Genome-wide identification and characterization of the aquaporin gene family in Sorghum bicolor (L.)

Reddy, Palakolanu Sudhakar; Rao, Tata Santosh Rama Bhadra; Sharma, Kiran K.; Vadez, Vincent

doi:10.1016/j.plgene.2014.12.002

Cited by 76 publications

(51 citation statements)

References 63 publications

(76 reference statements)

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“…6a-f). Our findings are also supported by the review of Afzal et al [59] the argues that AQP genes play an important role in plant defense responses against biotic and abiotic stressors and the report of Reddy et al [60] of the functions of this gene family in abiotic stress tolerance in Sorghum.…”

Section: Discussionsupporting

confidence: 89%

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa

et al. 2017

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BackgroundPlants contain a range of aquaporin (AQP) proteins, which act as transporter of water and nutrient molecules through living membranes. AQPs also participate in water uptake through the roots and contribute to water homeostasis in leaves.ResultsIn this study, we identified 59 AQP genes in the B. rapa database and Br135K microarray dataset. Phylogenetic analysis revealed four distinct subfamilies of AQP genes: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs). Microarray analysis showed that the majority of PIP subfamily genes had differential transcript abundance between two B. rapa inbred lines Chiifu and Kenshin that differ in their susceptibility to cold. In addition, all BrPIP genes showed organ-specific expression. Out of 22 genes, 12, 7 and 17 were up-regulated in response to cold, drought and salt stresses, respectively. In addition, 18 BrPIP genes were up-regulated under ABA treatment and 4 BrPIP genes were up-regulated upon F. oxysporum f. sp. conglutinans infection. Moreover, all BrPIP genes showed down-regulation under waterlogging stress, reflecting likely the inactivation of AQPs controlling symplastic water movement.ConclusionsThis study provides a comprehensive analysis of AQPs in B. rapa and details the expression of 22 members of the BrPIP subfamily. These results provide insight into stress-related biological functions of each PIP gene of the AQP family, which will promote B. rapa breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-0979-5) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 89%

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa

et al. 2017

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“…We identified a total of 40 putative aquaporin encoding genes chickpea genome, namely, thereafter, as CaAQPs (Table 1 and Supplementary File S1). The number of AQP identified in this study are slightly higher than the 35 AQP genes reported in Arabidopsis (Johanson et al, 2001), 33 in rice (Sakurai et al, 2005), 35 in Medicago and 30 in lotus genome, then again almost same in number as reported 41 AQP genes in potato (Venkatesh et al, 2013), Sorghum (Reddy et al, 2015), common bean (Ariani and Gepts, 2015), and 40 AQP genes in Pigeonpea (Deshmukh et al, 2015). …”

Section: Resultssupporting

confidence: 52%

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

Deokar

Tar’an

2016

Front. Plant Sci.

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Aquaporins (AQPs) are essential membrane proteins that play critical role in the transport of water and many other solutes across cell membranes. In this study, a comprehensive genome-wide analysis identified 40 AQP genes in chickpea (Cicer arietinum L.). A complete overview of the chickpea AQP (CaAQP) gene family is presented, including their chromosomal locations, gene structure, phylogeny, gene duplication, conserved functional motifs, gene expression, and conserved promoter motifs. To understand AQP's evolution, a comparative analysis of chickpea AQPs with AQP orthologs from soybean, Medicago, common bean, and Arabidopsis was performed. The chickpea AQP genes were found on all of the chickpea chromosomes, except chromosome 7, with a maximum of six genes on chromosome 6, and a minimum of one gene on chromosome 5. Gene duplication analysis indicated that the expansion of chickpea AQP gene family might have been due to segmental and tandem duplications. CaAQPs were grouped into four subfamilies including 15 NOD26-like intrinsic proteins (NIPs), 13 tonoplast intrinsic proteins (TIPs), eight plasma membrane intrinsic proteins (PIPs), and four small basic intrinsic proteins (SIPs) based on sequence similarities and phylogenetic position. Gene structure analysis revealed a highly conserved exon-intron pattern within CaAQP subfamilies supporting the CaAQP family classification. Functional prediction based on conserved Ar/R selectivity filters, Froger's residues, and specificity-determining positions suggested wide differences in substrate specificity among the subfamilies of CaAQPs. Expression analysis of the AQP genes indicated that some of the genes are tissue-specific, whereas few other AQP genes showed differential expression in response to biotic and abiotic stresses. Promoter profiling of CaAQP genes for conserved cis-acting regulatory elements revealed enrichment of cis-elements involved in circadian control, light response, defense and stress responsiveness reflecting their varying pattern of gene expression and potential involvement in biotic and abiotic stress responses. The current study presents the first detailed genome-wide analysis of the AQP gene family in chickpea and provides valuable information for further functional analysis to infer the role of AQP in the adaptation of chickpea in diverse environmental conditions.

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“…In mature S. viridis internode tissues, the transcript levels of TIPs and NIPs was generally low with the exception of SvNIP2;2, SvTIP4;2 , and SvTIP1;2. In a sorghum stem transcriptome report investigating SWEET gene involvement in sucrose accumulation, we note that transcripts for all 41 sorghum aquaporins were detected in pith and rind tissues in 60-day-old plants (Reddy et al, 2015; Mizuno et al, 2016). Of those 41 aquaporins the expression of 16, primarily NIPs and TIPs, was relatively low.…”

Section: Discussionmentioning

confidence: 87%

“…On the basis of amino acid sequence comparison with known aquaporins in Arabidopsis , rice and maize, the genomes of sugarcane, sorghum and S. italica include 42, 41, and 42 predicted aquaporin encoding genes, respectively (da Silva et al, 2013; Reddy et al, 2015; Azad et al, 2016). In S. viridis 41 aquaporin encoding genes were identified that group into four clades corresponding to NIPs, TIPs, SIPs, and PIPs ( Figure 1 ).…”

Section: Discussionmentioning

confidence: 99%

Roles of Aquaporins in Setaria viridis Stem Development and Sugar Storage

et al. 2016

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Setaria viridis is a C4 grass used as a model for bioenergy feedstocks. The elongating internodes in developing S. viridis stems grow from an intercalary meristem at the base, and progress acropetally toward fully expanded cells that store sugar. During stem development and maturation, water flow is a driver of cell expansion and sugar delivery. As aquaporin proteins are implicated in regulating water flow, we analyzed elongating and mature internode transcriptomes to identify putative aquaporin encoding genes that had particularly high transcript levels during the distinct stages of internode cell expansion and maturation. We observed that SvPIP2;1 was highly expressed in internode regions undergoing cell expansion, and SvNIP2;2 was highly expressed in mature sugar accumulating regions. Gene co-expression analysis revealed SvNIP2;2 expression was highly correlated with the expression of five putative sugar transporters expressed in the S. viridis internode. To explore the function of the proteins encoded by SvPIP2;1 and SvNIP2;2, we expressed them in Xenopus laevis oocytes and tested their permeability to water. SvPIP2;1 and SvNIP2;2 functioned as water channels in X. laevis oocytes and their permeability was gated by pH. Our results indicate that SvPIP2;1 may function as a water channel in developing stems undergoing cell expansion and SvNIP2;2 is a candidate for retrieving water and possibly a yet to be determined solute from mature internodes. Future research will investigate whether changing the function of these proteins influences stem growth and sugar yield in S. viridis.

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Genome-wide identification and characterization of the aquaporin gene family in Sorghum bicolor (L.)

Cited by 76 publications

References 63 publications

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa

Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa

Genome-Wide Analysis of the Aquaporin Gene Family in Chickpea (Cicer arietinum L.)

Roles of Aquaporins in Setaria viridis Stem Development and Sugar Storage

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