
@article {124206,
	title = {A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance.},
	journal = {Sci Rep},
	volume = {13},
	year = {2023},
	month = {2023 Feb 07},
	pages = {2195},
	abstract = {<p>Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group.\&nbsp;The miRNA-miRNA* duplex region is completely conserved across eleven\&nbsp;Oryza\&nbsp;species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the {\textquoteright}A{\textquoteright} allele may promote better processing vis-{\`a}-vis the structure conferred by {\textquoteright}G{\textquoteright} allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.</p>
},
	keywords = {MicroRNAs, Oryza, Polymorphism, Single Nucleotide, Salt-Tolerant Plants},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-28836-1},
	author = {Jaganathan, Deepa and Rajakani, Raja and Doddamani, Dadakhalandar and Saravanan, Divya and Pulipati, Shalini and Vivek Hari Sundar G and Sellamuthu, Gothandapani and Jayabalan, Shilpha and Kumari, Kumkum and Parthasarathy, Pavithra and S, Punitha and Ramalingam, Sivaprakash and Shivaprasad, Padubidri V and Venkataraman, Gayatri}
}
@article {78101,
	title = {Homology modeling identifies crucial amino-acid residues that confer higher Na+ transport capacity of OcHKT1;5 from Oryza coarctata Roxb.},
	journal = {Plant Cell Physiol},
	year = {2020},
	month = {2020 May 07},
	abstract = {<p>HKT1;5 loci/alleles are important determinants of crop salinity tolerance. HKT1;5s encode plasmalemma-localized Na+-transporters, retrieving xylem Na+ into xylem parenchyma cells, reducing shoot Na+ accumulation. Allelic variation in rice OsHKT1;5 sequence in specific landraces (Nona Bokra OsHKT1;5-NB/Nipponbare OsHKT1;5-Ni) correlates with variation in salt tolerance. Oryza coarctata, a halophytic wild rice, grows in fluctuating salinity at the seawater-estuarine interface in Indian and Bangladeshi coastal regions. The distinct transport characteristics of the shoots and roots expressing O. coarctata OcHKT1;5 transporter, are reported vis-{\`a}-vis OsHKT1;5-Ni. Yeast sodium extrusion-deficient cells expressing\&nbsp;OcHKT1;5 are sensitive to increasing Na+ (10-100 mM). Electrophysiological measurements in Xenopus oocytes expressing O. coarctata or rice HKT1;5 transporters indicates that OcHKT1;5, like OsHKT1;5-Ni is a Na+-selective transporter, but displays 16-fold lower affinity for Na+ and 3.5-fold higher maximal conductance than OsHKT1;5-Ni. For Na+ concentrations greater than 10 mM, OcHKT1;5 conductance is higher than that of OsHKT1;5-Ni, indicating potential of OcHKT1;5 for increasing domesticated rice salt tolerance. Homology modeling/ simulation suggests that four key amino acid changes in OcHKT1;5 (in loops on the extracellular side; E239K, G207R, G214R, L363V), account for its lower affinity and higher Na+ conductance vis-{\`a}-vis OsHKT1;5-Ni. Of these, E239K in OcHKT1;5, confers lower affinity for Na+ transport, as evidenced by Na+ transport assays of reciprocal site directed mutants for both transporters (OcHKT1;5- K239E, OsHKT1;5-Ni- E270K) in Xenopus oocytes. Both transporters have analogous roles in xylem sap desalinization and differences in Na+ transport affinity/ conductance between the transporters is attributable to differences in xylem sap Na+ concentrations in both species.</p>
},
	issn = {1471-9053},
	doi = {10.1093/pcp/pcaa061},
	author = {Somasundaram, Suji and V{\'e}ry, Anne-Ali{\'e}nor and Vinekar, Rithvik S and Ishikawa, Tetsuya and Kumari, Kumkum and Pulipati, Shalini and Kumaresan, Kavitha and Corratg{\'e}-Faillie, Claire and Sowdhamini, R and Parida, Ajay and Shabala, Lana and Shabala, Sergey and Venkataraman, Gayatri}
}
