Genome-wide characterization and expression analysis of HAK K+ transport family in Ipomoea

Rong Jin; Wei Jiang; Mengxiao Yan; Aijun Zhang; Ming Liu; Peng Zhao; Xiaoguang Chen; Zhonghou Tang

doi:10.1007/s13205-020-02552-3

Genome-wide characterization and expression analysis of HAK K⁺ transport family in Ipomoea

3 Biotech. 2021 Jan;11(1):3. doi: 10.1007/s13205-020-02552-3. Epub 2020 Nov 27.

Authors

Rong Jin¹, Wei Jiang¹, Mengxiao Yan², Aijun Zhang¹, Ming Liu¹, Peng Zhao¹, Xiaoguang Chen¹, Zhonghou Tang¹

Affiliations

¹ Chinese Academy of Agricultural Sciences/Xuzhou Sweetpotato Research Center, Jiangsu/Key Laboratory of Sweetpotato Biology and Gentic Breeding, Sweetpotato Research Institute, Ministry of Agriculture, Xuzhou, 221121 China.
² Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai, China.

Abstract

The potassium transporter high-affinity K⁺ transporter/K⁺ uptake permease/K⁺ transporter (HAK/KUP/KT) family plays a vital role in potassium uptake, and potassium ion (K⁺)-mediated environmental stress. In the present study, we identified 22 IbHAK/KUP/KT (HAK) genes in sweet potato [Ipomoea batata (L.) Lam] and the same number of HAK genes from sweet potato wild relative Ipomoea trifida. Phylogeny analysis indicated that the HAKs can be divided into five clades. Chromosomal distribution and genome synteny analyses revealed two tandem-duplicated gene pairs IbHAK16/17 and IbHAK17/18 on chromosomes 13 and eight segmental-duplicated gene pairs on chromosomes 1, 3, 5, 8, 10, 12, 14 among the IbHAK gene family. Eleven orthologous HAK gene pairs between I. batata and I. trifida were involved in the duplication of genomic blocks based on comparative genomic analysis. The Ka/Ks ratios of these IbHAK genes ranged from 0.02 to 0.55(< 1), further indicated that purifying selection was the primary force driving the evolution of HAKs in Ipomoea. A heat map based on RNA-seq data showed that 13 HAKs in Xushu32 (a K⁺-tolerant sweet potato genotype) and 10 HAKs in Ningzi1 (a K⁺-sensitive sweet potato genotype) in response to K⁺ deficiency stress. Quantitative real-time PCR (qRT-PCR) analysis revealed IbHAK2, -3, -8, -10, -11, -18, -19, and -21 were induced in both Xushu32 and Ningzi1 under low K⁺ stress. Compared with other IbHAK genes, IbHAK8 showed more strongly upregulation after exposure to drought and salt stress. Furthermore, co-expression analysis showed that only IbHAK8 of 22 IbHAK genes involved in network interactions with 30 genes related to abiotic and biotic stresses. Taken together, these results are helpful for further functional studies on IbHAK and molecular breeding of sweet potato.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-020-02552-3.

Keywords: Gene expression; HAK/KUP/KT family; IbHAK; Identification; Sweet ptotato.