Publications by authors named "Kumkum Kumari"

8 Publications

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To exclude or to accumulate? Revealing the role of the sodium HKT1;5 transporter in plant adaptive responses to varying soil salinity.

Plant Physiol Biochem 2021 Dec 19;169:333-342. Epub 2021 Nov 19.

School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia.

Arid/semi-arid and coastal agricultural areas of the world are especially vulnerable to climate change-driven soil salinity. Salinity tolerance in plants is a complex trait, with salinity negatively affecting crop yield. Plants adopt a range of mechanisms to combat salinity, with many transporter genes being implicated in Na-partitioning processes. Within these, the high-affinity K (HKT) family of transporters play a critical role in K and Na homeostasis in plants. Among HKT transporters, Type I transporters are Na-specific. While Arabidopsis has only one Na  -specific HKT (AtHKT1;1), cereal crops have a multiplicity of Type I and II HKT transporters. AtHKT1; 1 (Arabidopsis thaliana) and HKT1; 5 (cereal crops) 'exclude' Na from the xylem into xylem parenchyma in the root, reducing shoot Na and hence, confer sodium tolerance. However, more recent data from Arabidopsis and crop species show that AtHKT1;1/HKT1;5 alleles have a strong genetic association with 'shoot sodium accumulation' and concomitant salt tolerance. The review tries to resolve these two seemingly contradictory effects of AtHKT1;1/HKT1;5 operation (shoot exclusion vs shoot accumulation), both conferring salinity tolerance and suggests that contrasting phenotypes are attributable to either hyper-functional or weak AtHKT1;1/HKT1;5 alleles/haplotypes and are under strong selection by soil salinity levels. It also suggests that opposite balancing mechanisms involving xylem ion loading in these contrasting phenotypes exist that require transporters such as SOS1 and CCC. While HKT1; 5 is a crucial but not sole determinant of salinity tolerance, investigation of the adaptive benefit(s) conferred by naturally occurring intermediate HKT1;5 alleles will be important under a climate change scenario.
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http://dx.doi.org/10.1016/j.plaphy.2021.11.030DOI Listing
December 2021

Reduced apoplastic barriers in tissues of shoot-proximal rhizomes of Oryza coarctata are associated with Na + sequestration.

J Exp Bot 2021 Oct 4. Epub 2021 Oct 4.

Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai, India.

Oryza coarctata is the only wild rice species with significant salinity tolerance. The present work examines the role of the substantial rhizomatous tissues of O. coarctata in conferring salinity tolerance. Transition to an erect phenotype (shoot emergence) from prostrate growth of rhizome tissues is characterized by marked lignification and suberization of supporting sclerenchymatous tissue, epidermis and bundle sheath cells in aerial shoot proximal nodes and internodes in O. coarctata. With salinity however, aerial shoot proximal internodal tissues show reductions in lignification and suberization, most likely related to re-direction of carbon flux towards synthesis of osmporotectant proline. Concurrent with hypolignification and reduced suberization, the aerial rhizomatous biomass of O. coarctata appears to have evolved mechanisms to store Na + in these specific tissues under salinity. This was confirmed by histochemical staining, RT-qPCR expression patterns of genes involved in lignification/suberization, Na +, K + contents of internodal tissues as well as non-invasive microelectrode ion flux measurements of NaCl-induced net Na +, K + and H + flux profiles of aerial nodes. In O. coarctata, aerial proximal internodes appear to act as 'traffic controllers', sending required amounts of Na +, K + into developing leaves for osmotic adjustment and turgor-driven growth while more deeply positioned internodes assume a Na + buffering/storage role.
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http://dx.doi.org/10.1093/jxb/erab440DOI Listing
October 2021

Homology Modeling Identifies Crucial Amino-Acid Residues That Confer Higher Na+ Transport Capacity of OcHKT1;5 from Oryza coarctata Roxb.

Plant Cell Physiol 2020 Jul;61(7):1321-1334

Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600113, India.

HKT1;5 loci/alleles are important determinants of crop salinity tolerance. HKT1;5s encode plasmalemma-localized Na+ transporters, which move 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 the O. coarctata OcHKT1;5 transporter are reported vis-à-vis OsHKT1;5-Ni. Yeast sodium extrusion-deficient cells expressing OcHKT1;5 are sensitive to increasing Na+ (10-100 mM). Electrophysiological measurements in Xenopus oocytes expressing O. coarctata or rice HKT1;5 transporters indicate 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 >10 mM, OcHKT1;5 conductance is higher than that of OsHKT1;5-Ni, indicating the 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-à-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 likely analogous roles in xylem sap desalinization, and differences in xylem sap Na+ concentrations in both species are attributed to differences in Na+ transport affinity/conductance between the transporters.
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http://dx.doi.org/10.1093/pcp/pcaa061DOI Listing
July 2020

Genomic marker assisted identification of genetic loci and genes associated with variation of grain zinc concentration in rice.

J Genet 2019 Dec;98

Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848 125, India.

A study was conducted to examine the genetic divergence and to determine the genetic loci and genes associated with natural variation of grain zinc (Zn) concentration among 28 landraces, improved varieties and advanced breeding lines of rice using candidate gene specific primers. Field evaluation of the experimental material was conducted in randomized block design with three replications and Zn content in unpolished grains of the entries was determined by addition of nitric acid and perchloric acid (1:3) following the procedure of diacid digestion method. Statistical analysis revealed the exploitable extent of variability with respect to grain Zn concentration among the entries. Eighteen entries were selected from the two extremes of grain Zn distribution range and subjected to molecular profiling using a panel of 14 candidate genes specific 12 reported and 14 designed primer pairs. Only eight (OsZIP1-1, OsZIP3a, OsZIP4a, OsZIP5-3, OsZIP7-2, OsZIP8b, OsNRAMP7 and OsNAAT1) reported and eight (OsZIP3K, OsZIP4K, OsZIP5K, OsZIP7K, OsNRAMP7K, OsNAAT1K, OsNACK and OsYSL14K) designed primers generated polymorphic amplified products showing sequence length variation due to targeted amplification of candidate genes specific genomic regions. Ample genetic differentiation and divergence were revealed among the entries, which were accommodated into similarity coefficient-based six clusters, remarkably consistent with grain Zn concentration of the entries. Hierarchical classification pattern of entries was almost completely corroborated by principal co-ordinate analysis based spatial distribution pattern of their genetic profiles. Molecular analysis based on candidate genes specific primers appeared to be an efficient approach for the elucidation of genetic differentiation and divergence in relation to variation of grain Zn concentration among entries. Hence, these markers can be effectively and efficiently utilized for grain Zn concentration related discrimination of rice genotypes and selection of parental genotypes for grain Zn biofortification. Microsatellites were detected within the candidate genes and amplicons, thereby providing a basis to deduce that the repeat sequence length variation in candidate genes may be a role player in the differential grain Zn accumulation in rice varieties. Single marker analysis established the association of OsNACK, OsZIP1-1, OsNRAMP7 and OsNRAMP7K with grain Zn concentration. Thus, these four markers can be effectively used in marker-assisted selection programme for grain Zn biofortification in rice.
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December 2019

Analysis of genetic diversity and population structure using SSR markers and validation of a Cleavage Amplified Polymorphic Sequences (CAPS) marker involving the sodium transporter OsHKT1;5 in saline tolerant rice (Oryza sativa L.) landraces.

Gene 2019 Sep 12;713:143976. Epub 2019 Jul 12.

Plant Molecular Biology Laboratory, Department of Biotechnology, M. S. Swaminathan Research Foundation (MSSRF), Taramani, Chennai 600113, Tamil Nadu, India. Electronic address:

Naturally evolved saline tolerant rice landraces found along the coastline of India are a valuable genomic resource to explore the complex, polygenic nature of salinity tolerance. In the present study, a set of 28 genome wide SSR markers, 11 salt responsive genic SSR markers and 8 Saltol QTL linked SSR markers were used to estimate genetic relatedness and population structure within a collection of 47 rice landraces (including a tolerant and 2 sensitive checks) originating from geographically divergent coastal regions of India. All three marker types identified substantial genetic variation among the landraces, as evident from their higher PIC values (0.53 for genomic SSRs, 0.43 for Genic SSRs and 0.59 for Saltol SSRs). The markers RM431, RM484 (Genomic SSRs), OsCAX (D), OsCAX (T) (Genic SSRs) and RM562 (Saltol SSR) were identified as good candidates to be used in breeding programs for improving salinity tolerance in rice. STRUCTURE analysis divided the landraces into five distinct populations, with classification correlating with their geographical locations. Principal coordinate and hierarchical cluster analyses (UPGMA and neighbor joining) are in close agreement with STRUCTURE results. AMOVA analysis indicated a higher magnitude of genetic differentiation within individuals of groups (58%), than among groups (42%). We also report the development and validation of a new Cleavage Amplified Polymorphic Sequence (CAPS) marker (OsHKT1;5V395) that targets a codon in the sodium transporter gene OsHKT1;5 (Saltol/SKC1 locus) that is associated with sodium transport rates in the above rice landraces. The CAPS marker was found to be present in all landraces except in IR29, Kamini, Gheus, Matla 1 and Matla 2. Significant molecular genetic diversity established among the analyzed salt tolerant rice landraces will aid in future association mapping; the CAPS marker, OsHKT1;5V395 can be used to map rice landraces for the presence of the SNP (Single Nucleotide Polymorphism) associated with increased sodium transport rates and concomitant salinity tolerance in rice.
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http://dx.doi.org/10.1016/j.gene.2019.143976DOI Listing
September 2019

Expression of wild rice Porteresia coarctata PcNHX1 antiporter gene (PcNHX1) in tobacco controlled by PcNHX1 promoter (PcNHX1p) confers Na-specific hypocotyl elongation and stem-specific Na accumulation in transgenic tobacco.

Plant Physiol Biochem 2019 Jun 12;139:161-170. Epub 2019 Mar 12.

Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai, 600113, India. Electronic address:

Soil salinization is a major abiotic stress condition that affects about half of global agricultural lands. Salinity leads to osmotic shock, ionic imbalance and/or toxicity and build-up of reactive oxygen species. Na⁺/H⁺ antiporters (NHXs) are integral membrane transporters that catalyze the electro-neutral exchange of K⁺/Na⁺ for H⁺ and are implicated in cell expansion, development, pH/ion homeostasis and salt tolerance. Porteresia coarctata is a salt secreting halophytic wild rice that thrives in the coastal-riverine interface. P. coarctata NHX1 (PcNHXI) expression is induced by salinity in P. coarctata roots and shows high sequence identity to Oryza sativa NHX1. PcNHX1 confers hygromycin and Li sensitivity and Na tolerance transport in a yeast strain lacking sodium transport systems. Additionally, transgenic PcNHX1 expressing tobacco seedlings (PcNHX1 promoter) show significant growth advantage under increasing concentrations of NaCl and MS salts. Etiolated PcNHX1 seedlings also exhibit significantly elongated hypocotyl lengths in 100 mM NaCl. PcNHX1 expression in transgenic tobacco roots increases under salinity, similar to expression in P. coarctata roots. Under incremental salinity, transgenic lines show reduction in leaf Na, stem specific accumulation of Na and K (unaltered Na/K ratios). PcNHX1 transgenic plants also show enhanced chlorophyll content and reduced malondialdehyde (MDA) production in leaves under salinity. The above data suggests that PcNHX1 overexpression (controlled by PcNHX1p) enhances stem specific accumulation of Na, thereby protecting leaf tissues from salt induced injury.
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http://dx.doi.org/10.1016/j.plaphy.2019.03.014DOI Listing
June 2019

T-homoeolog specific plasma membrane protein 3 [Nt(t)PMP3-2] in polyploid Nicotiana tabacum shows conserved alternative splicing, derived from extant Nicotiana tomentosiformis parent.

Plant Physiol Biochem 2017 Oct 18;119:338-345. Epub 2017 Sep 18.

Institute of Life Sciences, NALCO Nagar Road, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India.

Abiotic stress induced plasma membrane protein 3 (PMP3) genes occur as multigene families in plants, coding for hydrophobic proteins. Group I PMP3s code for shorter ORFs while Group II PMP3s code for proteins with C-terminal extensions. Allotetraploid Nicotiana tabacum (SSTT; 2n = 48) derives its parentage from extant ancestors related to Nicotiana sylvestris (SS) and Nicotiana tomentosiformis (TT). Polyploidization triggers complex genetic and epigenetic changes, often leading to homoeolog-specific retention or loss of function, sub-functionalization or neo-functionalization. Genomic sequences of Nt(t)PMP3-1/Nt(t)PMP3-2 cloned from N. tabacum show near identity with N. tomentosiformis NtoPMP3-1/NtoPMP3-2 genomic sequences respectively (distinct from N. sylvestris NsPMP3-1/NsPMP3-2 genomic regions). RT-PCR with exon 1,2 primer pairs amplified only single fragments for Nt(t)PMP3-1 and Nt(t)PMP3-2. In contrast, for Nt(t)PMP3-2, three variants were detected using exon 2,3 primers by RT-PCR. Cloning revealed (i) a transcript coding for a Group I PMP3 [Nt(t)PMP3-2CS], (ii) a transcript with complete retention of the second intron [Nt(t)PMP3-2IR] and (iii) a transcript with an alternative (exon 2) 5' splice site [Nt(t)PMP3-2AS], coding for a longer protein, similar to ORFs of Group II PMP3 genes. All three Nt(t)PMP3-2 variants have conserved counterparts in the N. tomentosiformis transcriptome, suggesting the transcriptional machinery governing alternative splicing of Nt(t)PMP3-2 in N. tabacum has conserved origins, derived from a N. tomenosiformis lineage. The above data shows alternative splicing of PMP3 genes contributes to transcript and ORF diversity in plants. All three Nt(t)PMP3-2 splice variants show increased root-specific expression. Implications of Nt(t)PMP3-2 alternative splicing on transcript stability and ORF features are discussed.
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http://dx.doi.org/10.1016/j.plaphy.2017.09.011DOI Listing
October 2017

A Direct Metal-Free Decarboxylative Sulfono Functionalization (DSF) of Cinnamic Acids to α,β-Unsaturated Phenyl Sulfones.

Org Lett 2015 Jun 8;17(11):2656-9. Epub 2015 May 8.

Department of Chemistry (Centre of Advanced Study), Banaras Hindu University, Varanasi 221005, India.

A metal-free room temperature decarboxylative cross-coupling between cinnamic acids and arylsulfonyl hydrazides has been realized for the first time for the synthesis of (E)-vinyl sulfones. The scope and versatility of the reaction has been demonstrated by the regio- and stereoselective synthesis of 22 derivatives with diverse structural features.
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http://dx.doi.org/10.1021/acs.orglett.5b01037DOI Listing
June 2015
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