Quinoa represents a valuable gift from the "New World" to the "Old World." Although some breeding programs exist worldwide, they have seen limited growth and impact on their genetic improvement. Large-scale hybridization, hindered by the crop's complex floral morphology, remains the primary bottleneck in quinoa breeding. This study compared manual and natural crossing schemes, incorporating hybridity testing with morphological and molecular markers. The results indicate that a facilitated open-pollinated strategy combined with hand emasculation and hybridity confirmation using morphological or indel markers offers a feasible approach to establishing a quinoa breeding pipeline. We also concluded that characterizing panicles by the arrangement of hermaphrodite and pistillate flowers could be a game-changer for improving breeding efficiency. Additionally, interspecific crosses (Chenopodium quinoa × Chenopodium giganteum) achieved efficiencies of 5–26%. Both inter- and intraspecific crosses can feasibly generate variation for genetic improvement in quinoa. Breeding quinoa for Asian environments should follow a step-wise strategy: (1) characterize flowering in crossing blocks, (2) apply natural crossing or hand emasculation, (3) confirm hybridity using morphological or molecular markers, (4) pursue genetic enhancement, and (5) select for traits of interest.

Genetic variability is a fundamental prerequisite for successful plant breeding and crop improvement. This investigation assessed genetic variability parameters, including genotypic and phenotypic coefficients of variation (GCV and PCV), heritability, and genetic advance in 40 geographically diverse wheat (Triticum aestivum L.) genotypes across three sowing environments (normal, late, and very late sowing). Pooled analysis of variance revealed highly significant differences among genotypes for all morphological, yield-attributing, and quality traits, indicating the presence of substantial genetic variability in the experimental material. PCV values were consistently higher than GCV values for all traits, though the narrow gap between them suggested a predominance of genetic control over environmental influence. Heritability estimates ranged from 63.37% (seed yield per plant) to 95.55% (iron content in seed), indicating strong genetic control for most traits. Genetic advance as a percentage of mean (GAM) was highest for 1000-seed weight (24.70%) and effective tillers per plant (21.36%), suggesting that these traits are governed predominantly by additive gene effects and can be effectively improved through simple phenotypic selection. Results indicated that traits such as days to maturity, zinc content, and seed yield per plant exhibited high heritability coupled with low GAM, suggesting significant non-additive gene action. These findings provide valuable insights for designing effective selection strategies in wheat breeding programmes aimed at improving yield and nutritional quality across variable agro-climatic conditions in India.

Water salinity and scarcity constitute major limitations to crop production in arid and semi-arid regions. Introduction of nutritious and stress-tolerant underutilized crops is a promising approach for dietary enrichment, cropping system diversification, remediation of marginal and degraded lands, and building climate resilience. The primary objectives of this study were to investigate the effect of water salinity and managed water-deficit stress on grain and fodder yield, identify multi-trait ideotypes, and validate the stability and genetic gain in finger millet ideotypes over a 2-year period. A total of 80 finger millet accessions were evaluated under fresh water (0 dS/m) and two saline irrigation water (6 and 10 dS/m) in Dubai during the 2020/2021 cropping season. Validation of a selected elite subset was conducted under a combination of optimum, salinity, and drought-stress regimes (0 dS/m, 6 dS/m, 10 dS/m, and 50% irrigation) during the 2021/2022 cropping season. Initial analysis showed a grain yield (GYLD) reduction of 87% under 10 dS/m saline irrigation water compared with the control, and the genotype-by-treatment (G × T) interaction revealed highly significant effects for GYLD. Using multi-trait genotype–ideotype distance index (MGIDI), 20 elite accessions were identified, demonstrating a remarkable increase in mean GYLD under high saline irrigation water, corresponding to a genetic gain of 167% over the reference population mean. Validation trials confirmed the success of the selection by showing a non-significant G × T for GYLD and dry fodder yield (DFYLD) across the four validation treatments, alongside a significant increase in heritability (H2) for GYLD from 0.60 to 0.78. Comparative analysis revealed that managed water-deficit stress was the most limiting factor for GYLD in the elite subset, causing an average loss of 42.7% compared to 20.4% under high saline water irrigation. However, DFYLD displayed exceptional stability across both saline water and water-deficit stress types. The comparative analysis presented in Venn diagrams ultimately identified a core group of stable, broadly adapted accessions, including IE 4028 and IE 4570, which are recommended as high- impact parental lines for combined stress tolerance. These findings establish a reliable selection framework for enhancing the climate-resilience of underutilized crops in marginal environments.

Phosphorus Starvation Tolerance 1 in rice (OsPSTOL1, known as Phosphorus uptake 1, Pup1) is a receptor-like cytoplasmic protein kinase that confers tolerance to phosphorus deficiency. The OsPSTOL1 gene possesses a Ser/Thr kinase and shows high amino-acid sequence similarity with the leaf rust receptor-like kinase (OsLrK10). We hypothesise that the putative wheat genes TaPSTOL1 and TaLrK10 have a common ancestral origin and that putative TaPSTOL1 diverged recently, acquiring new structural modifications and biological functions in the process. In this study, we identified all putative TaPSTOL1 homeologs and examined the evolutionary relationship between TaPSTOL1 and TaLrK10 in Triticum species. Our results indicate that the putative TaPSTOL1 diverged recently without possessing the amino-terminal domain, which is a typical characteristic of TaLrK10. We observed numerous conversion tracts between these two genes, and the substitution pattern of randomly selected amino acids indicates that dynamic selection pressures acted on both genes. The putative TaPSTOL1 shows high nucleotide diversity compared to TaLrK10 within Triticum species. Further, a multiple-sequence analysis reveals that the third exon of TaLrK10 appears to have been duplicated and diverged as a putative single-exon-based TaPSTOL1 in bread wheat. Overall, our comparative analysis indicates that both TaPSTOL1 and TaLrK10 appear to have diverged from a common ancestor, acquiring distinct structural organisations and biological functions.

[This corrects the article DOI: 10.3389/fpls.2026.1754820.].

Phosphorus (P) is a crucial nutrient for plants, but its deficiency can significantly reduce crop yields, especially in wheat. To understand the genetic basis of Phosphorus Use Efficiency (PUE) in wheat, we analyzed the gene expression patterns of plants under phosphorus stress. We identified and analyzed 1194 differentially expressed genes, constructing a network of these genes through cytoscape. We have extracted 26 hub genes from this network, which are key players in PUE. These hub genes are involved in various biological processes related to phosphorus uptake, transport and utilization, as revealed by KEGG pathway analysis. Our findings provide valuable insights into the genetic mechanisms underlying PUE in wheat and may contribute to the development of strategies for improving crop yields in phosphorus-deficient environments.

Impact of the green revolution genes on rice and wheat productivity under rainfed environments has been debated since past few decades. Here we made an attempt to assess the impact of two major green revolution genes Rht B1 and Rht D1 on grain yield under drought stress. A total of four recombinant inbred line (RIL) populations were analyzed for this objective including PBW343 × Muu, PBW343 × Kingbird, PBW343 × Kenyaswara and Jal 95.4.3 × Kachu/Kiritati/Kachu. These populations segregated for either or both the Rht gene alleles. Our results revealed an invariable non-association of tall/ dwarf alleles of Rht B1 and Rht D1 genes with grain yield under drought stress. Tightly linked sequence tags with Rht and Vrn genes were identified for future application in wheat breeding. A genetic linkage map of 1170 DArt-seq markers covering 2870 cM was constructed in Jal 95.4.3 × Ka-chu/Kiritati/Kachu RIL population and QTLs for yield related traits were identified. Study provides an insight for researchers involved in developing the next generation climate resilient wheat varieties that can cope well with rainfed/ drought prone en-vironments.

Editorial: Harnessing crop biodiversity and genomics assisted pre-breeding approaches for next generation climate-smart varieties, volume II

Paddy straw, which is produced after the harvest of rice, is a major agricultural waste in the world. Rice straw has a high C:N ratio and is more resistant to microbial degradation than other straws because its main constituents are cellulose and hemicelluloses encrusted by lignin. When paddy straw is burned, hazardous substances such as CO2, CH4, CO, and NO are released into the air as smoke (less than ten micrometer-sized particles). The rise in the burning of paddy straw has contributed to too many accidents and health issues in the general population residing in Haryana, Punjab, and Uttar Pradesh. These states are being urged by the National Green Tribunal (NGT) to generate money instead of burning paddy straw. Even though these Lignocellulosic materials might be beneficial, not much has been done with them. This overview covers the properties of rice straw and husks, the numerous procedures used to create valuable products, and various applications that may be made for them. These include energy generation, environmental adsorbents, building supplies, and specialist commodities.

White rust or white blister disease caused by oomycete fungi, [Albugo candida (Persoon) Roussal] is one of the major devastating fungal diseases of rapeseed (Brassica napus) mustard. The continuous emergence of new pathogenic races is responsible for the breaking down of the resistance in already existing resistant cultivars. So, for finding new resistant sources against the pathogen, molecular markers have become new tools. In the present study, validation of 29 simple sequence repeat (SSR) markers was done to know the presence or absence of resistance (R) genes against selected Brassica genotypes using PCR analysis. Marker trait association analysis and multiple regression analysis indicated a significant association of six markers, namely, At5g41560, Ni2BO3, BrgMS329, MB5, BRMS-017 and NI-F02a with the immune, highly resistant and moderately resistant Brassica cultivars. These molecular markers may be utilized for the identification of resistant genotypes against A. candida pathogens in rapeseed mustard.

Assessment of the efficiency of Agrobacterium tumefaciens mediated transformation in four bread wheat varieties was focused and upon optimization of experiments done to obtain tangible results. The four varieties, Fielder, Navojoa, Baj and Kachu/saul, were transformed with optimized protocols and randomly selected from a selection medium amalgamated with phosphinothricin (Glufosinate). Initially, the variety Fielder has proceeded with 36 different concentrations of synthetic auxins 2,4-D and picloram as 36 treatments. The treatment 30 (48 μg of 2,4-D and 64 μg of picloram) has shown higher efficiency and is comparable in terms of the three traits studied. Additionally, antioxidants and growth regulators were adjusted to obtain better results towards reasonable transformation frequency. Additional varieties were also tested and selected against the selectable marker PPT based on the optimization for the variety Fielder. Selected genotypes were subjected for gusA or Bar gene PCR amplification. The result revealed the frequency of transgenesis in the range of 60 to 70% with the varieties studied. However, the whole experiment needs further repetitions for confirmatory results. Transgenic genotypes of the Fielder variety showed moderate to strong GUS expression in leaves, anthers, seeds, seed coats, and roots compared to non-transgenic control plant tissues. PPT leaf painting assay showed the lack of necrosis on the painted area of leaves in transgenic genotypes compared to the non-transgenic ones.

Ug99 is a highly destructive race of stem rust fungus known as Puccinia graminis Pers. f. sp. tritici Eriks. E. Henn. (Pgt). To address this problem, the International Maize and Wheat Improvement Center, Mexico (CIMMYT) has extensively employed adult plant resistance (APR), which combines multiple genes that provide slow rusting resistance. CIMMYT’s advanced germplasm, “Diniza,” has proven to possess a good level of APR for the Ug99 race group. This study identified the genomic regions responsible for providing APR in the PBW343/Diniza RIL population. Study identified four quantitative trait loci (QTLs) that provide slow rusting APR on chromosomes 2B (QSr.cimm-2B), 3BS (QSr.cimm-3BP1 and QSr.cimm-3BP2), and 7DS (QSr.cimm-7D). These QTLs explained phenotypic variances of 17.0, 18, 8.9, and 11.6

Quinoa (Chenopodium quinoa Willd.), an Andean crop, is a facultative halophyte food crop recognized globally for its high nutritional value and plasticity to adapt to harsh conditions. We conducted a genome-wide association study on a diverse set of quinoa germplasm accessions. These accessions were evaluated for the following agronomic and biochemical traits: days to 50% flowering (DTF), plant height (PH), panicle length (PL), stem diameter (SD), seed yield (SY), grain diameter (GD), and thousand-grain weight (TGW). These accessions underwent genotyping-by-sequencing using the DNBSeq-G400R platform. Among all evaluated traits, TGW represented maximum broad-sense heritability. Our study revealed average SNP density of ≈ 3.11 SNPs/10 kb for the whole genome, with the lowest and highest on chromosomes Cq1B and Cq9A, respectively. Principal component analysis clustered the quinoa population in three main clusters, one clearly representing lowland Chilean accessions, whereas the other two groups corresponded to germplasm from the highlands of Peru and Bolivia. In our germplasm set, we estimated linkage disequilibrium decay to be ≈ 118.5 kb. Marker-trait analyses revealed major and consistent effect associations for DTF on chromosomes 3A, 4B, 5B, 6A, 7A, 7B and 8B, with phenotypic variance explained (PVE) as high as 19.15%. Nine associations across eight chromosomes were also found for saponin content with 20% PVE by qSPN5A.1. More QTLs were identified for PL and TGW on multiple chromosomal locations. We identified putative candidate genes in the genomic regions associated with DTF and saponin content. The consistent and major-effect genomic associations can be used in fast-tracking quinoa breeding for wider adaptation across marginal environments.

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.

Diseases adversely affect grain yield of crop plants. Leaf rust is a major disease of wheat. As race-specific resistance breaks down, introduction of newer sources of resistance often from older accessions is necessary. Linkage drag from the donor accessions adversely impacts grain yield. As a result, CIMMYT breeding effort has shifted to using durable resistance, also referred to as race non-specific host resistance, which allows slow rusting but maintains grain yield. One of the key genes for durable resistance is Lr67 and the resistant form of this gene is absent in CIMMYT elite lines. Hence, we have initiated efforts to convert the susceptible copy of Lr67 into its resistant form directly in these elite lines using gene editing. This would eliminate backcrossing and thus save time as well as eliminate linkage drag that would accompany the resistant copy of the gene if it were to be introgressed from an older accession. As first steps, we have isolated and sequenced the genomic copies from each of the A, B, and D genome of the Lr67 gene from three elite lines and an experimental line. Identification of more than 50 single nucleotide polymorphisms (SNPs) in the open reading frames (ORF) among these lines would be useful in designing the guide RNA molecules with precision. Further, we have streamlined genetic transformation of these elite lines, a prerequisite step for gene editing.

Orphan crops are indigenous and invariably grown by small and marginal farmers under subsistence farming systems. These crops, which are common and widely accepted by local farmers, are highly rich in nutritional profile, good for medicinal purposes, and well adapted to suboptimal growing conditions. However, these crops have suffered neglect and abandonment from the scientific community because of very low or no investments in research and genetic improvement. A plausible reason for this is that these crops are not traded internationally at a rate comparable to that of the major food crops such as wheat, rice, and maize. Furthermore, marginal environments have poor soils and are characterized by extreme weather conditions such as heat, erratic rainfall, water deficit, and soil and water salinity, among others. With more frequent extreme climatic events and continued land degradation, orphan crops are beginning to receive renewed attention as alternative crops for dietary diversification in marginal environments and, by extension, across the globe. Increased awareness of good health is also a major contributor to the revived attention accorded to orphan crops. Thus, the introduction, evaluation, and adaptation of outstanding varieties of orphan crops for dietary diversification will contribute not only to sustained food production but also to improved nutrition in marginal environments. In this review article, the concept of orphan crops vis-à-vis marginality and food and nutritional security is defined for a few orphan crops. We also examined recent advances in research involving orphan crops and the potential of these crops for dietary diversification within the context of harsh marginal environments. Recent advances in genomics coupled with molecular breeding will play a pivotal role in improving the genetic potential of orphan crops and help in developing sustainable food systems. We concluded by presenting a potential roadmap to future research engagement and a policy framework with recommendations aimed at facilitating and enhancing the adoption and sustainable production of orphan crops under agriculturally marginal conditions.

As one of the oldest fruit trees of the Arabian peninsula, other Middle-Eastern countries, and also North Africa, the date palm (Phoenix dactylifera L.), is highly significant for the economy of the region. Listed as part of UNESCO's Intangible Cultural Heritage of Humanity, the date palm is believed to be the first tree cultivated by human beings, and was probably first harvested for its fruit nearly 7,000 years ago. Initial research efforts in date palm genetics focused on understanding the genetic diversity of date palm germplasm collections and its phylogenetic history, both important prerequisites for plant improvement. Despite various efforts, the center of origin of the date palm is still unclear, although genomic studies suggest two probable domestication events: one in the Middle East and the other in North Africa, with two separate gene pools. The current review covers studies related to omics analyses that have sought to decipher the present genetic diversity of the date palm. With advances and cost reductions in sequencing technologies, rapid progress has been made in the past few years in date palm genomics research. Along with organellar genomes, several reference genomes of the date palm are now available. In addition, several genotypes have been re-sequenced, either to detect single nucleotide polymorphisms (SNPs), or to study domestication and identification of key genes/loci associated with important agronomic traits, such as sex, fruit color, and sugar composition. These genomics research progress has paved the way to perform fast-track and precise germplasm improvement processes in date palm. In this study, we review the advances made in the genetics and genomics of the date palm so as to strategize targeted crop improvement plans for marginal areas of the Middle Eastern peninsula, North Africa, and other parts of the world.

Resource depletion and agricultural pollution status in India and worldEconomic growth, population explosion and improvement in quality of life are accompanied with the environment and ecological tradeoffs.As an example, human pressure is compromising biodiversity loss despite continued international efforts, especially the Convention on Biological Diversity (CBD).According to an estimate, the cost of biodiversity loss and ecosystem degradation is in a range of 2 -4.5 trillion USD which is nearly 3.3-3.75% of global GDP (TEEB, 2008) [6] .Further estimates revealed that approximately 52 billion USD is being spent on biodiversity annually globally against an estimated annual financing requirement in the range of 150-440 billion USD (HLP, 2012) [8] .In the Indian context, a study estimated that country is spending nearly 2 billion USD annually on conservation of biodiversity, though requirement should be 15-45 billion USD/ year for continued efforts (BIOFIN 2015) [9] Human well-being depends on ecosystem services provided by biodiversity, such as agricultural pollination, water purification, flood protection, and carbon sequestration.These services are expected to be worth between USD 125 and USD 140 trillion (US) annually.According to estimates,