Annapurna Chitikineni

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Peanut ( Arachis hypogaea L.) is a globally significant leguminous oil crop. Here we present telomere-to-telomere genome assemblies for two diploid and four tetraploid peanut varieties, resulting in high-quality reference genomes, showing that the complex activities of transposable elements, chromosomal rearrangements and centromere expansions within subgenomes collectively contribute to the asymmetrical evolution of the tetraploid genome, and unique structural variants in the four tetraploid peanut varieties provide clear evidence of domestication. Population analyses of 521 peanut accessions revealed asymmetric selection events between subgenomes during breeding, and genome-wide association studies identified candidate genes linked to oil content, seed size and weight, kernel dehydration rate, and arachidic acid content. In addition, transcriptomic and metabolomic analyses revealed enhanced activity in lipidomic and anthocyanin biosynthetic pathways during seed development. These comprehensive findings provide insights into genome organization, evolutionary dynamics and phenotypic differentiation across peanut varieties that could inform future peanut breeding and improvement strategies.

Lipoxygenases (LOXs) play vital roles in plant growth and defense. In this study, through genomic and molecular analyses, we discover a major LOX gene (LOX-A4) differentially expressed in Triticum urartu (Tu), the diploid progenitor of A subgenome in polyploid wheat. Compared to Tu accessions carrying wild type gene (LOX-A4^W), those bearing mutant allele (LOX-A4^m) show better growth but lower stress tolerance. These differences concur with a wider geographical distribution of LOX-A4^m accessions than LOX-A4^W materials in the Fertile Crescent. Interestingly, only mutant LOX-A4 alleles are detected in 3,516 worldwide tetraploid and hexaploid wheat lines; restoring LOX-A4^W expression in common wheat inhibits growth but enhances stress tolerance. Furthermore, genome-wide identity-by-state analysis reveals that polyploid wheat A subgenome is more related to the A genome in 13 LOX-A4^m Tu accessions. Thus, our work provides evidence that LOX gene variation shapes plant gene pools and their contributions to polyploid genome formation via regulating growth-defense trade-offs.

Wheat is a major staple crop for over one-third of the world’s population, crucial for global food security, economic stability and cultural traditions. Recently, single-cell and spatial omics approaches have transformed biological discovery, primarily in medical and animal sciences, and they are now beginning to be applied in plant research. Here we summarize the technical innovations and feasibility of spatial omics applications in wheat research, particularly for understanding developmental and environmental responses, thereby potentially enhancing wheat breeding. We highlight how these tools can reveal spatial and temporal patterns in gene expression, cellular heterogeneity and tissue organization in wheat. Furthermore, we propose developing a spatially resolved single-cell atlas of wheat across its life cycle to facilitate breakthroughs in basic research and potential applications in breeding. To achieve these goals, we advocate for a Wheat Spatial Omics Consortium to foster worldwide collaboration for overcoming barriers and developing sustainable and climate-resilient wheat.

Bacterial genome analysis provides valuable insights into the identification of potential biomolecules for diverse biotechnological and therapeutic applications. Particularly, bacteria isolated from extreme environments such as mud volcanoes possess unique physiological and genetic traits that may offer novel opportunities for both in vitro studies and in silico drug target discovery. In this study, a total of 10 bacteria were isolated from Baratang mud volcano, located in Andaman and Nicobar Islands of India; of which strain BRTN was selected for further study based on its best ferrous sulfate (FeSO₄ MTC value 600 mg L⁻¹) tolerance capability and antibiotic sensitivity profile (resistant to Gentamycin, Streptomycin, Ceftriaxone, and Sulphatriad). Optimum growth of BRTN was found at pH 8.0 and it could tolerate up to 16% NaCl. The whole genome sequencing, assembly, and annotation identified that BRTN had the most proximity with Bacillus genera. The bacterium was associated with 3.35 Mb genome with 35.9% of GC content and harbored 3514 genes. Genome analysis revealed that Sulfur Utilization Factor (SUF) proteins was present in the accessory genome. Genome analyses confirmed the presence of SufB, SufC, SufD, SufE2, etc. SUF genes (non-homologous to human genome) that could be considered as potent targets to develop antimicrobial compounds. Furthermore, in silico analysis including homology modeling and receptor-ligand docking were carried out to characterize the selected SUF proteins and to assess their potentiality for functional inhibition by candidate ligands. Among all interactions, SufD showed best Vina score (−14.0) when it interacted with ChEMBL3921511, suggesting SufD protein as a potential drug target. Thus, the SUF system genes identified in this study may serve as promising targets for the development of novel antibacterial therapies.

Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.

Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated water of Purbasthali, West Bengal, India, and through draft genome sequence; it was identified as a strain of Micrococcus luteus that comprised of 2.4 Mb genome with 73.1% GC content and 2256 protein coding genes. As the accessory genome, about 22 genomic islands (GIs) associated with many metal-resistant genes were identified. This strain was capable to tolerate more than 46,800 mg/L arsenate and 390 mg/L arsenite salts as well as found to be tolerable to multi-metals such as Fe, Pb, Mo, Mn, and Zn up to a certain limit of concentrations. Strain AKS4c was able to oxidize arsenite to less toxic arsenate, and its arsenic adsorption property was qualitatively confirmed through X-ray fluorescence (XRF) and Fourier transform infrared spectroscopy (FTIR) analysis. Quantitative estimation of plant growth-promoting attributes like Indole acetic acid (IAA), Gibberellic acid (GA), and proline production and enhancement of rice seedling growth in laboratory condition leads to its future applicability in arsenic bioremediation as a plant growth-promoting rhizobacteria (PGPR).

Chickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.