method to remove organic/inorganic pollutants primarily from soils by the use of plants and some plant-associated microorganisms. Recent case studies on model organisms using molecular genetics will improve the knowledge of essential metal metabolism in plants. There is a strong need for a collective way for finding effective ways for removing these toxic metals from the soil and other polluted metals from the biosphere. This chapter will discuss in brief about the absorption and elimination of toxic metals from the environment using different phytoremediation techniques, further there will be discussion on strategies used for generating transgenic plants and evaluation of genome editing approaches to raise plants, which can survive in toxic environment.

Project Co-ordinators: Dr. Jose Alfonso Gómez Calero (Instituto de Agricultura Sostenible (IAS-CISC), Dr. Weifeng Xu (Fujian Agriculture and Forest University, FAFU)., Beneficial root-associated rhizospheric microbes play a key role in maintaining host plant growth and can potentially allow drought-resilient crop production. The complex interaction of root-associated microbes mainly depends on soil type, plant genotype, and soil moisture. However, drought is the most devastating environmental stress that strongly reduces soil biota and can restrict plant growth and yield. In this review, we discussed our mechanistic understanding of drought and microbial response traits. Additionally, we highlighted the role of beneficial microbes and plant-derived metabolites in alleviating drought stress and improving crop growth. We proposed that future research might focus on evaluating the dynamics of root-beneficial microbes under field drought conditions. The integrative use of ecology, microbial, and molecular approaches may serve as a promising strategy to produce more drought-resilient and sustainable crops., We are grateful for the grant support from the National Key R&D Program of China (Nos. 2017YFE0118100 and 2018YFD02003025), National Natural Science Foundation of China (Nos. 31761130073, 31872169, and 31600209), a Newton Advanced Fellowship, UK (NO. NA160430), Fujian Province Education Department Funding, China (No. JK2017015), Research Grant of Fujian Agriculture and Forestry University, China (No. KXGH17005), and European Union's Horizon 2020 Research and Innovation Programme under Project SHui (No. 773903).

To feed more than 9 billion people by 2050, increased food production must be accomplished with reduced agricultural inputs in the face of climate change. Wild relatives of wheat (Triticum aestivum L.) possess many potentially valuable traits for improvement of its yield, quality plus tolerance to both biotic and abiotic stresses. To enhance the genetic gains and make agricultural systems climate-resilient, an integrated approach is urgently needed, which entails the use of high-throughput (i.e., genomic and phenomic) technologies and development of innovative breeding strategies to rapidly introgress favorable alleles from the reservoir of genetic diversity prevalent in the wild wheat relatives into modern wheat. This review covers successful gene transfers from wild relatives and use of the available genetic diversity to overcome yield barriers and improve modern wheat cultivars. We summarize the most recent advances in genomic and phenomic approaches and discuss the importance of exploiting the latest reference genomes of wheat and its wild relatives, computational resources and genome-editing technologies (such as CRISPR/Cas9) to enhance the efficiency of plant breeding, thus introducing desired alien genes without deleterious effects. We envision that the integration of various technologies will be critical in improving and stabilizing wheat yields and in meeting the future food demands of the growing human population, particularly in the face of climate change and the wheat production goals set for 2050 food security.

Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes.This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169 bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types.The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties.

Abscisic acid (ABA) is a plant growth regulator known for its functions, especially in seed maturation, seed dormancy, adaptive responses to biotic and abiotic stresses, and leaf and bud abscission. ABA activity is governed by multiple regulatory pathways that control ABA biosynthesis, signal transduction, and transport. The transport of the ABA signaling molecule occurs from the shoot (site of synthesis) to the fruit (site of action), where ABA receptors decode information as fruit maturation begins and is significantly promoted. The maximum amount of ABA is exported by the phloem from developing fruits during seed formation and initiation of fruit expansion. In the later stages of fruit ripening, ABA export from the phloem decreases significantly, leading to an accumulation of ABA in ripening fruit. Fruit growth, ripening, and senescence are under the control of ABA, and the mechanisms governing these processes are still unfolding. During the fruit ripening phase, interactions between ABA and ethylene are found in both climacteric and non-climacteric fruits. It is clear that ABA regulates ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism controlling the interaction between ABA and ethylene has not yet been discovered. The effects of ABA and ethylene on fruit ripening are synergistic, and the interaction of ABA with other plant hormones is an essential determinant of fruit growth and ripening. Reaction and biosynthetic mechanisms, signal transduction, and recognition of ABA receptors in fruits need to be elucidated by a more thorough study to understand the role of ABA in fruit ripening. Genetic modifications of ABA signaling can be used in commercial applications to increase fruit yield and quality. This review discusses the mechanism of ABA biosynthesis, its translocation, and signaling pathways, as well as the recent findings on ABA function in fruit development and ripening.