Molecular Genetics and Genomics

, Volume 290, Issue 5, pp 1771–1785 | Cite as

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

Original Paper


Plant aquaporins are a large and diverse family of water channel proteins that are essential for several physiological processes in living organisms. Numerous studies have linked plant aquaporins with a plethora of processes, such as nutrient acquisition, CO2 transport, plant growth and development, and response to abiotic stresses. However, little is known about this protein family in common bean. Here, we present a genome-wide identification of the aquaporin gene family in common bean (Phaseolus vulgaris L.), a legume crop essential for human nutrition. We identified 41 full-length coding aquaporin sequences in the common bean genome, divided by phylogenetic analysis into five sub-families (PIPs, TIPs, NIPs, SIPs and XIPs). Residues determining substrate specificity of aquaporins (i.e., NPA motifs and ar/R selectivity filter) seem conserved between common bean and other plant species, allowing inference of substrate specificity for these proteins. Thanks to the availability of RNA-sequencing datasets, expression levels in different organs and in leaves of wild and domesticated bean accessions were evaluated. Three aquaporins (PvTIP1;1, PvPIP2;4 and PvPIP1;2) have the overall highest mean expressions, with PvTIP1;1 having the highest expression among all aquaporins. We performed an EST database mining to identify drought-responsive aquaporins in common bean. This analysis showed a significant increase in expression for PvTIP1;1 in drought stress conditions compared to well-watered environments. The pivotal role suggested for PvTIP1;1 in regulating water homeostasis and drought stress response in the common bean should be verified by further field experimentation under drought stress.


Aquaporin Drought response Gene expression Gene structure Water homeostasis 



This project was supported by Agriculture and Food Research Initiative (AFRI) Competitive Grant No. 2013-67013-21224 from the USDA National Institute of Food and Agriculture.

Ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

438_2015_1038_MOESM1_ESM.pdf (10.8 mb)
Supplementary material 1 (PDF 11075 kb). Supplementary File S1 Multiple sequence alignment of the first NPA region in the putative aquaporins of P. vulgaris. Phytozome jbrowse RNA-Sequencing log-coverage link and Phytomine FPKM expression link refers to link of RNA-Sequencing coverage and FPKM expression of Phvul.003G040100
438_2015_1038_MOESM2_ESM.pdf (21 kb)
Supplementary material 2 (PDF 21 kb). Supplementary File S2 FPKM expression of PvPIP1;4 in the different organs and genotypes analyzed
438_2015_1038_MOESM3_ESM.pdf (12 kb)
Supplementary material 3 (PDF 12 kb). Supplementary File S3 Pairwise protein alignment of the putative tandemly duplicated aquaporins
438_2015_1038_MOESM4_ESM.pdf (716 kb)
Supplementary material 4 (PDF 716 kb). Supplementary File S4 Expression heatmap of the 41 aquaporins in different domesticated and wild common bean genotypes. The expression values of each aquaporins are log2 transformed
438_2015_1038_MOESM5_ESM.pdf (25 kb)
Supplementary material 5 (PDF 24 kb). Supplementary File S5 Putative interacting aquaporins with a Pearson’s correlation coefficient (r) > 0.9
438_2015_1038_MOESM6_ESM.pdf (20 kb)
Supplementary material 6 (PDF 19 kb). Supplementary File S6 Aquaporin normalized expression and expression-fold change under drought stress and in background ESTs. P value, based on 2 × 2 χ2 tests, is shown
438_2015_1038_MOESM7_ESM.pdf (21 kb)
Supplementary material 7 (PDF 20 kb). Supplementary File S7 Summary of BARCBean6K_3 SNPs that have an aquaporin gene locus as the nearest annotated genomic feature. Distance between the markers and the aquaporins, as well as genomic positions of both, is shown
438_2015_1038_MOESM8_ESM.pdf (22 kb)
Supplementary material 8 (PDF 22 kb). Supplementary File S8 Distance and genomic positions of the drought QTLs identified by Mukeshimana et al. (2014) and the nearest annotated aquaporins


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of Plant Sciences/MS1University of CaliforniaDavisUSA

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