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Genome-wide identification, characterization, and expression analyses of the HAK/KUP/KT potassium transporter gene family reveals their involvement in K+ deficient and abiotic stress responses in pear rootstock seedlings

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Abstract

High-affinity K+ (HAK)/K+ uptake (KUP)/K+ transporters (KT) play crucial roles in the regulation of cellular K+ levels. However, little is known about these genes in the Rosaceae family. In this study, 56 putative HAK/KUP/KT genes were identified in genome sequences from Pyrus bretschneideri, Fragaria vesca, and Vitis vinifera, 21 of which were from P. bretschneideri (designated PbHAK1-21). HAK/KUP/KTs from these species, as well as from Arabidopsis and rice, were grouped into five major clusters with eight subclades. Whole-genome duplication/segmental duplication and dispersed duplication largely accounts for the expansion of HAK/KUP/KT families in these five species. Orthologous relationships between pear and Arabidopsis genes suggest that some PbHAKs function as high-affinity K+ transporters or mediators of abiotic stress responses. Cis-regulatory motifs upstream of PbHAK genes also suggest that members of this family respond to environment changes. PbHAK2 and PbHAK12 mRNAs are abundant in roots exposed to normal levels of K+ and are rapidly up-regulated under conditions of K+ deficiency, suggesting that they have crucial roles in K+ uptake, especially at low K+ concentrations. PbHAK12 (orthologous to AtHAK5 from Arabidopsis) is predominately localized in the plasma membrane, consistent with a role in mediating K+ uptake. Some PbHAK mRNA levels also change in response to abiotic stresses such as salt, cold, and drought. Our data reveals potential candidate genes for further functional characterization, and may be useful for breeding pear rootstocks that utilize potassium more efficiently.

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Acknowledgements

This work was supported by an award from the China Agriculture Research System (CARS-28-10).

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Authors and Affiliations

  1. Jiangsu Provincial Key Lab for Organic Solid Waste Utilization/National Engineering Research Center for Organic-based Fertilizers/Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, 210095, China

    Yan Li, Lirun Peng, Changyan Xie, Xiaoqian Shi, Caixia Dong, Qirong Shen & Yangchun Xu

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  1. Yan Li
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  2. Lirun Peng
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  3. Changyan Xie
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Contributions

YX, CD and QS conceived and designed the experiments; YL, LP and CX performed the experiments; YL and XS analysed the data; YL contributed reagents/materials/analysis tools; YL wrote the paper.

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Correspondence to Caixia Dong.

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Fig. S1

Phylogenetic tree showing HAK/KUP/KTs from Arabidopsis thaliana, Oryza sativa, and Pyrus bretschneideri. The tree was generated with Clustal X2.0 using the NJ method with MEGA6.0. Supplementary material 1 (TIF 1263 KB)

Fig. S2

Phylogenetic tree and PbHAK gene structures. The phylogenetic tree on the left side was generated by MEGA 6.0 using the NJ method with 1000 bootstrap replicates. The percentage bootstrap scores are indicated on the nodes. The exon and intron organization for each PbHAK gene was obtained from the Gene Structure Display Server (http://gsds.cbi.pku.edu.cn/). Exons and introns are represented by pink boxes and black lines, and untranslated regions (UTRs) are indicated by blue boxes. Supplementary material 2 (TIF 698 KB)

Fig. S3

Distribution of conserved motifs within PbHAKs. The phylogenetic tree on the left side was generated by MEGA 6.0 using the NJ method with 1000 bootstrap replicates. Motifs are represented by colored boxes. Motifs were detected using MEME (http://meme-suite.org/tools/meme) with the following parameters: 5 ≤ optimum motif width ≤ 200; the number of motifs = 15; zero or one occurrence per sequence. Supplementary material 3 (TIF 658 KB)

Fig. S4

Chromosomal localization of PbHAK genes. Each bar represents a chromosome, and chromosome numbers are shown at the top of each chromosome. Tandem duplications are shown using red text. The black lines connect segmentally duplicated gene pairs, and the segmental duplication regions were estimated using the Plant Genome Duplication Database (PGDD). Additionally, one pair of segmentally duplicated genes (PbHAK4/PbHAK5) was located on Chr 07 and the other pair (PbHAK10/PbHAK11) was located on Chr 11. Supplementary material 4 (TIF 1187 KB)

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Li, Y., Peng, L., Xie, C. et al. Genome-wide identification, characterization, and expression analyses of the HAK/KUP/KT potassium transporter gene family reveals their involvement in K+ deficient and abiotic stress responses in pear rootstock seedlings. Plant Growth Regul 85, 187–198 (2018). https://doi.org/10.1007/s10725-018-0382-8

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