Explore the vast range of titles available.

Background Grain amaranth has recently gained global attention as a promising crop alternative to traditional cereals due to its nutritional value and adaptability to various growing conditions. Although gene banks conserve extensive collections of amaranth germplasm, the genomic and phenotypic characterization of these resources is limited, which hinders their full utilization in breeding programs. A major challenge is the lack of high-throughput genotyping assays essential for comprehensive genomic characterization and trait mapping. High-density SNP arrays have become standard tools for genome-wide analysis across multiple loci, enabling molecular breeding across a range of crop species. Results In this study, we developed a 64 K high-throughput SNP genotyping array named “AmahySNP”, using Affymetrix ® Axiom ® technology. The array contains 64,069 high-density SNPs distributed across both genic (55.17%) and non-genic (44.83%) regions of the Amaranthus hypochondriacus genome. The genic region includes 8,879 genes, which consist of 4,830 single-copy genes and 4,049 multi-copy genes distributed across 16 scaffolds. These genes cover various functional regions, including exons (10.5%), introns (40.1%), 5’UTRs (1.6%), and 3’UTRs (2.9%), respectively. The AmahySNP array was effectively utilized for population structure analysis, genetic diversity studies, core development, and genome wide association studies (GWAS) in amaranth germplasm. A representative core set of 112 accessions was identified, which includes two released varieties (Annapurna and Suvarna) and 100 diverse accessions from 12 different regions, representing 12% of the total 917 accessions evaluated. Phylogenetic analysis revealed three major genetic clusters, independent of their geographical origins. GWAS conducted using 22,763 polymorphic SNPs from 540 genotypes identified 13 novel loci associated days to flowering (DTF) trait, seven of which were located within annotated genes. Conclusions The AmahySNP 64 K SNP chip a valuable genomic tool for amaranth research and breeding with a strong potential to accelerate its genetic improvement. It enables high-throughput genotyping for a wide range of applications, including GWAS and other genomic studies, and will significantly advance the exploration of natural genetic variations. Ultimately, this resource will empower amaranth breeders to develop improved amaranth cultivars with enhanced crop yield, resilience, and nutritional quality, contributing to global food security and sustainable agriculture.

Vigna stipulacea (Lam.) Kuntz., commonly known as Minni payaru is an underutilized legume species and has a great potential to be utilized as food crop. To evaluate and select the best germplasm to be harnessed in the breeding programme, we assessed the genetic diversity of V . stipulacea (94 accessions) conserved in the Indian National Genebank, based on morphological traits and microsatellite markers. Significant variation was recorded for the morphological traits studied. Euclidean distance using UPGMA method grouped all accessions into two major clusters. Accessions were identified for key agronomic traits such as, early flowering (IC331436, IC251436, IC331437); long peduncle length (IC553518, IC550531, IC553557, IC553540, IC550532, IC553564); and more number of seeds per pod (IC553529, IC622865, IC622867, IC553528). To analyse the genetic diversity among the germplasm 33 SSR primers were used anda total of 116 alleles were detected. The number of alleles varied from two to seven, with an average of 3.52 per loci. The polymorphic information content values varied from 0.20 to 0.74, with a mean of 0.40. The high number of alleles per locus and the allelic diversity in the studied germplasm indicated a relatively wider genetic base of V . stipulacea . Phylogenetic analysis clustered accessions into seven clades. Population structure analysis grouped them into five genetic groups, which were partly supported by PCoA and phylogenetic tree. Besides, PCoA and AMOVA also decoded high genetic diversity among the V . stipulacea accessions. Thus, morphological and microsatellite markers distinguished V . stipulacea accessions and assessed their genetic diversity efficiently. The identified promising accessions can be utilized in Vigna improvement programme through introgression breeding and/or can be used for domestication and enhanced utilization of V . stipulacea .

Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters in one place. The AGRDB database contains functionally annotated gene information with their sequence details, genic as well as genomic SSRs with their three sets of primers, transcription factors classified into different families with their sequence information and annotation details, putative miRNAs with their family, sequences, and targeted gene details, transporter genes with their superfamily, trans-membrane domain details, and details of genic as well as nongenic SNPs with 3′ and 5′ flanking sequence information of five amaranth species. A database search can be performed using the gene ID, sequence ID, sequence motif, motif repeat, family name, annotation keyword, scaffold or chromosome numbers, etc. This resource also includes some useful tools, including JBrowse for the visualization of genes, SSRs, SNPs, and TFs on the respective amaranth genomes and BLAST search to perform a BLAST search of the user’s query sequence against the amaranth genome as well as protein sequences. The AGRDB database will serve as a potential platform for genetic improvement and characterization of this futuristic crop. The AGRDB database will be accessible via the link: http://www.nbpgr.ernet.in:8080/AmaranthGRD/.

The medicinal plant Abrus precatorius L. was traditionally used in the Siddha and Ayurvedic systems of medicine in India. The Indian center of origin holds a vast variability in its seed color. The objective of this study was to assess the total monomeric anthocyanin, flavonol, as well as the antioxidative potential, protein content and ash content among the accessions. A total of 99 accessions conserved in the Indian National Genebank were used in this study. The methods used for the estimation of total monomeric anthocyanin, flavonol, as well as the antioxidative potential, protein content and ash content were the pH differential method, Oomah method, Ferric Reducing Antioxidant Potential, Dumas method and gravimetric method, respectively. The completely black colored accession was recorded with highest total monomeric anthocyanin (51.95 mg/100 g of cyanidin 3-glucoside equivalent) and flavonol content (66.41 mg/g of quercetin equivalent). Red + black colored accessions have recorded the maximum value with respect to antioxidants (14.18 mg/g of gallic acid equivalent). The highest amount of protein content was found in a completely white colored accession (20.67%) and the maximum ash content was recorded in red + black colored accession (4.01%). The promising accessions identified can be used by pharmaceutical companies in drug development and in curing degenerative diseases.

Lentil ( Lens culinaris Medik.) is one of the major cool-season pulse crops worldwide. Its increasing demand as a staple pulse has led to the unlocking of diverse germplasm collections conserved in the genebanks to develop its superior varieties. The Indian National Genebank, housed at the Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India, currently has 2,324 accessions comprising 1,796 indigenous and 528 exotic collections. This study was conducted to unveil the potential of lentil germplasm by assessing its agro-morphological characteristics and diversity, identifying trait-specific germplasm, and developing a core set. The complete germplasm set was characterized for two years, i.e., 2017–2018 and 2018–2019, and data were recorded on 26 agro-morphological traits. High phenotypic variability was observed for nine quantitative and 17 qualitative traits. A core set comprising 170 accessions (137 Indian and 33 exotic) was derived based on the characterization data as well as geographical origin using a heuristic method and PowerCore software. This core set was found to be sufficiently diverse and representative of the entire collection based on the comparison made using Shannon–Weaver diversity indices and χ 2 test. These results were further validated by summary statistics. The core set displayed high genetic diversity as evident from a higher coefficient of variance in comparison to the entire set for individual traits and overall Shannon–Weaver diversity indices (entire: 1.054; core: 1.361). In addition, the total variation explained by the first three principal components was higher in the core set (70.69%) than in the entire collection (68.03%). Further, the conservation of pairwise correlation values among descriptors in the entire and core set reflected the maintenance of the structure of the whole set. Based on the results, this core set is believed to represent the entire collection, completely. Therefore, it constitutes a potential set of germplasm that can be used in the genetic enhancement of lentils.

Seed health testing, using the blotter method, revealed some fungal growth on the seed surface of one accession of Indian trumpet flower/Broken bones tree (Oroxylum indicum (L.) Kurz) collected from Kokrajhar, Assam, India. The fungus was identified as Diaporthe phaseolorum (Cooke & Ellis) Sacc. based on morphological characters. Later, the identity was re-confirmed by DNA sequencing using ITS gene sequencing (NCBI Sequence Id: MT154253.1) and a large subunit of rRNA (NCBI Sequence Id: OL798081.1). Literature reveals that D. phaseolorum is a destructive pathogen causing severe yield losses in various host crops. However, detection of D. phaseolorum in Indian trumpet flower seed followed by pathogenicity on its seedlings confirms that O. indicum is a new host record. Being a destructive pathogen of several other crops, such as seed decay and stem canker in soybean, it may pose a serious threat to future cultivation of this herbal plant.

The genus Vigna has several crop species that could be used to feasibly address nutritional security challenges in the subtropical and tropical regions of the world, particularly in climate-changing scenarios. Wild taxa of Vigna are a source of economically important traits and need to be studied. Out of the 34 wild Vigna species reported in India, 928 indigenous accessions belonging to 19 wild Vigna are conserved in India’s National Genebank (INGB) housed at the National Bureau of Plant Genetic Resources, New Delhi. Geospatial mapping has identified diversity-rich areas and the Western Ghats region exhibits the highest Shannon diversity values (H = 1.65–3.0). Using the complementarity procedure, six diversity hotspots were identified for the 34 wild Vigna, and these require utmost priority for exploration and germplasm collection. Due to the meagre amount of information available for wild Vigna, the BioClim model was used to successfully predict the Idukki district of Kerala as a suitable site for germplasm-collecting expeditions. Coastal areas identified as rich in twelve wild taxa, V. bourneae, V. dalzelliana, V. marina, V. sublobata, V. subramaniana, V. vexillata, V. stipulacea, V. trilobata, and V. trinervia, require immediate attention to protect hotspots as well as to collect accessions from these areas for ex situ conservation. A hotspot in the protected forest of Anshi National Park and Bhagwan Mahavira Wildlife Sanctuary was identified as an ideal spot for possible in situ conservation of V. konkanensis, V silvestris, and V. sublobata. The 15 wild Vigna species do not have representation in the INGB, and 11 Vigna species have been identified as endemic species to India. Priority needs to be given to these species for focussed exploration and germplasm collection. This paper discusses the future focus on explorations to be carried out for the collection of the germplasm of wild Vigna species.

Background Kala bhat (Black soybean) is an important legume crop in Uttarakhand state, India, due to its nutritional and medicinal properties. In the current study, the genetic variabilities present in Kala bhat were estimated using SSR markers and its variability was compared with other improved soybean varieties cultivated in Uttarakhand state, India. Results Seventy-five genotypes cultivated in different districts of Uttarakhand were collected, and molecular analysis was done using 21 SSR markers. A total of 60 alleles were amplified with an average of 2.85 alleles per locus. The mean value of gene diversity and PIC was estimated to be 0.43 and 0.36, respectively. The unrooted phylogenetic tree grouped soybean genotypes into three major clusters, where, yellow seed coat (improved varieties) genotypes were grouped in one cluster, while reddish brown (improved varieties) and Kala bhat showed intermixing. Population structure divided the soybean genotypes into six different populations. AMOVA analysis showed 12% variance among the population, 66% variance among individual and 22% variance was observed within individuals. Principal Coordinate Analysis (PCoA) also showed that yellow seed coat genotypes were grouped in one cluster, whereas, the Kala bhat showed scattered distribution and few genotypes of Kala bhat showed grouping with red and yellow genotypes. Conclusions The different genetic diversity parameters used in the present study indicate that Kala bhat genotypes were more diverse than the yellow seed coat and brown seed coat colour genotypes. Therefore, Kala bhat genotypes can be a good source for the soybean breeding programme due to its better genetic diversity as well as its medicinal properties.

Micronutrient malnutrition or hidden hunger is a serious challenge toward societal well-being. Vigna stipulacea (Lam.) Kuntz (known locally as Minni payaru ), is an underutilized legume that has the potential to be a global food legume due to its rich nutrient profile. In the present study, 99 accessions of V. stipulacea were tested for iron (Fe), zinc (Zn), calcium (Ca), protein, and phytate concentrations over two locations for appraisal of stable nutrient-rich sources. Analysis of variance revealed significant effects of genotype for all the traits over both locations. Fe concentration ranged from 29.35–130.96 mg kg –1 whereas Zn concentration ranged from 19.44 to 74.20 mg kg –1 across both locations. The highest grain Ca concentration was 251.50 mg kg –1 whereas the highest grain protein concentration was recorded as 25.73%. In the case of grain phytate concentration, a genotype with the lowest value is desirable. IC622867 (G-99) was the lowest phytate containing accession at both locations. All the studied traits revealed highly significant genotypic variances and highly significant genotype × location interaction though less in magnitude than the genotypic variance. GGE Biplot analysis detected that, for grain Fe, Zn, and Ca concentration the ‘ideal’ genotypes were IC331457 (G-75), IC331610 (G-76), and IC553564 (G-60), respectively, whereas for grain protein concentration IC553521 (G-27) was the most “ideal type.” For phytate concentration, IC351407 (G-95) and IC550523 (G-99) were considered as ‘ideal’ and ‘desirable,’ respectively. Based on the desirability index, Location 1 (Kanpur) was identified as ideal for Fe, Zn, Ca, and phytate, and for grain protein concentration, Location 2 (New Delhi) was the ideal type. A significant positive correlation was detected between grain Fe as well as grain Zn and protein concentration considering the pooled analysis over both the locations where as a significant negative association was observed between phytate and protein concentration over the locations. This study has identified useful donors and enhanced our knowledge toward the development of biofortified Vigna cultivars. Promoting domestication of this nutrient-rich semi-domesticated, underutilized species will boost sustainable agriculture and will contribute toward alleviating hidden hunger.