Crop Improvement Research Articles

'Emerging into the World' - the regulation and control of dormancy and sprouting in geophytes.

Geophytic plants synchronize growth and quiescence with the external environment to survive and thrive under changing seasons. Besides seasonal growth adaptation, dormancy and sprouting are critical factors determining crop yield and market supply as various geophytes also serve as major food, floriculture, and ornamental crops. Dormancy in such crops decides crop availability in the market, as most of such crops are consumed during the dormant stage. On the other hand, uniform/maximal sprouting is crucial for maximum yield. Thus, dormancy and sprouting regulation have great economic importance. Dormancy-sprouting cycles in geophytes are regulated by genetic, exogenous (environmental), and endogenous (genetic, metabolic and hormonal, etc.) factors. Comparatively, the temperature is more dominant in regulating dormancy and sprouting in geophytes, unlike aboveground tissues, where both photoperiod and temperature control are involved. Despite huge economic importance, studies concerning the regulation of dormancy and sprouting are scarce in the majority of geophytes. To date, only a few molecular factors involved in the process have been suggested. Recently, omics studies on molecular and metabolic factors involved in dormancy and growth regulations of underground vegetative tissues have provided more insight into the mechanism. Here, we discuss current knowledge of the environmental and molecular regulation and control of dormancy and sprouting in geophytes and discuss challenges/questions that need to be addressed in the future for crop improvement.

Assessment of Genetic Diversity of Brinjal (Solanum melongena L.) in the coastal region of Karaikal, India

Genetic divergence among 25 brinjal genotypes for 13 characters was evaluated in a breeding programme aimed at improving yield potential by using Mahalanobis D2 statistics. The genotypes were grouped into six clusters suggesting considerable amount of genetic diversity in the study material. The cluster I had constituted maximum of 17 genotypes followed by cluster II which had three genotypes and cluster IV with two genotypes. The cluster III, cluster V and cluster VI each had one genotype. The intra-cluster D2 value ranged from 0.00 to 61.67 and the inter-cluster D2 value ranged from 89.49 to 343.51. The maximum intra-cluster distance of 61.67 was exhibited by the cluster I followed by cluster IV and cluster III, V, VI. The inter cluster distance was found to be high between cluster II and IV followed by cluster IV and V, cluster II and VI and cluster II and V. The contribution of different characters towards divergence indicated that, fruit yield per plant contributed the maximum percentage of 79.00 towards genetic divergence followed by individual fruit weight (8.00 percent) and number of fruits per cluster (3.00 percent). Thus, it indicated that the genotypes from cluster IV (fruit yield per plant), cluster VI (individual fruit weight) and cluster IV (number of fruits cluster-1) could be selected for crop improvement in brinjal as they recorded higher cluster mean values for traits contributing maximum towards genetic divergence.

Advances in Breeding for Oil Quality Enhancement in Indian Mustard (Brassica spp. L.): Achievements, Challenges, and Research Opportunities

Major objectives in oil crop improvement are enhancement of seed and oil yield, quality of oil according to its use, i.e. edible or industrial uses, breeding of varieties that fit in different cropping systems and breeding biotic and abiotic stress resistant/tolerant varieties. Despite traditional breeding approaches, including pure line breeding, yielding only modest gains in productivity, recent advancements in mustard breeding have led to significant breakthroughs in both productivity and oil quality. This review discusses the innovative breeding strategies that have contributed to these advancements, with a focus on hybrid development, oil quality enhancement, and biotechnological approaches. To enhance productivity, researchers at the University of Delhi have developed hybrid seed production techniques using transgenic Barnase-barstar systems and cytoplasmic male sterility (CMS) systems. These systems enable large-scale hybrid seed production, with field trials demonstrating significant yield heterosis ranging from 31% to 55% compared to national check varieties. In addition to productivity, improving oil and meal quality has been a key objective. By integrating genes from canola-quality mustard lines, breeders have achieved reductions in erucic acid and glucosinolates, enhancing the health profile and industrial applicability of mustard oil. A high-density linkage map developed using an F1 double haploid mapping population has facilitated the marker-assisted backcross breeding of desirable traits, enabling precise transfer of key quality traits. Transgenic approaches, such as antisense RNA technology, have led to the development of high-oleic, low-linoleic mustard lines with improved fatty acid profiles. These advancements reflect a strategic combination of conventional and biotechnological methods, demonstrating a clear pathway for boosting mustard yields while enhancing oil quality. Molecular markers reported for genetic diversity assessment, mapping and tagging genes/QTLs for different qualitative and quantitative traits and their use in marker-assisted selection have been presented. This progress not only addresses current challenges but also sets the stage for future research aimed at further optimizing productivity, oil quality, and resistance to pests and diseases in mustard cultivation.

MpNAC1, a transcription factor from the mangrove associate Millettia pinnata, confers salt and drought stress tolerance in transgenic Arabidopsis and rice

Pongamia (Millettia pinnata Syn. Pongamia pinnata), a mangrove associate plant, exhibits good stress tolerance, making it a treasure of genetic resources for crop improvement. NAC proteins are plant-specific transcription factors, which have been elucidated to participate in the regulation and tolerance of abiotic stresses (such as salt and drought). Here, we identified a salt-induced gene from Pongamia, MpNAC1, which encodes an NAC factor sharing five highly conserved domains with other NACs and exhibits close homology to AtNAC19/AtNAC55/AtNAC72 in Arabidopsis. MpNAC1 showed nuclear localization and transcriptional activator activity. MpNAC1-overexpressing Arabidopsis exhibited significantly stronger salt and drought tolerance compared with wild-type plants. The expression levels of stress-responsive genes were activated in transgenic Arabidopsis. Furthermore, the heterologous expression of MpNAC1 also enhanced the salt and drought tolerance of transgenic rice. The major agronomic traits, such as plant height and tiller number, panicle length, grain size, and yield, were similar between the transgenic lines and wild type under normal field growth conditions. RNA-Seq analysis revealed that MpNAC1 significantly up-regulated stress-responsive genes and activated the biosynthesis of secondary metabolites such as flavonoids, resulting in increased stress tolerance. Taken together, the MpNAC1 increased salt and drought stress tolerance in transgenic plants and did not retard the plant growth and development under normal growth conditions, suggesting the potential of MpNAC1 in breeding stress-resilient crops.

Enhancing genetic variability in Trigonella species through sodium azide induction: morpho-physiological and chromosomal amelioration

Plant breeding, aimed at enhancing desired traits, depends on genetic diversity. Mutation breeding is a powerful method of rapidly expanding genetic diversity, facilitating crop improvement, and ensuring food security. In a recent study, researchers evaluated the genetic variability of Trigonella species using different doses of sodium azide (SA) (0.2%, 0.4%, 0.6%, 0.8%, and 1.0%) through morphological, physiological, and cytogenetic studies. Morphological variations were observed in cotyledonary leaves, vegetative leaves, and overall plant growth and habit. Several quantitative parameters, such as plant height, fertile branches per plant, pods per plant (or clusters), seeds per pod, and seed yield, increased when treated with 0.2% and 0.4% SA compared to the control. Furthermore, the total chlorophyll content and carotenoids increased in the sample treated with 0.2% SA over the control but decreased with higher concentrations. Scanning electron microscopy revealed that stomatal aperture and seed dimensions increased at lower concentrations of sodium azide treatment. The study found a positive correlation between the different parameters studied in the Trigonella species, as indicated by high r-values. Based on their findings, it was concluded that the genotype of fenugreek can be improved by using 0.2% and 0.4% concentrations of sodium azide. However, the evaluation of observed variants in successive generations is a critical and necessary process to validate their potential as keystones for crop genetic improvements.

Mean Performance and Genetic Variability Exploration for Fruit Yield and its Attributing Traits in Tomato (Solanum lycopersicum L.)

The present study was conducted to access the relative performance, genetic variability, genetic advance and heritability in thirty genotypes of tomato crop. The crop was sown under Randomized Block Design (RBD) in three replications at Regional Research Station Karnal, CCS Haryana Agricultural University, during the Autumn Winter season of 2021-22. The observations were recorded for eight parameters pertaining to the fruit yield and its attributing traits in tomato. Statistics from analysis of variance showed substantial differences among the genotypes that unveils the plausible presence of significant genetic variability which could be positively exploited in crop improvement programs. The results obtained in the experiment showed that Pusa Ruby (38 days) was earliest to flower in 50% plants followed by EC-631351 (40 days). Genotype Selection 7 took the least (66) number of days to first picking and genotype Kashi Hemant took the maximum (155 days) number of days to last picking. Genotype EC-615056 recorded the maximum (57.71 g) average fruit weight and genotypes namely EC-631457, EC-631357 and Pusa Early Dwarf observed highest fruit yield per plant. Narrow differences were recorded for the phenotypic and genotypic coefficients of variation for all the characters, which denotes that environment had very little influence in expression of the characters and phenotype truly represents the genotype. High to moderate magnitude of genotypic coefficient of variation and phenotypic coefficient of variation was recorded for almost all the characters in our investigation. Plant characters days to first picking, days to 50% flowering, days to last picking, plant height at harvest recorded high (>70%) magnitude of heritability in broad sense implying least influence of environment over these characters. High heritability coupled with high genetic advance was observed for characters like days to 50% flowering and plant height at harvesting.

Morphological and genetic characterization of jackfruit (Artocarpus heterophyllus) in the Kayunga and Luwero districts of Uganda

BackgroundJackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers.ResultsThe results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the ‘partitioning around medoids’ (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances.ConclusionsBoth morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers’ incomes. However, selecting germplasm based on morphology alone may be misleading.

The Function of RNA Interference (RNAi) in Crop Enhancement- Mechanism and Applications: A Review

RNA interference (RNAi) is a conserved molecular mechanism that plays a critical role in post-transcriptional gene silencing across diverse organisms. This review delves into the role of RNAi in plant functional genomics and its applications in crop improvement, highlighting its mechanistic insights and practical implications. The overview starts with the fundamental finding of the mechanism of RNAi, following its journey from petunias to its ubiquitous presence in a wide range of species. The discovery of several kinds of regulatory non-coding small RNAs, including as phasiRNAs, miRNAs, and siRNAs, has broadened our knowledge of RNAi-mediated gene regulation beyond what is previously thought. These RNA types have an impact on gene expression through complex post-transcriptional and epigenetic mechanisms. RNA interference (RNAi) has become a potent tool for comprehending gene activities in the context of crop improvement. It has shown to be useful in determining the functions of genes for metabolic pathways, stress tolerance, and more. Furthermore, RNAi-based strategies have potential for sustainable agriculture and integrated pest management, supporting international efforts to ensure food security. The many uses of RNA interference (RNAi) are covered in this article, including improving crop nutrition, changing plant architecture, and increasing shelf life. The challenges and future prospects of RNAi technology are also explored. The worldwide geography of RNA interference research is emphasized, with notable contributions from North America, Europe, and China. In conclusion, RNA interference (RNAi) continues to be a flexible and essential tool in contemporary plant research, providing new pathways for understanding gene activities and enhancing crop characteristics. Its combination with other biotechnological techniques, such as gene editing, might influence how agriculture and sustainable food production develop in the future.

Unlocking Genetic Diversity and Germplasm Characterization with Molecular Markers: Strategies for Crop Improvement

Molecular markers have emerged as the most useful tools in assessment of genetic diversity and characterizing germplasm, for crop improvement. This review paper comprehensively analyzes the applications of molecular markers in diversity analysis and germplasm characterization. It underscores the significance of genetic diversity as the bedrock for plant breeding programs, enabling the development of improved varieties with desirable attributes such as higher yields, stress tolerance, and enhanced nutritional profiles. The paper provides an overview of various types of molecular markers, including hybridization-based markers (e.g., RFLPs) and PCR-based markers (e.g., RAPDs, AFLPs, SSRs, and SNPs). It discusses marker selection strategies, emphasizing the consideration of factors like polymorphism, informativeness, and the potential for multiplexing and high-throughput genotyping. Diversity analysis techniques, including principal component analysis (PCA), cluster analysis methods (UPGMA and Neighbor-Joining), and population structure analysis (model-based approaches like STRUCTURE), are detailed. These methods enable the assessment of genetic relationships, identification of subpopulations, and selection of diverse parents based on molecular marker data. The review further explores the applications of molecular markers in germplasm management, conservation, and utilization. It discusses the role of markers in targeted introgression of desirable traits from diverse sources, as well as the integration of genotypic and phenotypic data for association mapping, genomic prediction, and selection. Additionally, the paper addresses emerging technologies, such as next-generation sequencing (NGS) and the integration of molecular markers with other omics data. It also highlights the practical applications and impact of molecular markers in crop improvement programs, including marker-assisted selection (MAS), genomic selection, and the development of genetically modified crops. Finally, the review outlines challenges and future perspectives, including limitations0 of current technologies, the potential of emerging techniques like NGS, and the integration of molecular markers with other omics approaches for a comprehensive understanding of complex traits.

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF < 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 < 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

Genomic Approaches for Enhancing Yield and Quality Traits in Mustard (Brassica spp.): A Review of Breeding Strategies

Mustard, a vital oilseed crop, plays a significant role in global agriculture due to its versatile applications in food, feed, and biofuel industries. However, meeting the increasing demands for yield and quality traits poses a substantial challenge to mustard breeders. In response, genomic approaches have emerged as powerful tools to expedite mustard breeding programs by unraveling the genetic basis of key agronomic traits. This review provides a comprehensive overview of genomic strategies aimed at enhancing yield and quality traits in mustard. Beginning with an exploration of traditional breeding methods and their limitations, we delve into the advancements in genomics, including next-generation sequencing technologies, marker-assisted selection (MAS), and genome editing techniques. We discuss how these tools are leveraged to identify yield-related genes, quantitative trait loci (QTLs), and markers for efficient trait selection. Furthermore, we examine genomic approaches for improving oil content, nutritional profiles, and phytochemical composition, crucial for enhancing mustard quality. Case studies demonstrating the successful integration of genomics into breeding programs are highlighted, along with discussions on challenges such as regulatory concerns and technical hurdles. Finally, we outline future directions and the potential of genomic approaches to revolutionize mustard breeding, paving the way for sustainable crop improvement. This study offers valuable insights into the application of genomics in mustard breeding and underscores its importance in addressing the evolving needs of agriculture in the 21st century.

Influence of plant growth regulators on qualitative attributes of acid lime Kuliana local in Odisha

Kuliana lime is an outstanding Odisha cultivar with significant potential to be included in future crop improvement operations due to its flavor and juice content. This research was conducted at the Horticultural Research Station, Department of Fruit Science and Horticultural Technology, Orissa University of Agriculture and Technology, Bhubaneswar during 2019–2020 and 2020–2021 to determine the optimal growth regulator in terms of quality metrics. certain growth regulators 2,4-D (2,4-D @ 10 ppm and 20 ppm) and GA3 (GA3 @ 50 ppm and 100 ppm) and NAA (NAA @ 100 ppm and 200 ppm) and SA (SA @ 100 ppm and 200 ppm) and SPMD (SPMD @ 0.01 ppm and 0.5 ppm) and PUT (PUT @ 0.01 ppm and 0.5 ppm) and BR (BR @ 0.1 ppm and 0.5 ppm) quality of Acid Lime kuliana local. The biometrical observations on various quality features were recorded in the same seasons over 2 years. The best was for fruit quality, which has been determined on the basis of growth regulators performances, as growth regulator variation has a significant effect on the quality of fruit. Brassinosteroids showed the best effects for TSS (7.17 oBrix), acidity (6.05 %), total sugar content (0.61 %), reducing sugar content (0.41 %), ascorbic acid (36.35 mg per 100 mL of juice), chlorophyll content (33.03 mg/100 g), flavonoid content (119.91 mg/100 g), protein (0.82 mg/100 g) and carbohydrate content (10.29 mg/100g) with the other treatments, including the untreated fruits in both years of the study. Our results revealed that the BR gave superior results in quality attributes for Kuliana lime in the East and Southeast Coastal Plain Zones of Odisha.

Assessment of induced allelopathy in crop-weed co-culture with rye-pigweed model

This study evaluates induced allelopathy in a rye-pigweed model driven by rye’s (Secale cereale L.) allelopathic potential as a cover crop and pigweed’s (Amaranthus retroflexus L.) notoriety as a weed. The response of rye towards pigweed’s presence in terms of benzoxazinoids (BXs) provides valuable insight into induced allelopathy for crop improvement. In the 2 week plant stage, pigweed experiences a significant reduction in growth in rye’s presence, implying allelopathic effects. Rye exhibits increased seedling length and BXs upsurge in response to pigweed presence. These trends persist in the 4 week plant stage, emphasizing robust allelopathic effects and the importance of different co-culture arrangements. Germination experiments show rye’s ability to germinate in the presence of pigweed, while pigweed exhibits reduced germination with rye. High-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis identifies allelopathic compounds (BXs), 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) in rye. Rye significantly increases BX production in response to pigweed, age-dependently. Furthermore, pigweed plants are screened for possible BX uptake from the rhizosphere. Results suggest that allelopathy in rye-pigweed co-cultures is influenced by seed timing, and age-dependent dynamics of plants’ allelopathic compounds, providing a foundation for further investigations into chemical and ecological processes in crop-weed interactions.

Response of grain amaranth (Amaranthus hypochondriacus) to irrigation schedules under sprinkler irrigation

A field experiment was conducted during winter (rabi) seasons of 2019–20 and 2020–21 at the Centre for Crop Improvement, Sardarkrushinagar Dantiwada Agricultural University, Banaskantha, Gujarat to study the response of grain amaranth (Amaranthus hypochondriacs L.) to irrigation schedules under sprinkler irrigation system. The experiment was conducted in a randomised block design (RBD) comprised of 6 irrigation treatments, viz. I0 , Surface irrigation; I1 , Control (only pre-sowing irrigation); I2 , Sprinkler irrigation at 0.2 IW: CPE; I3 , Sprinkler irrigation at 0.4 IW: CPE; I4 ,Sprinkler irrigation at 0.6 IW: CPE; and I5 ,Sprinkler irrigation at 0.8 IW:CPE with 4 replications. The results revealed that application of irrigation at IW: CPE ratio of 0.8 had significant effect on plant height, inflorescence length (83.4 cm), grain yield (1,625 kg/ha) and straw yield (7,497 kg/ha) compared with control treatment (surface irrigation). Treatment 0.8 IW: CPE resulted in the 28.15% higher grain yield than the control. The highest water-use efficiency (WUE) (12.8 kg/ha-mm) was achieved by the treatment I1 (only pre-sowing irrigation). Consumptive use (mm) was found increased with increase in irrigation scheduling from I0 to I5 . The highest consumptive use of 179.3 mm was recorded under the treatment of 0.8 IW: CPE ratio. Irrigation at 0.8 IW: CPE ratio fetched highest net returns of `54,701/ha, with benefit: cost (B:C) ratio 3.06 during both the years in pooled analysis.

Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea.

Genetic diversity and environmental factors are long believed to be the dominant contributor to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.

Morphological and molecular diversity analysis vis-a-vis phylogenetic correlation among pomegranate (Punica granatum L.) varieties

Abstract Identification of different pomegranate (Punica granatum L.) genotypes using morphological descriptors and further substantiated through molecular means is essential for a breeding program. Characterization using molecular markers has an advantage over its morphological counterpart due to its low expense, quick and reliable results, and the requirement of less sophisticated equipment. In this study, eight different pomegranate cultivars were characterized based on their morphological and molecular characters in sub-tropical regions between 2018 and 2019. Morphological experiments were conducted in a randomized block design replicated thrice for each cultivar, whereas RAPD markers were employed for molecular studies. Principal component analysis revealed significant morphological variation (79.61%) among the cultivars. A high level of polymorphism, similar to PCA, was observed with RAPD analysis (80.49%). Some discrepancies between morphological and molecular results were noted in UPGMA cluster analysis. However, eight primers (total = 41) distinctively separated the Bhagwa variety from others, with the maximum similarity coefficient value (ca. 0.54) and superior fruit quality distinguished in PCA analysis with the maximum mean Euclidean distance (ca. 16). Hence, RAPD markers could be used along with morphological markers for a quick screening of germplasms in further crop improvement programs.

A Single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis

The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and the genetic improvement of crops. This developmental process incorporates a series of cell fate transitions and reprogramming. However, our knowledge of cell heterogeneity and of the mechanisms of cell fate transition during callus induction remains quite limited. Here, we performed a time series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0 days, 1 day, and 4 days, and we constructed a detailed single-cell transcriptional atlas of the callus induction process. We identified the cell types responsible for initiating the early callus: lateral root primordia-initiating (LRPI)-like cells and quiescent center (QC)-like cells. LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia. We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells. QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration. We further inferred the transcription factors that regulating QC-like cells and the gene expression signatures that are related to cell fate decisions. Overall, our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transition during callus formation, and significantly improves understanding of callus formation.

Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants

CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution in rapid genetic improvement of crops. The editing capabilities of base editors strictly rely on the performance of various nucleotide modification enzymes. Compared to the well-developed adenine base editors (ABEs), cytosine base editors (CBEs) and dual base editors suffer from unstable editing efficiency and pattern at different genomic loci in rice, significantly limiting their application. Here, the activities of multiple evolved TadA8e variants in base editing have been comprehensively examined in rice. We found that both TadA-CDd and TadA-E27R/N46L achieve more robust C-to-T editing than previously reported hyperactive hAID*Δ, whereas TadA-CDd outperformed TadA-E27R/N46L. Also, the C-to-G base editor (CGBE) engineered with TadA-CDd and OsUNG performs highly efficient C-to-G editing in rice compared to TadA-N46P. In addition, the dual base editor, which was constructed with a single protein TadDE, enables simultaneously edit C-to-T and A-to-G at high efficiency in rice. Collectively, our study demonstrates that TadA8e derivatives improve both CBE and dual base editor in rice, provide a powerful way in inducing diverse nucleotide substitutions for plant genome editing.

Insight into the genomic diversity: Genome wide association study unveils the SNP diversity in horsgram germplsam

Genome wide association study (GWAS) was performed to identify loci associated with three agronomic traits namely seeds per pod, pods per plant and number of seeds per plant of horsegram (Macrotyloma uniflorum). Total 87 accesions of horsegram from different geographical regions of India and one wild relative from Australia were utilised for the genome wide association studies. The genotyping was carried out using genotype-by-sequencing technology and after high quality filtering, minor allele frequency of 0.05, a total of 55,656 quality SNPs were utilised for determining Marker-Trait Association. The LD decay varied across the chromosomes form 8 kb to 300 kb. Further, the population structure analysis has clustered the accession into three subpopulations. All the 88 accessions of horsegram were evaluated at Palampur (32.1109° N, 76.5363° E) and Bajaura (31.8465°N, 77.1605°E) locations of North-Western Himalayan region, India from. In the current study, 143 MTAs associations were observed for seeds per pod distributed on all 8 chromosomes, 2 for pods per plant at chromosomes 2 and 3 and 1 for number of seeds per plant at chromosome 7. However, total 11 stable QTLs (9 for number of seeds per plant and 2 for pods per plant) were also identified. These QTLs can serve as a potential source for marker assisted selection. The genes identified within and in proximity to the stable QTLs will serve as a bridge between genetic information and its practical application for crop improvement.

Sustainability concern in Indian agriculture: needs science-led innovation and structural reforms

Agriculture in India is facing several challenges which together are manifested into the sustainability issues. The broad contours of the agricultural production system in the country have been defined by the need to achieve food security which calls for close attention to rice–wheat (Triticum aestivum L.) cropping system of the Indo Gangetic Plains (IGP) whose sustainability is under threat. Degradation of natural resources, severe biotic and abi otic stresses specially drought, floods, pest infestations with accompanying impacts on biodiversity and agricultural productivity are the major constraints to agricultural development. Further, climate change has gained significant global attention over the past decade due to concerns of deleterious long-term impacts on agriculture, water sup ply, human welfare, regional and political stability. All the related issues need to be addressed on priority, with par ticular emphasis on soil-carbon through a holistic approach. As the strategy brings focus on income of farmers, the agricultural technology needs to move from “Production oriented-Green Revolution” to “Farmer’s Income oriented Revolution” and environmentally sustainable farming. Therefore, for long-term sustainability in agriculture, 4 pil lars/ components (good agricultural practices, climate-change mitigation and adaptation, diversification of high value crops and biodiversity management) needs to be addressed properly, more importantly good agricultural practices (GAP). The GAPs are based on the principles of risk prevention, risk analysis, sustainable agriculture, and integrated crop management (ICM), which are of utmost importance in present time. The GAPs for agricultural sustainability are reduced tillage, conservation agriculture, resource-conservation technologies (RCTs), erosion control measures, diversified cropping system, micro-irrigation, balanced fertilization, manuring, watershed man agement, organic farming, and integrated farming systems etc. Now that the vision is to impart income security to the farmers of the country, diversification of the system across all the sub-sectors of agriculture assumes impor tance which is, indeed a de-risking mechanism capable of negotiating both endogenous and exogenous risks as sociated with the system. The effective and efficient management of agro-biodiversity is also essential through management of genebanks, science-led innovations; livelihood, food and nutrition security though crop diversifica tion, use of lesser-known crops and wild relatives in crop improvement; dealing appropriately with quarantine, bio safety and bio-security.