
@article {149951,
	title = {Genome-wide association study reveals effect of nsSNPs on candidate genes in rice during iron deficiency.},
	journal = {Funct Integr Genomics},
	volume = {24},
	year = {2024},
	month = {2024 Oct 25},
	pages = {198},
	abstract = {<p>Resource-poor areas with moisture deficit lands following aerobic and direct seeded rice (DSR) methods of cultivation face severe problems of iron deficiency. In this study, Bengal and Assam Aus rice panel was phenotyped at the seedling stage using an iron-deprived hydroponic medium for various shoot and root traits. A novel iron deficiency scoring scale was used to classify the tolerance reaction and could range anywhere between 0 and 9, indicating the most tolerant and susceptible, respectively. The GWAS results identified four putative candidate genes; OsFLA for number of leaves and shoot length, OsBIDK1 for root traits; average diameter, volume, biomass, projected area, and surface area, OsHPL3 for chlorophyll index of the third leaf and AKR2B (XBOS252) was for Fe score, (which was earlier reported in relation to Xa21). The nsSNP (nsSNPs) variations in these gene sequences were used to group the panel and identify superior haplotypes and donors. BR16 was identified as a superior donor, with higher chlorophyll index and shoot length than RA23, also higher values for root traits like root average diameter, root volume, root projected area and root surface area followed by Shete Bhado. The impact of identified nsSNPs on protein structure and stability was investigated. The conserved domains detected in the mutated proteins of the superior haplotypes are very informative, highlighting that natural selection favors abiotic stress tolerant variants in resource poor areas. Thus, justifying our choice of Aus landraces for association mapping of Fe deficiency tolerant genes in rice.</p>
},
	keywords = {Chlorophyll, Genome-Wide Association Study, Iron Deficiencies, Oryza, Plant Proteins, Plant Roots, Polymorphism, Single Nucleotide},
	issn = {1438-7948},
	doi = {10.1007/s10142-024-01478-w},
	author = {Panda, Siddharth and Anandan, Annamalai and Shafi, K Mohamed and Naika, Mahantesha B N and Sowdhamini, R and Vanishree, G and Sarkar, Sutapa and Travis, Anthony J and Norton, Gareth J and Price, Adam H}
}
@article {3554,
	title = {Genome-wide survey of putative RNA-binding proteins encoded in the human proteome.},
	journal = {Mol Biosyst},
	volume = {12},
	year = {2016},
	month = {2016 Jan 26},
	pages = {532-40},
	abstract = {<p>RNA-binding proteins (RBPs) are involved in various post-transcriptional gene regulatory processes and are also functionally important members of the ribosome and the spliceosome. However, RBPs and their interactions with RNA are less well-studied in comparison to DNA-binding proteins. We have classified the existing RBP structures, available in complexes with RNA and RNA/DNA hybrids, into different structural families and created Hidden Markov Models (HMMs). These structure-centric family HMMs, along with the sequence-centric family HMMs, were used as a primary database to systematically search the human proteome for the presence of putative RBPs. We have found more than 2600 gene products with RBP signatures in humans, of which around 28\% are likely to bind to RNA but not DNA, whereas 9\% might bind to both RNA and DNA. 11\% of them do not contain an explicit functional annotation yet. Nearly 30\% of the putative RBPs are exclusively nuclear, 15\% have known disease associations and around 30\% are enzymes. Around 40\% of the proteins identified in this study are novel and have not been reported by recent large-scale studies on human RBPs.</p>
},
	issn = {1742-2051},
	doi = {10.1039/c5mb00638d},
	author = {Ghosh, Pritha and Sowdhamini, R}
}
