Development of prolific male sterile baby corn hybrids through conventional breeding is a time-consuming and resource-intensive process, and is made further cumbersome by the need to identify or introduce the appropriate cytoplasmic-nuclear gene combinations. The application of doubled haploidy (DH) in baby corn breeding programmes can facilitate generation of completely homozygous lines carrying the desired trait combinations in a relatively short time. The objective of this study was to develop prolific sterility maintainer lines from heterozygous (Rf/rf) maize hybrids using doubled haploidy and to evaluate their stability and breeding utility across environments. In this study, a total of 217 DH lines were generated from four maize hybrids heterozygous for fertility restoration genes (Rf/rf) and screened for prolificacy. The DH lines showed substantial genetic variability for prolificacy along with expression of transgressive segregation, leading to the selection of 30 superior DH lines for fertility evaluation. Fertility behaviour was assessed using anther exsertion and pollen fertility assays with a C-cytoplasmic male sterile tester across multiple environments (Hyderabad and Almora). The DH lines grouped into 11 sterility maintainers (36.7

Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus, is an emerging threat to rice production in Asia. Since its first outbreak in 2022, the virus has raised concerns due to its potential impact on rice ecosystems in India. However, limited genomic data exist on its establishment, ecology and evolution, particularly in alternative hosts. In this study, high-throughput sequencing (HTS) and RT-PCR were used to perform a comparative genomic segmental analysis of SRBSDV in symptomatic rice (Oryza sativa) and asymptomatic monocot weeds from the vicinity of rice fields in North India. Complete SRBSDV genomes (segments S1-S10) were recovered from rice samples, while seven near-complete segments were identified in the monocot weeds during the two subsequent rice growing seasons. Viral segment accumulation, copy number and FPKM analyses revealed significantly higher SRBSDV loads in rice than in weeds. SNV profiling indicated active viral replication and intra-host evolution in rice, whereas limited SNV in weeds suggested viral stability and a reservoir role. Phylogenetic analysis of SRBSDV segments S8 and S10 confirmed close relatedness to the Chinese isolates. Diversity analysis of the S8 segment using DnaSP demonstrated high haplotype richness, moderate nucleotide diversity, and strong purifying selection, with Indian isolates forming a low-diversity subgroup relative to highly polymorphic Chinese populations. RT-PCR validation across additional samples supported HTS findings and segment-specific variability in detection. This study provides the first genomic evidence of SRBSDV establishment in weed hosts in Indian rice agroecosystem post its first outbreak and highlights the role of asymptomatic weeds as potential reservoirs. Furthermore, the detection of all ten SRBSDV genomic segments in the white-backed planthopper (WBPH) vector collected from these fields confirms its role in viral transmission. These findings provide the first genomic evidence of SRBSDV persistence in weed hosts in India and underscore the importance of integrated disease and vector management strategies to safeguard rice productivity, contributing to sustainable agriculture.

Several stress factors influence the yield of a key legume crop common bean. To pact with the food insecurity for future generations, there is a need to exploit crop wild relatives and landraces. Advanced methods of crop genetic improvement and identification of novel variations must be explored admirably for improving common bean cultivars. Crop sustainability despite changing climatic conditions and exposure to emerging or existing stress entities could be effectively met with the involvement of common bean wild relatives or landraces and closely related domesticated Phaseolus species in introgression programmes. Though a substantial sum of literature related to common bean origin and exploitation of wild relatives is available, the profound understanding of the concept is still edged. Here, efforts were made to compile information on the utilization of common bean wild relatives in crop procreation programmes.

Liguleless mutants produce defective ligules and auricles and, consequently, have more upright leaves than their ligulate counterparts, making them useful genetic material for plant architectural studies. Besides, owing to the recessive nature and amenability of the liguleless trait to phenotyping at the seedling stage, liguleless mutants are popularly used for 'proof-of-concept' demonstration and assessment of haploid induction rate (HIR) of haploid inducer lines (HILs) in maize. The commonly used liguleless testers in maize are of temperate origin and are challenging to use and maintain under tropical/sub-tropical conditions. In the present study, liguleless lines (V 601, V 602, V 603 and V 604) derived from crosses between agronomically superior locally adapted tropical ligulate lines (V 407 and CM 152) and liguleless donors of temperate origin (PDH-3 and PDH-8) were evaluated for different agro-morphological traits. Liguleless line V 602 was also used as a tester to assess the HIR of haploid inducer line EC937890 (CIM2GTAILP2). The results showed a mean HIR of 12.42% for EC937890, consistent with the HIR reported in other studies, thus demonstrating the efficacy of V 602 as a tester for determining HIR. The agronomically superior liguleless maize lines reported in this study will, therefore, be a valuable resource for leaf architectural studies, assessment of HIR of candidate HILs and maintenance of high HIR in the HILs presently in wide use in the doubled haploid (DH) programmes. Additionally, these genetic stocks carry the liguleless trait in genetic backgrounds with known heterotic affinity with early maturity Indian public maize germplasm and, therefore, can be used directly as parents in hybrid development programmes.

Various pathogenic microorganisms (such as fungi, bacteria, viruses and nematodes) affect plant viability and productivity. However, plants combat these pathogens by inducing their defense mechanism to sustain their fitness. The aggregation of pathogenesis-related (PR) proteins in response to invading pathogens is a crucial component of a plant’s self-defense mechanism. PR proteins induce innate resistance in plants through fungal cell wall disintegration, membrane permeabilization, transcriptional suppression, and ribosome inactivation. Earlier studies have demonstrated their crucial role in determining resistance against phytopathogens, making them a promising candidate for developing disease-resistant crop varieties. Plant genetic engineering is a potential approach for developing disease-resistant transgenic crops by employing several PR genes (thaumatin, osmotin-like proteins, chitinases, glucanases, defensins, thionins, oxalate oxidase, oxalate oxidases like proteins/germin-like proteins and LTPs). Furthermore, the overexpression of PR proteins enhances the resistance against phytopathogens. As a result, this chapter gives an overview of PR proteins, including their classification, functional characterization, signaling pathways, mode of action and role in defense against various phytopathogens. It also highlights genetic engineering advances in utilizing these genes singly or synergistically against various phytopathogens to impart disease resistance. Various challenges faced with the products of transgenic technology and synergistic expression of different groups of PR proteins were also discussed.

Doubled haploid (DH) technology is growingly becoming an integral component of maize breeding programmes worldwide. The currently popular method of DH production employs R1-nj-based haploid inducers lines (HILs) that enable segregation of induction cross seed into haploids and diploids based on anthocyanin pigmentation on kernel endosperm and scutellum. However, the presence of anthocyanin inhibitor gene/s in the source germplasm may cause weak or absence of anthocyanin pigmentation on the kernel endosperm and/or scutellum, which limits the use of this method by precluding distinction between true haploid seed and selfed/out-crossed seed. In induction crosses between R1-nj-based haploid inducer TAILP1 and a hybrid CMVL 55 and its female parent V 405 (the F-1 seeds of both of which express scutellum anthocyanin pigmentation, but kernel crown pigmentation is absent), classification of seed was attempted on the basis of kernel dorsal basal pigmentation and scutellum pigmentation. The ploidy status of the classified seed was determined using the 'gold standard' method in the field. The efficiency of haploid classification (as assessed by false discovery rate) using the combination of scutellum pigmentation and dorsal basal pigmentation was found to be 83.41%. The results suggested that kernel dorsal basal pigmentation may be used as a marker for seed classification in induction crosses where scutellum pigmentation is present, but kernel crown pigmentation is absent. However, assessing this marker's efficiency in a larger germplasm set would be required for its adoption for regular use in induction cross seed classification.

Identifying gene interactions and markers associated with physiological traits, especially at later stages of grain filling, can help develop effective breeding methodology in wheat crop. Six generations (P1, P2, F1, F2, BC1P1 and BC1P2) of four different spring wheat crosses (drought-responsive x drought susceptible) and F3 generation of a single cross, i.e., MACS6272 x UP2828 were phenotyped and genotyped to decipher gene action and associated markers. Ample variation in canopy temperature depression (CTD - 2.6 - 5.6?C), chlorophyll content by SPAD (39.6 - 51.3), relative water content (RWC - 51.5 - 75.4 %), grain filling period (GFP - 61.1 - 80.1 days), 100 seed weight (3.7 - 5.5 grams), harvest index (HI - 25.8 - 46.2 %), biological yield (BY - 35.5 - 89.8 grams) and grain yield (GY - 13.4 - 36.5 grams) per plant were observed in six generations. GY positively correlated with CTD, SPAD, 100SW, BY and HI (0.08* - 0.85**). BY had the maximum direct (0.82) and indirect effect via other traits on GY. Significant non-additive epistatic interactions (j & l) and duplicate gene action were found for most traits except GFP and 100SW. Seven different SSR markers associated with CTD, SPAD, NDVI, RWC, 100SW, and explained phenotypic variation (PVE) ranging from 10.1% to 18.4%, with marker Xcfd35 explaining highest PVE for RWC. The identified candidate genes (in silico) belonged to transmembrane proteins (Xcfd32, Xcfd50), nucleic acid binding domains (Xbarc124, Xgwm484) and having enzymatic activity (Xcfd35, Xwmc47, Xwmc728) important for abiotic stress tolerance. Complex inheritance deciphered by six generations indicated delaying the selection to later stages of segregation so that useful transgressive segregants can be selected for improving grain yields in wheat.

Finger millet (Eleusine coracana (L.) Gaertn.), popularly known as ragi or mandua in India, is an important crop used for food, forage, and industrial products, grown under a wide range of climatic conditions, generally cultivated in tropical and subtropical regions of the world. The crop is largely cultivated by resource-poor farmers, which serves as a food security crop because of rich nutrition and extraordinary storage qualities. Magnaporthe grisea is the most destructive pathogen causing blast disease on a variety of grasses including finger millet. Effective disease management requires identification of resistance source, and understanding the pathogen variability, ecology, and disease epidemiology. Despite a wide host range, presence of few AVR genes restricts the other M. grisea pathotypes from infecting finger millet. However, mutations of potential AVR genes resulting in skip towards new host remain a threat. Indeed, some isolates from other species of Poaceae are successful in infecting finger millet. This chapter provides precise information on the current status of finger millet blast and strategies for the management of disease.

Magnaporthe oryzae that causes blast disease in rice is one of the most notorious phytopathogenic fungi responsible for severe economic loss in rice production. The fungus is one among the top ten devastating biotic threats to food security worldwide. To counter the pathogen and minimize the losses, various biological, conventional, and advanced molecular approaches have been utilized. Conventional and marker-assisted selection (MAS) breeding methods were deployed and varieties having tolerance or resistance have been developed. Durable and broad-spectrum resistance is the demand of the hour to protect the crop against blast disease, and several studies have made significant progress in this direction. Identification and molecular characterization of different blast resistance genes (R) and defense regulators (DR), and their deployment in various cultivars, is the most preferred approach to breed the disease-resistant varieties. The inclusive approaches including quantitative trait locus (QTL), association mapping, allele mining, bioinformatics tools and genetic engineering, miRNA, genome editing, CRISPR/Cas9 etc. have contributed to the strengthening of molecular breeding and providing of new opportunities for the development of rice varieties resistant to blast. Recent advances show that R-genes Pikh, Pi-1, Pi9, Pi20, Pi27, Pi39, Pi40, and Pita impart broad-spectrum resistance against blast disease. The bsr-d1, bsr-k1, spl11, spl33, and OsBBI1 transcription factors have also been reported for broad-spectrum resistance. The R-genes are broadly classified into eight groups, and in plants, the NBS-LRR genes correspond to the major group. These R-genes are the master keys of the entire defense system of plants, act in multilayered surveillance, and are governed by various extra- and intracellular receptor molecules to ward off pathogen invasion. The updated information on rice blast pathogen provided here will help to understand the different mechanism, advancement in resistance gene research, and focus on the breeding program in rice against blast disease.

Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.

Maize (Zea mays ssp. mays) originated from Mexico and Central America and grew worldwide for food, feed and industrial products components. It possesses ten chromosomes with a genome size of 2.3 gigabases. Teosinte (Z. mays ssp. parviglumis) is the probable progenitor of the modern-day maize. The maize domestication favored standing gain of function and regulatory variations acquired the convergent phenotypes. The genomic loci teosinte branched 1 (tb1) and teosinte glume architecture 1 (tga1) played a central role in transforming teosinte to modern-day maize. Under domestication and crop improvement, only 2% (~1200) genes were undergone selection, out of ~60000 genes. Around ~98% of the genes have not experienced selection; there is enormous variation present in the diverse inbred lines that can be potentially utilized to identify QTLs and crop improvement through plant breeding. The genomic resources of wild relatives and landraces harbor the unexplored genes/alleles for biotic/abiotic tolerance, productivity and nutritional quality. The human-made evolution led to the transformation of wild relatives/landraces to the modern-day maize. This chapter summarized the maize’s wild relatives/landraces and the genetic gain over time in biotic/abiotic, productivity, and nutritional quality traits.

Exponential upsurge in the global population growth rate claims sustainable means to fulfill their food requirements. Therefore, the collaboration of beneficial microorganisms with their host plants have been of interest for years as these associations can be helpful in the development of sustainable agriculture. However, the endophytic microorganisms develop a strong and persistent interaction with the host plants compared to epiphytic microbes. The origin of plant-associated endophytes was supposed to be from seeds as the endophytic microbes were found inside seeds of several plant species although, endophytes do not necessarily come from seeds only but can also enter the roots or other parts during plant growth. In any case, the richness of seed with the microbes and their dynamics can edify innovative research potentials in the field of plant-microbe associations. Yet, the seed microbiome is often underrepresented in plant microbial studies and is least studied up till now compared to phyllospheric or rhizospheric microbial population. The revival of exploring the seed microbiome is stimulating new insights related to the dynamics and diversity of seed microbiome along with their interconnectedness with the soil and plant microbial community as well as the microbes associated with pollinators and dispersers. This review is an effort to acknowledge the research on seed associated microbial community including bacteria and fungi. It focuses on ecology of seed microbiome from sources to diversity, their association with the host plant, and their life cycle including mode of colonization, localization, and transmission. Both the horizontal and vertical means of transmission have been discussed in this paper whereas the significance of vertical transmission for rapid infection of beneficial microbial community to next generations of plants through seeds is emphasized. Moreover, the applications of seed endophytes for growth promotion of plants, as biocontrol agents and in phytoremediation are discussed. Finally, the association of seed endophytes with seed quality is linked.

Main conclusion Parastagonospora nodorum is one of the important necrotrophic pathogens of wheat which causes severe economical loss to crop yield. So far, a number of effectors of Parastagonospora nodorum origin and their target interacting genes on the host plant have been characterized. Since targeting effector-sensitive gene carefully can be helpful in breeding for resistance. Therefore, constant efforts are required to further characterize the effectors, their interacting genes, and underlying biochemical pathways. Furthermore, to develop effective counter-strategies against emerging diseases, continuous efforts are required to determine the qualitative resistance that demands to screen of diverse genotypes for host resistance. Stagonospora nodorum blotch also refers to as Stagonospora glume blotch and leaf is caused by Parastagonospora nodorum. The pathogen deploys necrotrophic effectors for the establishment and development on wheat plants. The necrotrophic effectors and their interaction with host receptors lead to the establishment of infection on leaves and extensive lesions formation which either results in host cell death or suppression/activation of host defence mechanisms. The wheat Stagonospora nodorum interaction involves a set of nine host gene-necrotrophic effector interactions. Out of these, Snn1-SnTox1, Tsn1-SnToxA and Snn-SnTox3 are one of the most studied interaction, due to its role in the suppression of reactive oxygen species production, regulating the cytokinin content through ethylene-dependent wayduring initial infection stage. Further, although the molecular basis is not fully unveiled, these effectors regulate the redox state and influence the ethylene biosynthesis in infected wheat plants. Here, we have discussed the biology of the wheat pathogen Parastagonospora nodorum, role of its necrotrophic effectors and their interacting sensitivity genes on the redox state, how they hijack the resistance mechanisms, hormonal regulated immunity and other signalling pathways in susceptible wheat plants. The information generated from effectors and their corresponding sensitivity genes and other biological processes could be utilized effectively for disease management strategies.

Genetic improvement along with widened crop base necessitates for the detailed understanding of the genetic diversity and population structure in wheat. The present investigation reports the discovery of a total of 182 alleles by assaying 52 simple sequence repeats (SSRs) on 40 genotypes of bread wheat. Unweighted neighbour-joining method grouped these genotypes into two main clusters. Highly heat tolerant and intermediate tolerant cultivars were grouped in the same cluster, whereas remaining genotypes, particularly sensitive ones, were assigned different cluster. Similarly, the entire population was structured into two sub-populations (K = 2), closely corresponding with the other distance-based clustering patterns. The marker-trait association was discovered for four important physiological parameters, viz. canopy temperature depression, membrane thermostability index (MSI), normalized difference vegetation index and heat susceptibility index, indicating for heat stress (HS) tolerance in wheat. Both general and mixed linear models of association studies during 2017 and 2018, revealed the association of SSR markers, wmc222 (17.60%, PV) and gwm34 (20.70%, PV) with the mean phenotypic value of MSI. Likewise, SSR markers barc183, gwm75, gwm11 and cfd7 revealed a unique relationship with four selected physiological traits. Candidate genes discovered using in silico tools had nine SSR markers within the genic regions reported to play a role in heat and drought stress responses in plants. The information generated about these genic regions may be explored further in expression studies in-vivo to impart HS tolerance in bread wheat.