Biology subjects

Rani, P. S.

Publications and source records attributed to Rani, P. S..

2 recordsLinked to original sources

bioRxiv2025

Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut

Malnutrition is a major global challenge, especially in the developing regions, where improving the nutritional content of staple crops is a significant step towards alleviating hidden hunger. Groundnut, a nutrient rich legume contains several mineral nutrients, high protein, essential amino-acids and vitamins that are required for human health. In this study, multi-season phenotyping data for kernel iron (Fe), zinc (Zn) content and protein content (PC) and whole genome re-sequencing (WGRS) data on mini-core collection, were used to perform genome-wide association study (GWAS) analysis. Phenotypic variability analysis revealed a large variation in the Fe (7.6 - 42.8 ppm), Zn (10.9 - 62.4 ppm) and PC (12.7 - 33.6%). GWAS analysis identified a total of 15 marker-trait associations (MTAs) and 28 candidate genes for pooled season data, as well as 44 MTAs and 62 candidate genes for individual seasons. Key candidate genes like MYB transcription factor (Arahy.QI0PHV, Arahy.1I6ZSS), Zn finger MYM type protein, RING finger MYM type protein (Arahy.7P97F6, Arahy.9R964H, Arahy.I3B88T) and NAC domain protein (Arahy.LV3APC), associated with the Fe and Zn homeostasis pathway, genes related to protein homeostasis, such as protein kinase family protein (Arahy.4D7KBI), and E3 ubiquitin-protein ligase (Arahy.PE3CF6), were also identified within significant MTA regions. These findings provide basis for the detection and characterization of the possible candidate genes related to the nutritional quality traits. Single nucleotide polymorphism (SNP)-based KASP (Kompetitive Allele Specific Polymerase Chain Reaction) markers for 9 SNPs were designed and validated. Of these, three markers (snpAH00636, snpAH00641 and snpAH00644) showed polymorphism which could be deployed in the genomics-assisted breeding for the development of nutrient-rich groundnut varieties.

plant biology↗

bioRxiv2024

Insight into the regulatory mechanism of the MFS transporter, SCO4121 by the MarR regulator, SCO4122

MarR group of transcriptional regulators are ubiquitous in bacteria and found to be involved in regulation of efflux pumps that confer multidrug resistance phenotype. While most characterized MarR regulators act as transcriptional repressors, we earlier identified a MarR regulator SCO4122 in Streptomyces coelicolor, playing an essential role in transcriptional activation of the MFS transporter SCO4121 in response to multiple substrates of the latter, including streptomycin, ciprofloxacin and chloramphenicol. In this study, using Surface Plasmon Resonance, we demonstrate that SCO4122 interacts directly with the diverse substrates of SCO4121 with the highest affinity for streptomycin with a KD of 0.73 M. Further, in-vitro and in-vivo studies reveal that SCO4122 also binds to the intergenic region between sco4121 and sco4122, where the interaction is dependent on the cooperative binding of SCO4122 to three motifs in this region. A conserved Methionine, M93, in SCO4122 is identified to be an integral amino acid residue that is involved in activation of SCO4121 in response to ciprofloxacin, streptomycin and EtBr but not chloramphenicol. Furthermore, our studies also indicate that upon binding to different substrates, the affinity of SCO4122 to the sco4121 promoter increases 50-1000 fold, thereby leading to enhanced expression of the transporter, SCO4121. This study thus highlights that SCO4122 is a novel MarR regulator that functions as a strong transcriptional activator of an efflux pump, SCO4121, through intricate molecular mechanisms in presence of structurally dissimilar substrates. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/577416v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@3394e2org.highwire.dtl.DTLVardef@73afb1org.highwire.dtl.DTLVardef@113c724org.highwire.dtl.DTLVardef@1772ac9_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗