Codon usage bias (CUB) is a phenomenon that shows variation both within the genes of a species and across different species, wherein particular codons are preferred over their synonymous counterparts. Genomic nucleotide configuration provides insights into the molecular basis of genes and their evolutionary relationships in distinct plant species. In this study, the VTE4 gene, responsible for enhancing the nutritional quality and oil stability of oilseed Brassica , sequences from six Brassica species were extracted through the NCBI GenBank database. Subsequently, various CUB-related parameters, including nucleotide composition (AT and GC content), relative synonymous codon usage (RSCU), effective number of codons (ENC), frequency of optimal codons (Fop), relative codon usage bias (RCBS), neutrality plot (GC12 vs. GC3), parity rule-2 [(A3/(A3 + T3) vs. (G3/(G3 + C3)], and correspondence analysis, were assessed to analyse codon biasness within the U’s triangle of Brassica species. The results showed AT bias across the Brassica species and moderate codon usage frequency for specific amino acids based on RSCU values in the VTE4 gene. An evolutionary study confirmed a similarity in codon usage preference among species clustered together. The elevated ENC value, along with low Fop and RSCU values, indicated a low level of gene expression and a moderate bias in codon usage preference within the Brassica genus. Moreover, the results from the neutrality plot, parity rule, and correspondence analysis revealed that natural selection pressure had a more significant influence on shaping codon usage bias (CUB) in the VTE4 gene than mutation pressure. This research contributes to understanding codon optimization, enhancing exogenous gene expression, and advancing transgenic engineering for improved α-tocopherol content profiling in Brassica species to enhance seed oil quality.

Additive effects of three candidate genes—SAMBA, NAC TF25, and ARF18—significantly influenced seed weight in Brassica juncea, collectively accounting for 35.79

Elevated temperatures adversely affect the growth and productivity of Brassica juncea at various developmental stages. Breeding heat-tolerant varieties presents an economically viable strategy to reduce the impacts of heat stress. Therefore, a genome-wide association study was conducted, focusing on agro-morphological traits under late-sown conditions, exerting heat stress at the reproductive phase. A diverse panel of 142 genotypes was used for phenotyping and SNP genotyping. During late-sown conditions of 2020-2021, 2021-2022 and 2022-2023, a total of 59 significant marker-trait associations were identified. Among these, 11 SNPs were consistently associated with key traits across the seasons. These stable SNPs were further analysed through gene annotation and in silico expression profiling. The SNPs were linked to several important agro-morphological traits affected by heat stress. In silico analysis of SNPs revealed important candidate genes directly involved in stress response and trait regulation. Expression profiling confirmed predominant expression of these genes in corresponding tissues, indicating their functional relevance. The identified candidate genes will be subsequently used for the development of heat-tolerant B. juncea varieties through molecular breeding approaches.

Oats (Avena sativa L.) is a multipurpose, popular, nutritionally rich cereal crop widely used for food, feed, and fodder. In India, it is cultivated on nearly 0.25 M ha in the northern, northwestern, and central regions and has recently expanded to the eastern region, mainly for fodder purposes. Breeder seed (BS) production data were collected from the AICRP on Forage Crops and Utilization (FC&U) for a period of 24 years (1998-1999 to 2021-2022). Several fodder oat varieties have been developed and introduced into the seed chain in India over the past 24 years to suit different agro-climatic conditions. However, analysis reveals a narrow genetic base at the varietal level, with a few old and popular varieties (Kent, OS-6, and OS-7) sharing > 70% of the genome in varietal development. To encourage the cultivation of new varieties and replace older ones, adequate BS production is vital to ensure a regular supply of quality seeds for sustainable livestock production, providing nutritious and cost-effective fodder. With a few exceptions, the amount of BS indent and the number of varieties has increased, indicating growing demand and awareness of new varieties. At the institutional level, Indian Grassland and Fodder Research Institute (IGFRI) (Jhansi) contributed the highest to BS production (29.8%), followed by Punjab Agricultural University (PAU) (Ludhiana; 13.7%), AAU (Anand; 10.8%), and G.B. Pant University of Agriculture and Technology (GBPUAT) (Pantnagar; 9.9%). A moderate varietal replacement rate (22.9%) was observed for recently developed varieties (< 5 years) over the past 3 years (2019-2020 to 2021-2022). However, their contribution has significantly increased from 0.2% (2018-2019) to 26.2% (2021-2022). We estimated certified seed production (194,040 q) for 2023-2024 based on the available BS (485.1 q), assuming the seed chain operates at 100% efficiency. This production could cover 0.19 M ha of fodder oats in 2024-2025. The ARIMA model estimated that BS production and the number of varieties in the seed chain would reach 734.2 q and 28, respectively, by 2026-2027. Additionally, breeding approaches and improved management practices for enhanced seed production were discussed, and a roadmap was proposed to meet the demand for quality fodder oat seed in India.

Indian mustard [Brassica juncea (L.) Czern. and Coss.] is a vital oilseed crop in India, comprising over 90

In Indian mustard, improving agro-morphological and quality traits through conventional methods are both cumbersome and resource-intensive. Marker-aided breeding presents a promising solution to these challenges. Hence, the present research aimed to identify genomic regions governing agro-morphological and quality traits using genome-wide association studies (GWAS). The GWAS panel comprised 142 diverse genotypes of Indian mustard were evaluated for 20 different agro-morphological and quality traits, revealing significant difference among genotypes. Subsequently, the GWAS panel genotyped using the Brassica 90K SNP array (Illumina). Structure and diversity analysis grouped the GWAS panel into 3 sub-populations or groups, and LD decay of 1.05 Mb was confirmed through genotypic analysis. GWAS using the BLINK model revealed a total of 49 marker-trait associations (MTAs), in which 28 and 21 MTAs were observed during rabi 2020-21 and rabi 2021-22 for various agro-morphological and quality traits, respectively. Amongst them, twelve MTAs demonstrated stable associations with the studied traits, including days to 50% flowering (DF), days to 100% flower termination (DFT), days to maturity (DM), plant height (PH), main shoot length (MSL), siliqua length (SL), seeds per siliqua (SPS), oil content (OC), and glucosinolates content (Glu) in both years. Moreover, in silico analysis of nearby regions of these stable SNPs revealed their association with 31 candidate genes known to be involved in various molecular, physiological, and biochemical pathways relevant to the studied traits. These genes can be further characterized and deciphered for more precise utilization in breeding programs in the future.

Tocopherols, together with tocotrienols and plastochromanols, constitute a category of lipophilic substances referred to as tocochromanols or vitamin E. Tocochromanols, celebrated for their strong antioxidant characteristics, are solely synthesized by photosynthetic entities, including plants, algae, and cyanobacteria, rendering them essential elements of the human diet. Their exceptional antioxidative functions arise from their capacity to engage with polyunsaturated acyl groups, efficiently neutralizing lipid peroxyl radicals and diminishing reactive oxygen species (ROS), thus protecting fatty acids from lipid peroxidation. Recent scientific investigations have uncovered novel understandings of the biosynthetic pathways of vitamin E and associated processes, presenting possible approaches for improving the nutritional quality of vital crops via biofortification. This review offers a comprehensive examination of the tocopherol biosynthesis pathway in plants, the importance of vitamin E levels in staple crops, and the variations in both levels and composition found among different crops. Additionally, the review emphasizes research focused on enhancing tocopherol content through genetic modifications, including the overexpression of critical enzymes within the biosynthetic pathway, and discusses the potential of diverse breeding strategies for crop enhancement.

Diverse uses of maize oil attracted various stakeholders, including food, feed, and bioenergy, highlighting the increased demand for sustainable production. Here, 48 diverse sub-tropical maize genotypes varying for dgat1-2 and fatb genes governing oil attributes, were evaluated in three diverse locations to assess trends of oil content, fatty acid (FA) profile, the effect of environment on oil attributes, the impact of different gene combinations and determine FA health and nutritional properties. The genotypes revealed wide variation in oil content (OC: 3.4-6.8 %) and FA compositional traits, namely palmitic (PA, 11.3-24.1 %), oleic (OA, 21.5-42.7 %), linoleic (LA, 36.6-61.7 %), and linolenic (ALA, 0.7-2.3 %) acids. Double-mutants with both favourable alleles (dd/ff) exhibited 51.6 % higher oil, 33.2 % higher OA, and 30.2 % reduced PA compared to wild-types (d(+)d(+)/f(+)f(+)) across locations. These double-mutants had lower saturated FA (12.2 %), and higher unsaturated FA (87.0 %), indicating reduced susceptibility to autooxidation, with lower atherogenicity (0.14), thrombogenicity (0.27) and peroxidisability (48.15), higher cholesterolemic index (7.16), optimum oxidability (5.27) and higher nutritive-value-index (3.35) compared to d(+)d(+)/f(+)f(+), making them promising for significant health and nutritional benefits. Locally adapted stable novel double-mutants with high-oil and better FA properties identified here can expedite the maize breeding programs, meeting production demands and addressing long-standing challenges for breeders.

Millets gained a great attention at the global level in 2023 which is celebrated as the "International Year of Millets" to create awareness to eventually promote consumption and production. An attempt is made here to understand the cultivation and production dynamics of millets as influenced by their demand and supply. We also assess challenges and emerging opportunities to make millets more productive, competitive, and relevant to future farming. Millets registered a 60% decline in area and a 200% rise in productivity, but production has remained the same during the last seven decades. The demand of millets decreased as food due to greater incentives (purchasing grain at a pre-determined price) and policies (distribution of grains to the public at a subsidized rate) in favor of wheat and rice. Millets would play a greater role in future agriculture due to challenges posed by climate change, limited water supply, and reduced agro-biodiversity. This would need a much greater intensity of investment in millet research and adequate support as extended to wheat and rice. Increased emphasis on their genetic improvement and agronomic management is required to develop cultivars, using new tools and technologies, with high production potential and adequate environmental adaptation to make millets competitive with other crops. Mainstreaming the nutritional traits in millet breeding is also critically important to develop high-yielding cultivars with improved grain quality traits. Promoting millet consumption would remain the key issue for increasing their demand as food, feed, and industrial raw materials through policies and awareness programs. Strengthening of value chain will help in diversifying agri-food production system and creating an ecosystem for millet promotion. There have been significant changes in millet cultivation in India during last seven decades. Millets registered a 60% decline in area and 200% rise in productivity. Production of millets has remained same during last seven decades. Millets would play a greater role in future agriculture due to anticipated challenges posed by climate-change. Increasing millet productivity and promoting consumption are the key issues to be addressed.

Background: This study is meant to examine the energy requirement and energy input- output of different cropping sequences .The crucial objective to conduct experiment to understand energy efficiency using inputs and outputs which were disbursed in cropping sequences. Hence, it is need of the hour to identify the most remunerative and cost effective cropping sequence with high energy efficient for UGP of India. Methods: This study was carried out at the research farm of ICAR-Indian Institute of Farming Systems Research, Modipuram, during 2017-2021.The divergent cropping sequences viz. sugarcane-ratoon-wheat (CS1); rice-wheat-dhaincha (CS2); pigeonpea +maize-chickpea-okra (CS3); maize-berseem-black gram (CS4); sorghum-mustard-green gram (CS5) and Napier+cowpea/berseem (CS6) were compared in reference to curtail higher energy inputs through selected alternate cropping sequences. The obtained energy values were calculated by multiplying the amount of inputs and outputs by using energy conversion factors. Result: Maximum inputs energy consumed by sugarcane crop alone (33.14x103 MJ ha-1). Results shown that irrigation, seed, fertilizers and diesel required higher energy for the completion of cultural operations. However, higher inputs energy was used in irrigation followed by seed and fertilizers, respectively. In regard to per cent energy intake through inputs, the highest energy spent was for irrigation (35.30 MJ ha-1) and fertilizer (23.80 MJ ha-1).The wheat equivalent yield was higher in sugarcane-ratoon-wheat (125.58 t ha-1). Maximum output energy was with above system (596.70×103 MJ ha-1). Highest net energy returns was counted with sugarcane-ratoon-wheat (549.37x103 MJ ha-1), energy ratio (12.60) and energy profitability (11.60). Indeed, energy efficiency was highest in same system (1657.50) followed by maize-berseem-black gram (1421.96).

SUMMARYEnhancing maize kernel oil is vital for improving the bioavailability of fat‐soluble vitamins. Here, we combined favourable alleles of dgat1‐2 and fatb into parental lines of four multi‐nutrient‐rich maize hybrids (APTQH1, APTQH4, APTQH5 and APTQH7) using marker‐assisted selection (MAS). Parental lines possessed favourable alleles of crtRB1, lcyE, vte4 and opaque2 genes. Gene‐specific markers enabled successful foreground selection in BC1F1, BC2F1 and BC2F2, while background selection using genome‐wide microsatellite markers (127–132) achieved 93% recurrent parent genome recovery. Resulting inbreds exhibited significantly higher oil (6.93%) and oleic acid (OA, 40.49%) and lower palmitic acid (PA, 14.23%) compared to original inbreds with elevated provitamin A (11.77 ppm), vitamin E (16.01 ppm), lysine (0.331%) and tryptophan (0.085%). Oil content significantly increased from 4.80% in original hybrids to 6.73% in reconstituted hybrids, making them high‐oil maize hybrids. These hybrids displayed 35.70% increment in oil content and 51.56% increase in OA with 36.32% reduction in PA compared to original hybrids, while maintaining higher provitamin A (two‐fold), vitamin E (nine‐fold), lysine (two‐fold) and tryptophan (two‐fold) compared to normal hybrids. Lipid health indices showed improved atherogenicity, thrombogenicity, cholesterolaemic, oxidability, peroxidizability and nutritive values in MAS‐derived genotypes over original versions. Besides, the MAS‐derived inbreds and hybrids exhibited comparable grain yield and phenotypic characteristics to the original versions. The maize hybrids developed in the study possessed high‐yielding ability with high kernel oil and OA, low PA, better fatty acid health and nutritional properties, higher multi‐vitamins and balanced amino acids, which hold immense significance to address malnutrition and rising demand for oil sustainably in a fast‐track manner.

Photosynthetic traits can sense and signal abiotic stress at early growth stages of mustard [Brassica juncea (L.) Czern & Coss]. The integration stress responses with multiple selection indices can select the fittest/tolerant genotypes. With this goal, a set of 210 diverse mustard genotypes were phenotyped under control and salt-stress (electrical conductivity = 12 dS m(-1)). Significant dynamic response of the plant to salt stress with reduction for all morpho-physiological traits and genotype x treatment interaction was observed under salinity. A higher accumulation of Na+ was recorded in the roots, followed by shoots. A close correspondence between phenotypic coefficient of variation and genotypic coefficient of variation under control and salt stress conditions results in high heritability (h(2)) in broad sense. A significant negative association between shoot and root Na+ content and rate of photosynthesis also indicated that Na+ was significantly restricted in the root. This was not found to be efficient because considerable Na+ buildup was observed in the shoot. Multiple trait-based indices, such as membership function value of salinity tolerance, classical Smith-Hazel index, factor analysis ideotype-best linear unbiased prediction index, and multi-trait genotype-ideotype distance index, deduced CS 2009-159, CS 2009-420, CS 2009-124, and Swarn Jyoti (RH-9801) are promising for identifying salt-tolerant genotypes that can serve as donors for the development of salt-tolerant cultivars.

KeyMessage: We identified QTLs for salinity tolerance in Indian mustard, paving the way for salt -tolerant mustard genotypes, enhancing crop resilience in saline environments. Soil salinity is a major abiotic stress that reduced the growth and productivity of numerous crops, including Indian mustard. Natural genetic variations in salt tolerance (ST) were observed but no QTL mapping has been done for ST related traits in Indian mustard. In this study, to identify QTLs for ST traits, 250 stabilized F7:8 recombinant inbred lines (RILs) mapping population of Indian mustard was developed from a cross CS 614-11-100-13 x CS 56 and evaluated them under control, and irrigated water salinity of ECiw 12 dSm- 1 for two Rabi seasons 2020-21, and 2021-22 for 18 traits. Most of traits were shown normal distribution curve, indicating population suitable for QTLs identification. Genotyping-by-sequencing (GBS) using ddRAD sequencing of the population was performed and total 2506 SNPs sorted from total 2594,666 variants after discarding markers as no progeny polymorphism and not passing chi square test which cover 1127.85 cM distance on linkage map. A total of 47 QTLs associated with ST traits were identified using composite interval mapping (CIM). Out of 47 QTLs, 12 QTLs were major QTL such as: for days to 50% flowering (qDFsB07.1), days to maturity (qDMsB08.1), number of primary branches per plant (qPBRcA05.1, and qPBRsA07.1), main shoot length (qMSLsB05.1, and qMSLcB05.1), seeds per siliqua (qSPScA09.1), yield per plant (qYPPsB06.1), transpiration rate (qEsA01.1), Na+ concentration of stem (qSNasA01.1), K+ concentration of stem (qSKsB03.1), and K+ concentration of root (qRKsB01.1) was identified with SNPs. This novel research findings will facilitate QTLs/genes mapping that can be used to identify candidate gene and transfer this with marker assistant selection (MAS).

The current scanty knowledge about the salt tolerance mechanism underlying the ability of plants to tolerate salt stress hinders the potential production of numerous crops, including Indian mustard. To explore the traits and mechanism for salt tolerance, high throughput phenotyping of 250 stabilized F7:8 recombinant inbred lines (RILs) mapping population of Indian mustard were conducted under control and salinity (ECiw 12 dS m-1 ) for 54 morpho-physio-seed-quality traits. Most of the traits were reduced with variable percentages under salt stress. The stress tolerance index (STI) of YPP showed a significant negative association with Na+ concentration of root (RNa), indicating that RILs with low Na+ concentration have high seed yield and a positive significant association with STI of yield-related traits, photosynthesis rate (Pn), intrinsic water use efficiency (inWUE), fresh weight of upper leaf (USFW), fresh weight of branches (BrFW), fresh weight of basal leaf (BLFW), and fresh weight of middle leaf (MLFW) revealed that by improving these traits seed yield per plant (YPP) was improved. Based on principal component analysis (PCA) of 54 STI and new index composite selection index (CSI), RILs viz., R114, R150, R164, R170, and R206 were identified as stable performers which can be exploited for quantitative trait loci (QTLs)/gene discovery and serve as potential donors to combat salt stress. Our research will serve to determine the relative importance of different functional traits of salt tolerance mechanisms that can be used to screen colossal germplasm.

This research explored the process of transforming banana peels into nano-sized filler particles used as a reinforcement for polymeric composite and measured the durability in corrosive environment. The composites were fabricated by varying the weight percentages of banana fillers (2.5, 5.0, 7.5, and 10wt

Tocopherol (vitamin E) is considered an important vitamin carrying antioxidant properties. It plays a vital role in maintaining the quality and stability of oil in Brassica species. Molecular mechanisms of tocopherol content have been studied in Brassicas; however, it is untapped in Indian mustard (Brassica juncea). In the experiment, the expression profile and sequence variation of the candidate gene VTE4 controlling alpha-tocopherol content (ATC) were studied between two diverse parents (RLC-3 and NPJ-203) of B. juncea. The VTE4 gene expression in different tissues was almost double in NPJ-203 (high ATC genotype) as compared to RLC-3 (low ATC genotype). Moreover, sequence analysis of VTE4 in NPJ-203 and RLC-3 revealed the presence of two SNPs in the 6th exon, resulting in a shorter coding sequence (CDS) in RLC-3 (996 bp) as compared to NPJ-203 (1044 bp). Using these SNPs, an allele-specific marker was developed and validated in the F3 population.The single marker analysis revealed that the marker was significantly linked to the tocopherol content, contributing 16.46% to the total phenotypic variance. Thus, the study suggested that VTE4 is the major gene contributing to the tocopherol content, and the developed marker can be effectively used in marker-assisted breeding to improve tocopherol content in B. juncea.

Egyptian clover/Berseem (Trifolium alexandrinum L.) is the most popular winter leguminous multi-cut fodder crop widely cultivated in the northwest and central parts of India. Quality seed significantly impacts farm productivity, farmers’ profitability, and socioeconomic welfare. Foundation and certified seeds enable high-quality seed production, making breeder seed (BS) the most important link in the seed supply chain. In India, berseem BS indent had increased from 1998 - 99 to 2012–13; afterwards, it followed a constant but decreasing trend. Of the 27 notified cultivars, 24 came into the seed supply chain between 1998–1999 and 2021–2022, indicating high varietal availability to stakeholders. The study examines the potential causes of the national decline in BS indent and production and the differences in these figures over time. The highest BS indent was received for the variety JB-1 (276.1 q), followed by BL-10 (205.1 q), Mescavi (165.6 q) and Wardan (153.7 q) from 1998 - 99 to 2021–22. The varietal replacement rate (VRR) is high, 43.30 %, for the varieties that have reached the age of five or less in the recent three years (2019–20 to 2021–22). Additionally, it has been calculated that if the seed chain operates at 100 % efficiency, the BS generated (48.1q) in 2021–22 can cover an area of almost 0.12 million hectares in 2024–25. The study offers an in-depth overview of berseem BS indent and production, an analysis of the difficulties encountered in BS production, and future directions for expanding variety and producing excess BS in the nation.

Deficiency of vitamin E results in several neurological and age-related disorders in humans. Utilization of maize mutants with favourable vte4-allele led to the development of several α-tocopherol (vitamin E) rich (16–19 µg/g) maize hybrids worldwide. However, the degradation of tocopherols during post-harvest storage substantially affects the efficacy of these genotypes. We studied the role of lipoxygenase enzyme and Lipoxygenase 3 (LOX3) gene on the degradation of tocopherols at monthly intervals under traditional storage up to six months in two vte4-based contrasting-tocopherol retention maize inbreds viz. HKI323-PVE and HKI193-1-PVE. The analysis revealed significant degradation of tocopherols across storage intervals in both the inbreds. Lower retention of α-tocopherol was noticed in HKI193-1-PVE. HKI323-PVE with the higher retention of α-tocopherol showed lower lipoxygenase activity throughout the storage intervals. LOX3 gene expression was higher ( 1.5-fold) in HKI193-1-PVE compared to HKI323-PVE across the storage intervals. Both lipoxygenase activity and LOX3 expression peaked at 120 days after storage (DAS) in both genotypes. Further, a similar trend was observed for LOX3 expression and lipoxygenase activity. The α-tocopherol exhibited a significantly negative correlation with lipoxygenase enzyme and expression of LOX3 across the storage intervals. HKI323-PVE with high tocopherol retention, low -lipoxygenase activity, and -LOX3 gene expression can act as a potential donor in the vitamin E biofortification program. Protein-protein association network analysis also indicated the independent effect of vte4 and LOX genes. This is the first comprehensive report analyzing the expression of the LOX3 gene and deciphering its vital role in the retention of α-tocopherol in biofortified maize varieties under traditional storage.

Field trial comprising of two integrated disease management module (based on bio-intensive input and Chemical fungicide) was conducted for disease management in mustard at regional research station, Bawal (Rewari) of CCSHAU, Hisar, Haryana during 2017 to 2019. The results showed that soil application (2.5 kg /ha) and seed treatment (10 g /kg) with Trichoderma viride (NCIPM / T-9 strain) followed by two foliage spray of freshly made garlic clove extract @2% (w/v) was better than seed treatment with carbendazim 50WP (1 g a.i. /kg) followed by its two foliar spray @ 0.5 g a.i. / l of water in significantly reducing the diseases and increasing the seed yield. Minimum white rust (32.2%) and Alternaria leaf spot (28.3%) disease severity, Sclerotinia stem rot (4.6%) incidence and maximum seed yield of 2433 kg / ha was observed in bio-intensive IDM module in comparison to corresponding values of 38.1%, 34.2%, 7.6% and 2202 kg /ha in chemical fungicide.