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Development of vitamin A-rich cereals can help in alleviating the widespread problem of vitamin A deficiency. We report here significant enhancement of kernel β-carotene in elite maize genotypes through accelerated marker-assisted backcross breeding. A favourable allele (543 bp) of the β-carotene hydroxylase (crtRB1) gene was introgressed in the seven elite inbred parents, which were low (1.4 µg/g) in kernel β-carotene, by using a crtRB1-specific DNA marker for foreground selection. About 90% of the recurrent parent genome was recovered in the selected progenies within two backcross generations. Concentration of β-carotene among the crtRB1-introgressed inbreds varied from 8.6 to 17.5 µg/g - a maximum increase up to 12.6-fold over recurrent parent. The reconstituted hybrids developed from improved parental inbreds also showed enhanced kernel β-carotene as high as 21.7 µg/g, compared to 2.6 µg/g in the original hybrid. The reconstituted hybrids evaluated at two locations possessed similar grain yield to that of original hybrids. These β-carotene enriched high yielding hybrids can be effectively utilized in the maize biofortification programs across the globe.

Malnutrition affects growth and development in humans and causes socio-economic losses. Normal maize is deficient in essential amino acids, lysine and tryptophan; and vitamin-A. Crop biofortification is a sustainable and economical approach to alleviate micronutrient malnutrition. We combined favorable alleles of crtRB1 and lcyE genes into opaque2 ( o2 )-based four inbreds viz . QLM11, QLM12, QLM13, and QLM14 using marker-assisted backcross breeding. These are parents of quality protein maize versions of two elite hybrids viz . Buland and PMH1, grown in India. Gene-based SSRs for o2 and InDel markers for crtRB1 and lcyE were successfully employed for foreground selection in BC 1 F 1 , BC 2 F 1 , and BC 2 F 2 generations. The recurrent parent genome recovery ranged from 88.9 to 96.0% among introgressed progenies. Kernels of pyramided lines possessed a high concentration of proA (7.14–9.63 ppm), compared to 1.05 to 1.41 ppm in the recurrent parents, while lysine and tryptophan ranged from 0.28–0.44% and 0.07–0.09%, respectively. The reconstituted hybrids (RBuland and RPMH1) showed significant enhancement of endosperm proA (6.97–9.82 ppm), tryptophan (0.07–0.09%), and lysine (0.29–0.43%), while grain yield was at par with their original versions. The dissemination of reconstituted hybrids holds significant promise to alleviate vitamin-A deficiency and protein-energy malnutrition in developing countries.

Maize ( Zea mays L.) is the leading cereal crop and staple food in many parts of the world. This study aims to develop nutrient-rich maize genotypes by incorporating crtRB1 and o2 genes associated with increased β-carotene, lysine, and tryptophan levels. UMI1200 and UMI1230, high quality maize inbreds, are well-adapted to tropical and semi-arid regions in India. However, they are deficient in β-carotene, lysine, and tryptophan. We used the concurrent stepwise transfer of genes by marker-assisted backcross breeding (MABB) scheme to introgress crtRB1 and o2 genes. In each generation (from F 1 , BC 1 F 1 –BC 3 F 1 , and ICF 1 –ICF 3 ), foreground and background selections were carried out using gene-linked ( crtRB1 3′TE and umc1066) and genome-wide simple sequence repeats (SSR) markers. Four independent BC 3 F 1 lines of UMI1200 × CE477 (Cross-1), UMI1200 × VQL1 (Cross-2), UMI1230 × CE477 (Cross-3), and UMI1230 × VQL1 (Cross-4) having crtRB1 and o2 genes and 87.45–88.41% of recurrent parent genome recovery (RPGR) were intercrossed to generate the ICF 1 -ICF 3 generations. Further, these gene pyramided lines were examined for agronomic performance and the β-carotene, lysine, and tryptophan contents. Six ICF 3 lines (DBT-IC-β 1 σ 4 -4-8-8, DBT-IC-β 1 σ 4 -9-21-21, DBT-IC-β 1 σ 4 -10-1-1, DBT-IC-β 2 σ 5 -9-51-51, DBT-IC-β 2 σ 5 -9-52-52 and DBT-IC-β 2 σ 5 -9-53-53) possessing crtRB1 and o2 genes showed better agronomic performance (77.78–99.31% for DBT-IC-β 1 σ 4 population and 85.71–99.51% for DBT-IC-β 2 σ 5 population) like the recurrent parents and β-carotene (14.21–14.35 μg/g for DBT-IC-β 1 σ 4 and 13.28–13.62 μg/g for DBT-IC-β 2 σ 5 ), lysine (0.31–0.33% for DBT-IC-β 1 σ 4 and 0.31–0.34% for DBT-IC-β 2 σ 5 ), and tryptophan (0.079–0.082% for DBT-IC-β 1 σ 4 and 0.078–0.083% for DBT-IC-β 2 σ 5 ) levels on par with that of the donor parents. In the future, these improved lines could be developed as a cultivar for various agro-climatic zones and also as good genetic materials for maize nutritional breeding programs.

Traditional yellow maize though contains high kernel carotenoids, the concentration of provitamin A (proA) is quite low (<2 μg/g), compared to recommended level (15 μg/g). It also possesses poor endosperm protein quality due to low concentration of lysine and tryptophan. Natural variant of (β ) and ( ε ) cause significant enhancement of proA concentration, while recessive allele, ( ) enhances the level of these amino acids. Development of biofortified maize enriched in proA, lysine and tryptophan thus holds significance in alleviation of micronutrient malnutrition. In the present study, marker-assisted stacking of and was undertaken in the genetic background of four maize hybrids (HQPM1, HQPM4, HQPM5, and HQPM7) popularly grown in India. HP704-22 and HP704-23 were used as donors, while four elite QPM parents viz., HKI161, HKI163, HKI193-1, and HKI193-2 were used as recipients. showed severe segregation distortion, while segregated as per the expectation. Recovery of recurrent parent genome (RPG) among selected backcross progenies ranged from 89 to 93%. Introgressed progenies possessed high concentration of proA (7.38-13.59 μg/g), compared to 1.65-2.04 μg/g in the recurrent parents. The reconstituted hybrids showed an average of 4.5-fold increase in proA with a range of 9.25-12.88 μg/g, compared to original hybrids (2.14-2.48 μg/g). Similar plant-, ear-, and grain- characteristics of improved versions of both inbreds and hybrids were observed when evaluated with their respective original versions. Mean lysine (0.334%) and tryptophan (0.080%) of the improved hybrids were with the original versions (lysine: 0.340%, tryptophan: 0.083%). Improved hybrids also possessed similar grain yield potential (6,301-8,545 kg/ha) with their original versions (6,135-8,479 kg/ha) evaluated at two locations. This is the first study of staking -, -, and -, favorable alleles in single genetic background. The improved inbreds can be effectively used as potential donor for independent and/or simultaneous introgression of , and in the future breeding programme. These biofortified maize hybrids, rich in proA, lysine and tryptophan will hold great promise for nutritional security.

Waxy maize rich in amylopectin has emerged as a preferred food. However, waxy maize is poor in lysine and tryptophan, deficiency of which cause severe health problems. So far, no waxy hybrid with high lysine and tryptophan has been developed and commercialized. Here, we combined recessive waxy1 ( wx1 ) and opaque2 ( o2 ) genes in the parental lines of four popular hybrids (HQPM1, HQPM4, HQPM5, and HQPM7) using genomics-assisted breeding. The gene-based markers, wx-2507F/RG and phi057 specific for wx1 and o2 , respectively were successfully used to genotype BC 1 F 1 , BC 2 F 1 and BC 2 F 2 populations. Background selection with > 100 SSRs resulted in recovering > 94% of the recurrent parent genome. The reconstituted hybrids showed 1.4-fold increase in amylopectin (mean: 98.84%) compared to the original hybrids (mean: 72.45%). The reconstituted hybrids also showed 14.3% and 14.6% increase in lysine (mean: 0.384%) and tryptophan (mean: 0.102%), respectively over the original hybrids (lysine: 0.336%, tryptophan: 0.089%). Reconstituted hybrids also possessed similar grain yield (mean: 6248 kg/ha) with their original versions (mean: 6111 kg/ha). The waxy hybrids with high lysine and tryptophan assume great significance in alleviating malnutrition through sustainable and cost-effective means. This is the first report of development of lysine and tryptophan rich waxy hybrids using genomics-assisted selection.

Harnessing the benefits of plant–microbe interactions towards better nutrient mobilization and plant growth is an important challenge for agriculturists globally. In our investigation, the focus was towards analyzing the soil–plant–environment interactions of cyanobacteria-based formulations ( Anabaena – Nostoc consortium, BF1–4 and Anabaena – Trichoderma biofilm, An–Tr) as inoculants for ten maize genotypes (V1–V10). Field experimentation using seeds treated with the formulations illustrated a significant increase of 1.3- to 3.8-fold in C–N mobilizing enzyme activities in plants, along with more than five- to six-fold higher values of nitrogen fixation in rhizosphere soil samples. An increase of 22–30% in soil available nitrogen was also observed at flag leaf stage, and 13–16% higher values were also recorded in terms of cob yield of V6 with An-Tr biofilm inoculation. Savings of 30 kg N ha −1  season −1 was indicative of the reduced environmental pollution, due to the use of microbial options. The use of cyanobacterial formulations also enhanced the economic, environmental and energy use efficiency. This was reflected as 37–41% reduced costs lowered GHG emission by 58–68 CO 2 equivalents and input energy requirement by 3651–4296 MJ, over the uninoculated control, on hectare basis. This investigation highlights the superior performance of these formulations, not only in terms of efficient C–N mobilization in maize, but also making maize cultivation a more profitable enterprise. Such interactions can be explored as resource-conserving options, for future evaluation across ecologies and locations, particularly in the global climate change scenario. Graphic abstract

Sweet corn has gained worldwide popularity. Traditional sweet corn possesses low concentration of essential nutrients such as lysine (0.15–0.25%), tryptophan (0.03–0.04%) and provitamin-A (proA 3–4 ppm), and deficiency leads to serious health problems in humans. Here, stacking of shrunken2 (sh2), opaque2 (o2), lycopene epsilon cyclase (lcyE) and β‐carotene hydroxylase (crtRB1) genes were undertaken in the parents of four hybrids viz., APQH1, APHQ4, APHQ5 and APHQ7 using marker-assisted backcross breeding (MABB). Gene-linked markers (umc2276 and umc1320) for sh2, while gene-based markers for o2 (umc1066 and phi057), lcyE (5′TE-InDel) and crtRB1 (3′TE-InDel), were used for genotyping in BC1F1, BC2F1 and BC2F2. Selected backcross progenies showed high recovery of recurrent parent genome (92.4–97.7%). The reconstituted sweet corn hybrids possessed significantly high lysine (0.390%), tryptophan (0.082%) and proA (21.14 ppm), coupled with high kernel sweetness (brix 18.96%). The improved sweet corn hybrids had high cob yield (12.22–15.33 t/ha) across three environments. These newly developed biofortified sweet corn hybrids possess great significance in providing balanced nutrition. This is the first report of combining sh2, o2, lcyE and crtRB1 genes for enrichment of sweet corn hybrids with multiple essential nutrients.

Sweet corn is popular worldwide as vegetable. Though large numbers of sugary1 (su1)-based sweet corn germplasm are available, allelic diversity in su1 gene encoding SU1 isoamylase among diverse maize inbreds has not been analyzed. Here, we characterized the su1 gene in maize and compared with allied species. The entire su1 gene (11,720 bp) was sequenced among six mutant (su1) and five wild (Su1) maize inbreds. Fifteen InDels of 2–45 bp were selected to develop markers for studying allelic diversity in su1 gene among 19 mutant- (su1) and 29 wild-type (Su1) inbreds. PIC ranged from 0.15 (SU-InDel7) to 0.37 (SU-InDel13). Major allele frequency varied from 0.52 to 0.90, while gene diversity ranged from 0.16 to 0.49. Phylogenetic tree categorized 48 maize inbreds in two clusters each for wild- type (Su1) and mutant (su1) types. 44 haplotypes of su1 were observed, with three haplotypes (Hap6, Hap22 and Hap29) sharing more than one genotype. Further, comparisons were made with 23 orthologues of su1 from 16 grasses and Arabidopsis. Maize possessed 15–19 exons in su1, while it was 11–24 exons among orthologues. Introns among the orthologues were longer (77–2206 bp) than maize (859–1718 bp). SU1 protein of maize and orthologues had conserved α-amylase and CBM_48 domains. The study also provided physicochemical properties and secondary structure of SU1 protein in maize and its orthologues. Phylogenetic analysis showed closer relationship of maize SU1 protein with P. hallii, S. bicolor and E. tef than Triticum sp. and Oryza sp. The study showed that presence of high allelic diversity in su1 gene which can be utilized in the sweet corn breeding program. This is the first report of comprehensive characterization of su1 gene and its allelic forms in diverse maize and related orthologues.

Domain membrane protein ( DMP ) gene is one of the key genes regulating in vivo haploid production in maize. Here, full-length sequence (931 bp) of DMP gene was sequenced in five mutant and five wild-type maize inbreds to study allelic variation. Two SNPs viz., T to C (SNP1) and G to A (SNP2) that distinguished wild-type and mutant- allele of DMP gene, converted methionine to threonine and alanine to threonine at positions 44 and 87, respectively. Two breeder-friendly PCR-based markers (DMP_SNP_TC and DMP_SNP_GA) specific to SNP1 and SNP2 were developed. These markers identified four haplotypes, viz., Hap-DMP-TG , Hap-DMP-CG , Hap-DMP-TA , and Hap-DMP-CA among a set of 48 diverse maize inbreds. Both SNP1 and SNP2 were present in DUF679_motif-2 and DUF679_motif-1, respectively and were conserved among maize and its paralogues, hence resulting in altered protein. Analysis with 11 paralogues of maize showed high similarity with DMP gene. Comparison with 11 paralogues revealed that maize DUF679 protein of DMP gene was more similar to dmp_Zm_Zm00001eb110420 paralogue . Gene structure analysis showed that most of the DMP genes have single exon. The breeder-friendly markers developed in the present study can be utilized in marker-assisted introgression of DMP gene to develop new haploid inducer lines in maize. This is the first report on identification of novel SNP differentiating the wild-type and mutant allele of DMP gene, besides comprehensive molecular characterization of the DMP gene in maize and its paralogues.

Adzuki bean, an underutilized grain legume, has a significant potential for enhancing food and nutritional security. The main obstacles to developing new cultivars and promoting the adzuki bean as a mainstream pulse crop are a lack of awareness about its potential and insufficient information on crop its genetic diversity. Here, we aimed to explore the untapped potential of adzuki bean germplasm by evaluating its agro-morphological traits and diversity at the molecular level and also to identify trait-specific germplasm by utilizing 100 adzuki bean accessions conserved in the Indian National Genebank. Significant variations was recorded for the morphological traits and identified promising accessions exhibiting desirable traits, such as early flowering (IC341945, EC340257 and EC340283), number of primary branches (IC341945 and IC469175), number of clusters per plant (EC000264, IC167611 and IC341939), number of pods per plant (IC469175, EC34264, EC000264), early maturity (EC340283; EC120460; IC341941) and number of seeds per pod (EC340240, IC455396 and IC341955). Molecular characterization of diverse accessions using 22 polymorphic SSR markers identified a total of 50 alleles, with a mean of 2.27 alleles per loci. The polymorphic information content (PIC) ranged from 0.03 to 0.46, indicating informativeness of markers in distinguishing diverse accessions. Further, the gene diversity among the accessions ranged from 0.03 to 0.57 with a mean of 0.19. Population structure analysis grouped the accessions into three genetic groups, supported by Principal Coordinate Analysis (PCoA) and a phylogenetic tree. Additionally, Analysis of Molecular Variance (AMOVA) confirmed a substantial genetic diversity among the adzuki bean accessions. Thus, the combined assessment of agro-morphological traits and molecular markers effectively distinguished adzuki bean accessions and provided valuable insights in understanding untapped variation at both morphological and molecular levels. The promising accessions identified in the study hold potential for integration into legume improvement programs through introgression breeding, contributing to the development of adzuki bean varieties with target trait.