Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.

Globally, about 20% of calories (energy) come from wheat. In some countries, it is more than 70%. More than 2 billion people are at risk for zinc deficiency and even more, people are at risk of iron deficiency, nearly a quarter of all children underage group of 5 are physically and cognitively stunted, and lack of dietary zinc is a major contributing factor. Biofortified wheat with elevated levels of zinc and iron has several potential advantages as a delivery vehicle for micronutrients in the diets of resource-poor consumers who depend on cereal-based diets. The conventional breeding strategies have been successful in the introduction of novel alleles for grain Zn and Fe that led to the release of competitive Zn enriched wheat varieties in South Asia. The major challenge over the next few decades will be to maintain the rates of genetic gains for grain yield along with increased grain Zn/Fe concentration to meet the food and nutritional security challenges. Therefore, to remain competitive, the performance of Zn-enhanced lines/varieties must be equal or superior to that of current non-biofortified elite lines/varieties. Since both yield and Zn content are invisible and quantitatively inherited traits except few intermediate effect QTL regions identified for grain Zn, increased breeding efforts and new approaches are required to combine them at high frequency, ensuring that Zn levels are steadily increased to the required levels across the breeding pipelines. The current review article provides a comprehensive list of genomic regions for enhancing grain Zn and Fe concentrations in wheat including key candidate gene families such NAS, ZIP, VLT, ZIFL, and YSL. Implementing forward breeding by taking advantage of the rapid cycling trait pipeline approaches would simultaneously introgress high Zn and Fe QTL into the high Zn and normal elite lines, further increasing Zn and Fe concentrations.

Utilization of “hidden genes” from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from ‘A’ genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids. Hybrids developed from recurrent parents were used as checks to compare the performance of 318 hybrids developed by hybridizing alien introgression lines with PMS17A. Seventeen hybrids expressed a significant increase in yield and its component traits over check hybrids. These 17 hybrids were re-evaluated in large-size replicated plots. Of these, four hybrids, viz., ILH299, ILH326, ILH867 and ILH901, having introgressions from O. rufipogon and two hybrids (ILH921 and ILH951) having introgressions from O. nivara showed significant heterosis over parental introgression line, recurrent parents and check hybrids for grain yield-related traits. Alien introgressions were detected in the lines taken as male parents for developing six superior hybrids, using a set of 100 polymorphic simple sequence repeat (SSR) markers. Percent introgression showed a range of 2.24 from in O. nivara to 7.66 from O. rufipogon. The introgressed regions and their putative association with yield components in hybrids is reported and discussed.

Rice is one of the most important crops in the world. The wild species of rice are expected to have novel beneficial alleles that have been lost from cultivated rice during the process of domestication. Therefore, wild species could be the potential source to induce lost genetic diversity in cultivated rice. Serving as an important reservoir of novel genes/QTLs, wild species, in general, are better adapted to different ecologies and can tolerate many biotic and abiotic stresses. Despite that, only a few wild species are studied and extensive characterization both at the molecular and morphological level is yet to be achieved. Several agronomically important genes/QTLs for improving biotic and abiotic stresses, resistance, productivity and grain quality traits were identified from AA genome donor wild species and were tagged with breeder friendly molecular markers for their transfer to elite genetic backgrounds. The present review provides information on the important wild rice species harbouring genes/QTLs for agriculturally important traits and their successful utilization in rice breeding programmes.

To sustainably increase wheat yield to meet the growing world population’s food demand in the face of climate change, Conservation Agriculture (CA) is a promising approach. Still, there is a lack of genomic studies investigating the genetic basis of crop adaptation to CA. To dissect the genetic architecture of 19 morpho-physiological traits that could be involved in the enhanced adaptation and performance of genotypes under CA, we performed GWAS to identify MTAs under four contrasting production regimes viz., conventional tillage timely sown (CTTS), conservation agriculture timely sown (CATS), conventional tillage late sown (CTLS) and conservation agriculture late sown (CALS) using an association panel of 183 advanced wheat breeding lines along with 5 checks. Traits like Phi2 (Quantum yield of photosystem II; CATS:0.37, CALS: 0.31), RC (Relative chlorophyll content; CATS:55.51, CALS: 54.47) and PS1 (Active photosystem I centers; CATS:2.45, CALS: 2.23) have higher mean values in CA compared to CT under both sowing times. GWAS identified 80 MTAs for the studied traits across four production environments. The phenotypic variation explained (PVE) by these QTNs ranged from 2.15 to 40.22%. Gene annotation provided highly informative SNPs associated with Phi2, NPQ (Quantum yield of non-photochemical quenching), PS1, and RC which were linked with genes that play crucial roles in the physiological adaptation under both CA and CT. A highly significant SNP AX94651261 (9.43% PVE) was identified to be associated with Phi2, while two SNP markers AX94730536 (30.90% PVE) and AX94683305 (16.99% PVE) were associated with NPQ. Identified QTNs upon validation can be used in marker-assisted breeding programs to develop CA adaptive genotypes.

Understanding genetic diversity and population structure is crucial for strategizing and enhancing breeding efficiency. Wheat, a globally cultivated crop, is a significant source of daily calories for humans. To overcome challenges such as extreme climatic fluctuations, stagnant yields, and diminishing genetic variation, it is essential to develop diverse germplasms with new alleles. Triticum sphaerococcum, an underutilized ancient hexaploid wheat species, shows promise for contributing beneficial alleles. However, the genetic diversity of its germplasms remains unstudied. This is the first report where we have examined the genetic diversity and population structure of 116 T. sphaerococcum accessions using a 35 K SNP Array. The objective of this study is to apply these findings to improve wheat breeding programs. Analysis of the population’s genetic structure identified four potential subpopulations, which was supported by principal coordinate analysis. Allele neutrality tests showed an abundance of intermediate genotypes, suggesting that many beneficial alleles are maintained through balancing selection. Among the three subgenomes, subgenome B exhibited the highest genetic diversity. AMOVA (Analysis of Molecular Variance) revealed significant variation both among (35%) and within (65%) the four subpopulations. The high genetic differentiation between subpopulations was corroborated by a moderate level of haploid migrant numbers (Nm = 1.286), indicating sufficient gene flow. SP4 emerged as the most diverse subpopulation, showing the highest values for allelic pattern indices due to its larger size and higher percentage of polymorphic loci. The D subgenome displayed a faster linkage disequilibrium (LD) decay rate compared to the A and B subgenomes. Haplotype block analysis identified 260 haplotype blocks of varying sizes distributed across the genome. This research demonstrates that Indian dwarf wheat accessions, sourced from three distinct gene banks and local collections, possess considerable genetic diversity. These germplasm collections offer valuable opportunities to investigate their unexplored genetic potential. They can be utilized in wheat improvement initiatives to tackle both present and future breeding challenges. Furthermore, these accessions can introduce new alleles to broaden the genetic base of modern wheat varieties, enhancing their overall diversity.