Abstract
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.
Highlights
Chickpea (Cicer arietinum L.) is second most important food legume crop grown globally over 13.5 Mha with the production of 13.1 Mt in 2013 (FAOSTAT 2013: http://faostat.fao.org/site/339/default.aspx)
We identified a total of 40 putative aquaporin encoding genes chickpea genome, namely, thereafter, as chickpea AQP (CaAQP) (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, 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)
Summary
Chickpea (Cicer arietinum L.) is second most important food legume crop grown globally over 13.5 Mha with the production of 13.1 Mt in 2013 (FAOSTAT 2013: http://faostat.fao.org/site/339/default.aspx). The productivity of chickpea has been limited by several biotic and abiotic factors, among them drought is one of the major abiotic stress causing a significant reduction in yield in the majority of chickpea growing areas (Krishnamurthy et al, 1999) Soil salinity is another increasing abiotic stress in many of the chickpea growing areas (Flowers et al, 2010). Understanding the genetic and molecular mechanisms of tolerance to drought and salinity will help to improve the adaptation of chickpea to these adverse conditions Both the drought and salinity stresses cause tissue dehydration instigated by the imbalance between root water uptake and leaf transpiration and modify root water uptake (Wahid and Close, 2007). Despite the importance of AQPs in regulating stress tolerance, very limited studies on understanding the role of AQPs in biotic and abiotic stresses were reported in chickpea. Differential regulation of some of the AQP genes under drought stress has been described (Molina et al, 2008; Deokar et al, 2011), suggesting the potential involvement of AQPs in drought and other osmotic related stresses in chickpea
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