Genome-Wide Identification and Expression Analysis of the KUP Family under Abiotic Stress in Cassava (Manihot esculenta Crantz)

Abstract

KT/HAK/KUP (KUP) family is responsible for potassium ion (K⁺) transport, which plays a vital role in the response of plants to abiotic stress by maintaining osmotic balance. However, our understanding of the functions of the KUP family in the drought-resistant crop cassava (Manihot esculenta Crantz) is limited. In the present study, 21 cassava KUP genes (MeKUPs) were identified and classified into four clusters based on phylogenetic relationships, conserved motifs, and gene structure analyses. Transcriptome analysis revealed the expression diversity of cassava KUPs in various tissues of three genotypes. Comparative transcriptome analysis showed that the activation of MeKUP genes by drought was more in roots than that in leaves of Arg7 and W14 genotypes, whereas less in roots than that in leaves of SC124 variety. These findings indicate that different cassava genotypes utilize various drought resistance mechanism mediated by KUP genes. Specific KUP genes showed broad upregulation after exposure to salt, osmotic, cold, H₂O₂, and abscisic acid (ABA) treatments. Taken together, this study provides insights into the KUP-mediated drought response of cassava at transcription levels and identifies candidate genes that may be utilized in improving crop tolerance to abiotic stress.

Keywords: KUP family; cassava; drought stress; gene expression; identification.

Figure 1

Phylogenetic analysis of KUPs from cassava, rice, and Arabidopsis using the complete protein sequences. The Neighbor-joining (NJ) tree was reconstructed using Clustal X 2.0 and MEGA 5.0 softwares with the pair-wise deletion option. One thousand bootstrap replicates were used to assess tree reliability.

Figure 2

The conserved motifs of cassava KUPs according to phylogenetic relationship. All motifs were identified by MEME database with the complete amino acid sequences of cassava KUPs.

Figure 3

Gene structure analyses of cassava KUPs according to phylogenetic relationship. Exon-intron structure analyses were performed by GSDS database. The blue boxes, yellow boxes, and the black lines indicate upstream/downstream, exons, and introns, respectively.

Figure 4

Expression profiles of cassava KUPs in different tissues of Arg7, KU50, and W14. Log2 based fold change was used to create the heat map. Fold changes in gene expression are shown in color as the scale.

Figure 5

Expression profiles of cassava KUPs in response to drought stress in leaves and roots of Arg7, SC124, and W14. Log2 based fold change was used to create the heat map. Fold changes in gene expression are shown in color as the scale.

Figure 6

Expression patterns of MeKUPs after osmotic, NaCl, cold, H₂O₂, and ABA treatments treatment in cassava. The mean fold changes of each gene between treated and control samples at each time point were used to calculate its relative expression levels. NTC indicates no treatment controls (mean value = 1). Data are means ± SD of n = 3 biological replicates. Means denoted by the same letter do not significantly differ at P < 0.05 as determined by Duncan's multiple range test.