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

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Abstract

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.

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Acknowledgments

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.

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  1. Department of Plant Sciences/MS1, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA

    Andrea Ariani & Paul Gepts

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  1. Andrea Ariani
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Correspondence to Andrea Ariani.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

438_2015_1038_MOESM1_ESM.pdf

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

Supplementary material 2 (PDF 21 kb). Supplementary File S2 FPKM expression of PvPIP1;4 in the different organs and genotypes analyzed

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Supplementary material 3 (PDF 12 kb). Supplementary File S3 Pairwise protein alignment of the putative tandemly duplicated aquaporins

438_2015_1038_MOESM4_ESM.pdf

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

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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

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

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

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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Ariani, A., Gepts, P. Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.). Mol Genet Genomics 290, 1771–1785 (2015). https://doi.org/10.1007/s00438-015-1038-2

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