Guava (Psidium guajava L.) is a popular fruit crop in Southeast Asia. Landrace Purple Local (PL), also known as Malaysian guava, is rich in anthocyanin content in all the plant parts but has poor yield. Genetic inheritance and physical location of the allele(s) controlling the constitutive purple trait in guava have not yet been reported. The F-1 plants generated by cross hybridizing PL x green cv. Allahabad Safeda (AS) and analysed for 7 years did not exhibit purple trait. Evaluation of F-1, F-2 and BC1F1 populations derived from the cross between PL x AS revealed that purple color is a recessive trait in guava. Equally spaced (similar to 10 Mb) co-dominant polymorphic markers developed by in silico analysis of AS and PL genome (mapped to AS genome assembly) into PCR-based assay mapped the purple color locus (pl) on pseudochromosome 11 (PC 11) of guava genome. Further mapping on PC 11 identified 2 InDel markers at 2.49 Mb (Pg11_INDL_2.49 M) and 4.99 Mb (Pg11_INDL_4.99 M) closely associated with pl. Also, QTLseqr for purple and non-purple bulks in F-2 provided two co-localized significant peak Delta SNP-indices at positions 2489072 and 4978573 on PC 11. The mapped genomic interval harbours 85 coding genes, including the potential candidates MYB-like ETC1, anthocyanidin reductase, MYB41-like transcription factors and F-box protein SKIP27-like. Markers flanking pl would potentiate the marker-assisted introgression of anthocyanin trait in popular cultivars of guava.

The rise of direct-seeded rice cultivation as a suitable alternative to transplanted puddled rice depends on developing genotypes with high seedling emergence under deep sown conditions. Two rice genotypes (IRGC 128442 and PR126) were screened for contrasting seedling emergence and subjected to high-throughput RNA sequencing under varying sowing depths (4 cm and 10 cm) and time intervals (5, 10, and 15 days after sowing). On average, a total of 2702 differentially expressed genes were identified across twelve inter- and intra-genotypic pairwise differential expression analyses, with a false discovery rate ≤ 0.05 and log2 fold change ≥ ± 2. The DEGs specifically showing differential expression under deep-sowing stress were prioritized and further refined based on their corresponding gene ontology terms, gene set enrichment analysis and KEGG and plant reactome pathway. From this pool of DEGs, 24 genes were validated using qRT-PCR. Among these, two genes (LOC_Os04g51460 and LOC_Os02g45450) contribute to cell wall remodelling and membrane stability, while three genes (LOC_Os04g48484, LOC_Os06g04399, and LOC_Os07g15440) play key roles in mitigating abiotic stress. Transcriptional regulators (LOC_Os06g33940 and LOC_Os01g45730) drive stress responses and growth. Notably, high fold changes in LOC_Os03g22720 and LOC_Os07g01960 underscore their importance in early stress responses and metabolic adjustments. The transcriptome analysis also highlighted the role of 29 heat shock proteins in response to deep sowing stress. Differential expression of key components in the abscisic acid (ABA)-mediated signalling pathway such as OsABI5 (LOC_Os01g64000), phosphatase 2C-like (PP2C) (LOC_Os09g15670) and OsPYL (LOC_Os06g36670) indicated downregulation of ABA signalling in the genotype IRGC 128442. Additionally, a role for miRNA-mediated regulation of auxin response factors was hypothesized in seedling emergence regulation. The study brings us closer to understanding the genetic control of seedling emergence under deep sown conditions. Functional validation of the key candidate genes and pathways could provide new targets for genetic improvement, potentially contributing to the development of rice cultivars optimized for direct-seeded rice cultivation.

The impact of the GpcB1/Yr36 gene on agronomic attributes, grain quality parameters, and stripe rust resistance was studied in the background of the popular Indian wheat cultivar PBW550. Introgression lines SABW159 showed 21.01% enhancement in protein with no yield penalty and stripe rust-resistant reaction (10s). Similarly, SABW141 registered a 14.19% increase in protein content along with a 6.17 % yield advantage over PBW550 and the terminal disease reaction of 10S. The corresponding disease score for PBW550 was 80S. Similar trends for improvement across all three traits, viz. grain yield, GPC, and stripe rust resistance, were observed for several introgression lines, and no single yield component showed a reduction on account of enhanced protein.

Interspecific plant hybridisation is a pivotal evolutionary process shaping speciation dynamics. In the context of bread wheat cultivation in India, stripe rust stands out as the predominant factor contributing to yield reduction. With the objective of improving stripe rust resistance and floral traits, diverse back-crossed population was meticulously developed through triticale-wheat crosses. The BC2F7 generation of rye-wheat derivatives underwent a comprehensive analysis encompassing genetic variability, trait associations, multiple regressions, and principal component, with a focus on floral and yield attributes. The meticulously chosen stripe rust-resistant derivative lines underwent comprehensive evaluation, including an assessment of chromosomal abnormalities, fluorescence in situ hybridisation, and rye genome-specific molecular markers analysis. The statistical analysis substantiates that the derived population exhibits significant variations for all the examined traits. Positive correlations were observed with anther size, pollen viability, tiller number, thousand kernel weight, and grain yield. Multiple regression analysis reveals that anther size, pollen viability, tiller number, and thousand kernel weights emerge as pivotal contributors influencing grain yield. Moreover, the three principal components exhibit more than one eigen-value, thereby signifying their capacity to encapsulate the maximum variability within the dataset. In addition, chromosomal abnormalities, encompassing univalent, multivalent, laggards, bridge chromosomes, and micronuclei, were observed within the PMCs of rye wheat derivative lines. Fluorescence in-situ hybridisation unequivocally demonstrated rye introgression by green signals. Furthermore, the affirmation of rye introgression was corroborated by rye genome-specific molecular markers. Hence, Comprehensive methods unveil promising traits in rye-wheat lines, advancing wheat breeding in India.

Hybrid breeding has the potential to overcome the yield barriers through hybrid vigor, improving yield instability and stress resilience. In wheat, a predominantly self-pollinating species, the cytoplasmic male sterility-restoration of fertility (CMS/Rf) system is a promising approach for reaping the benefits of hybrid vigor or heterosis. However, insufficient genetic diversity in the elite germplasm limits the exploitation of heterosis in wheat. This study aimed to expand the genetic diversity in locally adapted restorer germplasm by enriching the male parental gene pool carrying T. timopheevii cytoplasm. We used selected European winter wheat genotypes with desirable out-crossing characteristics to develop spring × winter wheat backcross derivatives. Phenotypic and genotypic assessments were conducted to evaluate genetic diversity and performance of new germplasm for key traits including anther extrusion (VAE), plant height (PH), spikelets per spike (SPS) and tiller number (TN) in the field trials. Significant phenotypic diversity was observed in the resultant germplasm for desirable floral and agronomic traits including anther extrusion, days to flowering, and plant height, along with sufficient molecular diversity as revealed by SSR markers. This diversified germplasm also exhibited enhanced performance for key out-crossing and agronomic traits (PH, VAE, SPS, TN) compared to original restorers, when evaluated over two field seasons. These findings indicate significant genetic improvement of the spring restorer germplasm through the winter-wheat facilitated diversity enhancement strategy. Therefore, this improved novel restorer germplasm has strong potential for CMS/Rf-based hybrid wheat breeding, paving way for the development of superior wheat hybrids with significant heterosis.

Improving the rate of genetic gain of cereal crop will rely on the accelerated crop breeding pipelines to allow rapid delivery of improved crop varieties. The laborious, time-consuming traditional breeding cycle, and the seasonal variations are the key factor restricting the breeder to develop new varieties. To address these issues, a revolutionized cost-effective speed breeding protocol for large-scale rice germplasm advancement is presented in the present study. The protocol emphasises on optimizing potting material, balancing the double-edged sword of limited nutritional dose, mode and stage of application, plant density, temperature, humidity, light spectrum, intensity, photoperiod, and hormonal regulation to accelerate rice growth and development. The plant density of 700 plants/m2, cost-effective halogen tubes (B:G:R:FR-7.0:27.6:65.4:89.2) with an intensity of ∼ 750–800 µmol/m2/s and photoperiod of 13 h light and 11 h dark during seedling and vegetative stage and 8 h light and 16 h dark during reproductive stage had a significant effect (P < 0.05) on reducing the mean plant height, tillering, and inducing early flowering. Our results confirmed that one generation can be achieved within 68–75 days using the cost-effective SpeedyPaddy protocol resulting in 4–5 generations per year across different duration of rice varieties. The other applications include hybridization, trait-based phenotyping, and mapping of QTL/genes. The estimated cost to run one breeding cycle with plant capacity of 15,680 plants in SpeedyPaddy was 2941 including one-time miscellaneous cost which is much lower than the advanced controlled environment speed breeding facilities. The protocol offers a promising cost-effective solution with average saving of 2.0 to 2.6 months per breeding cycle with an integration of genomics-assisted selection, trait-based phenotyping, mapping of QTL/genes, marker development may accelerate the varietal development and release. This outstanding cost-effective break-through marks a significant leap in rice breeding addressing climate change and food security.

Citrus reticulata Blanco also known as kinnow mandarin is a widely grown horticultural crop in Punjab. CRISPR/Cas9 technology is being widely used for generation of varieties with increased resilience towards abiotic and biotic stresses as well as improved horticultural traits. Xanthomonas citri subsp. citri ( Xcc )-mediated Agroinfiltration offers a fast and transgene-free method for the delivery of CRISPR/Cas9 constructs for systemic introduction into plants for functional genomics and expression studies. The technology is currently unexplored in kinnow mandarin. This study is aimed at establishing an efficient method of Cas9 delivery for transient knockout of PDS (phytoene desaturase) gene in kinnow mandarin. The construct pKO-119-PDS N-Cas9/sgRNA:PDS1 carrying sgRNA and Cas9 enzyme was delivered into the dorsal surface of young leaves of kinnow mandarin. The leaves showed albino patches at the point of injection within 60 h. Two surfactants (Triton-X and Silwet ™ ) were used to ease the Agroinfiltration process which resulted in variation in the expression of vector. The Sanger’s analysis of the treated plants showed a substitution within the sgRNA region which resulted in change in amino acid from proline to serine. The protocol provides a feasible and an efficient method for genome editing in C. reticulata which could be helpful in future studies aimed at genome editing as well as genetic transformation.

Triticale is a man-made cereal crop that combines the rye and wheat genome in a single crop. Rye is a cross pollinated cereal crop that has large anther size in comparison of wheat. To improve wheat anther size, cross with triticale is a noble practice to combine the A, B, D and R genome. In the current investigation wheat (AABBDD) were crossed with triticale (AABBRR) with the help of Ph suppressor Chinese Spring. Subsequently triticale wheat derivative lines populations were developed. The BC2F7 generations of the derived population were planted in alpha lattice design to further evaluation. With the help of fixative, the fresh spikes were collected from individual derivative lines to measure anther the size. The anther size was measured in millimeter by the help of ocular micrometer. Twenty-two triticale wheat derivative lines were identified with grater anther size in comparison of triticale anther. The TWD26 (5.7mm) has larger anther size followed by TWD18 (5.4mm) and TWD36 (5.3mm). These derivative lines may use as a donor parent in hybrid wheat breeding programme.

Globally, malnutrition has given birth to an alarming predicament, especially in developing countries, and has extensively shifted consumer preferences from conventional high-energy diets to a nutritionally balanced, cost-effective, sustainable, and healthy lifestyle. In keeping with this view and the mandate for developing high-yielding, disease-resistant biofortified staple food (wheat) for catering to the demand-driven market, the current research aimed at stacking together the enhanced grain protein content, carotenoid content, and disease resistance in an elite bread wheat background. The Y gene (PsyE1) and the GpcB1 gene were used as novel sources for enhancing the grain carotenoid and protein content in the commercial elite bread wheat cultivar HD2967. The combination also led to the stacking of resistance against all three foliar rusts owing to linked resistance genes. A stepwise hybridization using Parent 1 (HD2967 + PsyE1/Lr19/Sr25) with Parent 2 (PBW550 + GpcB1/Yr36+ Yr15), coupled with a phenotypic-biochemical selection, narrowed down 2748 F2 individuals to a subset of 649 F2 plants for molecular screening. The gene-specific markers PsyE1, PsyD1, Xucw108, and Xbarc8 for the genes PsyE1, PsyD1, GpcB1, and Yr15, respectively, were employed for forward selection. Four bread wheat lines positive for all the desired genes with high carotenoid (>8ppm) and protein (>13%) content were raised to the F5 generation and will be evaluated for yield potential after bulking. These improved advanced breeding lines developed following multipronged efforts should prove a valuable and unique source for the development of cultivars with improved nutritional quality and rust resistance in wheat breeding programs.

Triticum dicoccoides, the immediate tetraploid progenitor of durum (T. durum) and bread wheat (T. aestivum) is known to endure harsh environmental conditions. The present study was aimed at exploring the responsiveness of Triticum dicoccoides accessions to early vegetative stage water deficit stress. Relative water content (RWC) and malondialdehyde (MDA) content were evaluated from the leaves of field-grown rain-fed plants. Significant genotypic variation was observed in wild accessions along with cultivated durum PDW 291 and bread wheat PBW 621 included in the set. The relative water content ranged from 75.50% (acc 7054) to 83.78% (acc 5251). The average content of malondialdehyde was recorded as 30.85 nmole g−1 FW. Fourteen of the twenty-six T. dicoccoides accessions accumulated MDA less than the cultivated wheats. Overall, T. dicoccoides accessions 4655, 4667, 5251, 7054, 7079 and 14004 may be shortlisted to identify distinct allelic variants/stress-responsive loci for subsequent deployment in the wheat breeding program.

Improvement of grain protein content (GPC), loaf volume, and resistance to rusts was achieved in 11 Indian wheat cultivars that are widely grown in four different agro-climatic zones of India. This involved use of marker-assisted backcross breeding (MABB) for introgression and pyramiding of the following genes: (i) the high GPC gene Gpc-B1; (ii) HMW glutenin subunits 5 + 10 at Glu-D1 loci, and (iii) rust resistance genes, Yr36, Yr15, Lr24, and Sr24. GPC increased by 0.8 to 3.3%, although high GPC was generally associated with yield penalty. Further selection among high GPC lines allowed identification of progenies with higher GPC associated with improvement in 1000-grain weight and grain yield in the backgrounds of the following four cultivars: NI5439, UP2338, UP2382, and HUW468. The high GPC progenies (derived from NI5439) were also improved for grain quality using HMW glutenin subunits 5 + 10 at Glu-D1 loci. Similarly, progenies combining high GPC and rust resistance were obtained in the backgrounds of following five cultivars: Lok1, HD2967, PBW550, PBW621, and DBW1. The improved pre-bred lines developed following multi-institutional effort should prove a valuable source for the development of cultivars with improved nutritional quality and rust resistance in the ongoing wheat breeding programmes.

The periodic breakdowns of stripe rust resistance due to emergence of new virulent and more aggressive pathotypes of Puccinia striiformis f. sp. tritici have resulted in severe epidemics in India. This necessitates the search for new and more durable resistance sources against stripe rust. The three bread wheat cultivars PBW 343 (carries Yr9 and Yr27), PBW 621 (carries Yr17) and HD 2967 (gene not known) were highly popular among the farmers after their release in 2011. But presently all three cultivars are highly susceptible to stripe rust at seedling as well as at adult plant stages as their resistance has been broken down due to emergence of new pathotypes of the pathogen (110S119, 238S119). In previous study, the crosses of PBW 621 with PBW 343 and HD 2967 and evaluation of further generations (up to F4) against pathotype 78S84 resulted in resistant segregants. In the present study, the F5 and F6 RIL populations have been evaluated against new pathotypes of Pst. The RILs categorized based on the disease severity on the P (Penultimate leaf) and F (flag) leaf into three categories i.e., high, moderate and low level of APR (adult plant resistance) having 1–200, 201–400 and >400 values of AUDPC, respectively, upon infection with stripe rust. The various APR components (latent period, lesion growth rate, spore production and uredial density) were studied on each category, i.e., resistant, moderately resistant and susceptible. The values of APR parameters decreased as the level of resistance increased. Based on molecular analysis, the lines (representing different categories of cross PBW 621 X PBW 343) containing the genes Yr9 and Yr17 due to their interactive effect provide resistance. Based on BSA using 35k SNPs and KASP markers association with phenotypic data of the RIL population (PBW 621 X HD 2967) showed the presence of two QTLs (Q.Pst.pau-6B, Q.Pst.pau-5B) responsible for the residual resistance and two SNPs AX-94891670 and AX-94454107 were found to be associated with the trait of interest on chromosome 6B and 5B respectively. The present study concludes that in the population of both the crosses (PBW 621 X PBW 343 and PBW 621 X HD 2967) major defeated gene contributed towards residual resistance by interacting with minor gene/QTLs.

All stage resistance to stripe rust races prevalent in India was investigated in the European winter wheat cultivar 'Acienda'. In order to dissect the genetic basis of the resistance, a backcross population was developed between 'Acienda' and the stripe rust susceptible Indian spring wheat cultivar 'HD 2967'. Inheritance studies revealed segregation for a dominant resistant gene. High density SNP genotyping was used to map stripe rust resistance and marker regression analysis located stripe rust resistance to the distal end of wheat chromosome 1A. Interval mapping located this region between the SNP markers AX-95162217 and AX-94540853, at a LOD score of 15.83 with a phenotypic contribution of 60%. This major stripe rust resistance locus from 'Acienda' has been temporarily designated as Yraci. A candidate gene search in the 2.76 Mb region carrying Yraci on chromosome 1A identified 18 NBS-LRR genes based on wheat RefSeqv1.0 annotations. Our results indicate that as there is no major gene reported in the Yraci chromosome region, it is likely to be a novel stripe rust resistance locus and offers potential for deployment, using the identified markers, to confer all stage stripe rust resistance.

More than one-third of the global population suffers from iron and zinc deficiency, developing anaemia like diseases mostly in the developing countries. Therefore, the current study focuses on the investigation of variability and bioavailability of micronutrients such as iron and zinc in bread wheat mediated by lower levels of phytic acid which is often categorised as an antinutritional compound. Phytic acid in cereals acts as an chelator of major micronutrients such as iron and zinc, thus lowering their bioavailability both in humans and animals. In addition, drought is a major component affecting the micronutrient accumulation in wheat kernels. Therefore, a pre-breeding wheat germplasm set comprising 137 genotypes was grown under irrigated and restricted irrigated conditions for 2 years. This germplasm set was used to assess the variability for iron, zinc and phytic acid content in the wheat kernels. Mean iron and zinc content was 45.83 and 49.43 ppm under irrigated conditions, whereas it was 40.53 and 49.62 ppm under restricted irrigated conditions. Afterward, the molar ratios of phytate with iron and zinc were calculated to predict their bioavailability. Based on the daily recommended values, promising genotypes were shortlisted with low phytic acid combined with high iron and zinc content. These promising genotypes will be further used in wheat breeding programme to breed biofortified wheat cultivars with higher micronutrient and reduced phytic acid concentration combined with enchanted abiotic stress tolerance which can potentially help in alleviating the hidden hunger under changing climatic conditions.

Colored wheat has piqued the interest of breeders and consumers alike. The chromosomal segment from 7E of Thinopyrum ponticum , which carries a leaf rust resistant gene, Lr19 , has been rarely employed in wheat breeding operations due to its association with the Y gene, which gives a yellow tint to the flour. By prioritizing nutritional content over color preferences, consumer acceptance has undergone a paradigm change. Through marker-assisted backcross breeding, we introduced an alien segment harboring the Y ( PsyE1 ) gene into a high yielding commercial bread wheat (HD 2967) background to generate rust resistant carotenoid biofortified bread wheat. Agro-morphological characterization was also performed on a subset of developed 70 lines having enhanced grain carotene content. In the introgression lines, carotenoid profiling using HPLC analysis demonstrated a considerable increase in β-carotene levels (up to 12 ppm). Thus, the developed germplasm caters the threat to nutritional security and can be utilized to produce carotenoid fortified wheat.

One hundred twenty-five recombinant inbred lines of wheat derived from the cross of C 273 (heat tolerant) and PBW 343 (susceptible) together with check PBW 550 were evaluated under normal and heat stress (late sown) conditions. A significant reduction in chlorophyll content and increases in membrane injury index and lipid peroxidation were observed under heat stress. Higher buildup of sugars in peduncle of tolerant over susceptible lines resulted in higher transport of sugars for sink activity. However, grains of control plants showed higher lipoxygenase activities and total antioxidant activity with decreasing contents of lipid peroxide and H2O2 resulting in building of redox homeostasis to tolerate oxidative stress. High temperature significantly decreased yield and yield-related traits both in tolerant and susceptible lines. Chlorophyll content, peduncle sugars and peduncle weight were highly correlated with yield and grain weight under stress indicating a reliable screening tool for development of heat-tolerant genotypes.

Variability in enzymatic and non enzymatic antioxidants could be useful for breeding genotypes tolerant to different abiotic stresses. The objective of present study was to determine the variability in enzymatic and non enzymatic antioxidants in wheat at three different stages of development including leaves of vegetative stage, flag leaf stage after 5 days of anthesis and in mature grains. Forty wheat genotypes including 10 commercial cultivars, 5 rainfed cultivars, 17 advanced breeding lines and 8 Australian cultivars were raised under irrigated conditions. At vegetative stage, high activity of superoxide dismutase (SOD), peroxidase (POX), glutathione reductase (GR) and ascorbate peroxidase (APX) and low hydrogen peroxide (H2O2) content was observed in many of the advanced breeding lines, while high proline and low malondialdehyde (MDA) content was observed in many commercial cultivars. In flag leaf after 5 days of anthesis higher activity of SOD and APX was observed in many of rain-fed cultivars; many commercial cultivars showed high activity of POX and GR while low H2O2 content was observed in many of Australian cultivars. Ruby, Binnu and Datatine have low H2O2 and MDA content so they could be used for studying tolerance towards different types of abiotic stresses. PBW 550 showed high antioxidant activity in leaves during vegetative and flag leaf stage, it could be worthwhile to study the performance of this cultivar under different abiotic stresses. Variability was also observed in mature grains of different wheat genotypes. In mature grains high proline content was observed in many of rain-fed cultivars while less GR, CAT and APX activity was observed in many of Australian genotypes. Mature grains of wheat genotypes PBW 644, PBW542, DBW 16, DBW 17, WH 1021, PBW 676, BWL 73 and PBW 175 have high activity of APX, GR and some have high proline content. In general genotypes with high enzymatic antioxidants and low H2O2 and MDA content may be useful for studying tolerance towards different abiotic stresses. Genotypes with high antioxidants were identified for possible use in wheat breeding programme.