Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses

Singh, Alka; Kumar, Pramod; Gautam, Vibhav; Balakrishnan, Rengasamy; Adhikari, Bijan; Udayakumar, M.; Sarkar, Ananda K.

doi:10.1038/srep39266

Cited by 22 publications

(20 citation statements)

References 107 publications

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“…Similarly, the bet-like SNARE- AtBS14a has been found to be significant in controlling cell growth in Arabidopsis [ 56 ]. The overexpression of SNARE-like protein from the halophyte Salicornia brachitata conferred salinity/drought tolerance on transgenic tobacco lines by enhancing seed germination, membrane stability, antioxidant enzymes coding genes expression,and maintaining cell turgor [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic basis of drought tolerance during seed germination in barley

et al. 2018

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Drought is one of the harshest abiotic stresses hindering seed germination, plant growth, and crop productivity. A high rate and uniformity of germination under stressful conditions are vital for crop establishment and growth; thus, for productivity. A better understanding of the genetic architecture of seed germination under drought stress is a prerequisite for further increasing yield potential. Barley is considered one of the most abiotic stresses-tolerant cereals. Elucidating the drought tolerance of barley during seed germination would indeed pave the way towards improving the performance of all cereals. However, we still know relatively little about the genetic control of drought tolerance during the seed germination phase. In our study, 218 worldwide spring barley accessions were subjected to PEG-induced drought during seed germination. Induced drought stress "20% PEG" significantly reduced the seed germination parameters and seedling related traits. A genome-wide association scan (GWAS) was used to identify genomic regions associated with our trait of interest. In total, 338 single nucleotide polymorphisms (SNPs) were found to be associated with several traits distributed across seven barley chromosomes, of which 26 genomic regions were associated with candidate genes. The current study found some of the quantitative trait loci (QTL) that have previously been reported to be linked to seed germination-related traits under drought conditions, as well as some new associations. Noteworthy, the identified QTL colocalized with a number of genes (within interval ±0.5 Mbp) that are exclusively distributed on chromosomes 1H, 2H, and 5H. The annotation of these genes in barley shows their roles in drought tolerance through encoding different transcription factors. The function of the identified genes during seed germination was also confirmed by the annotation of their counterparts in Arabidopsis. The current analyses show the power of the GWAS both for identifying putative candidate genes and for improving plant adaptive traits in barley.

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Section: Discussionmentioning

confidence: 99%

Genetic basis of drought tolerance during seed germination in barley

et al. 2018

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“…RNA isolation and qRT-PCR for the transcript level of MIR166 gene family, HD-ZIP IIIs and KAN gene family were done as described previously 19, 46 . Primers specific for each of the seven MIR166 ( A – G ) precursors were designed as described earlier 47 .…”

Section: Methodsmentioning

confidence: 99%

Phytohormonal crosstalk modulates the expression of miR166/165s, target Class III HD-ZIPs, and KANADI genes during root growth in Arabidopsis thaliana

Singh

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Singh

et al. 2017

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Both phytohormones and non-coding microRNAs (miRNAs) play important role in root development in Arabidopsis thaliana. Mature miR166/165 s, which are derived from precursor transcripts of concerned genes, regulate developmental processes, including leaf and root patterning, by targeting Class III HOMEODOMAIN LEUCINE-ZIPPER (HD-ZIP III) transcription factors (TFs). However, their regulation through hormones remained poorly understood. Here, we show that several phytohormones dynamically regulate the spatio-temporal expression pattern of miR166/165 and target HD-ZIP IIIs in developing roots. Hormone signaling pathway mutants show differential expression pattern of miR166/165, providing further genetic evidence for multilayered regulation of these genes through phytohormones. We further show that a crosstalk of at least six different phytohormones regulate the miR166/165, their target HD-ZIP IIIs, and KANADI (KANs). Our results suggest that HD-ZIP IIIs mediated root development is modulated both transcriptionally through phytohormones and KANs, and post-transcriptionally by miR166/165 that in turn are also regulated by the phytohormonal crosstalk.

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“…The OsNRT2.3 is known to be involved in highaffinity nitrate transport system and nitrogen acquisition (Fan et al 2016). Under the anaerobic condition, significant nitrification on root surface has been observed when NH4 + dominates which may be responsible for its relative high expression in anaerobic compared to aerobic condition (Singh et al 2016). Another gene OsNPF2.2 has is known to be vascular specific transporter that unloads nitrate from xylem affecting root-to-shoot nitrate transport was highly expressed in aerobic condition (Li et al 2015).…”

Section: Validation Of Reference Genes For Relative Gene Expressionmentioning

confidence: 99%

Genes encoding membrane proteins showed stable expression in rice under aerobic condition: novel set of reference genes for expression studies

et al. 2018

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A set of reference genes expressing stably under aerobic and anaerobic conditions in rice is essential to execute omics studies relating to aerobic adaptations. Stability of expression of ten rice reference genes, viz. , and was validated across six experimental sets in shoot and root tissues at seedling, tillering, and panicle initiation stages. Comprehensively, (Membrane protein), (Tumor protein homolog), and (Expressed protein) were revealed as the most stable set with acceptable and value according to the gold standards of qRT-PCR using various algorithms/tools. The identified set of reference genes was validated using root trait genes, which showed concurrence with the functional expression patterns in the aerobic and anaerobic adapted cultivars. The (Membrane protein), (Tumor protein homolog), and (Expressed protein) genes are the most stable reference genes across the root and shoot at various developmental stages under aerobic and anaerobic conditions in rice. This is the first study for accurate and reliable relative gene expression analysis in rice grown in aerobic and anaerobic conditions.

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Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses

Cited by 22 publications

References 107 publications

Genetic basis of drought tolerance during seed germination in barley

Genetic basis of drought tolerance during seed germination in barley

Phytohormonal crosstalk modulates the expression of miR166/165s, target Class III HD-ZIPs, and KANADI genes during root growth in Arabidopsis thaliana

Genes encoding membrane proteins showed stable expression in rice under aerobic condition: novel set of reference genes for expression studies

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