Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Solanum tuberosum.

Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes' resistance to drought.

Identification and characterization of phosphate transporter genes in potato.

Phosphate transporter (PHTs) have important roles in Pi acquisition, allocation, and signal transduction. The aim of this study is to provide a comprehensive knowledge of PHTs in potato. Very strict homology search and subsequent domain verification using Hidden Markov Models revealed that the potato genome has 20 StPHT and StPHOs genes which were grouped into 5 phylogenetical clusters including 8 PHT1 homologs,1 PHT2 homolog, 2 PHT3 homologs, 5 PHT4 homologs and 4 PHO homologs. These genes were mapped on ten S. tuberosum chromosomes (chr1-9 and 12). Analysis of these genes led to identification of 20 conserved motifs and location prediction showed that PHT1 and PHT4 proteins have 12 transmembrane (TM) domains, PHT2 proteins have 13 TM domains, PHT3 proteins contain 4-5 TM domains, and PHO proteins contain 8-10 TM domains. Two tandem and 2 segmental duplications were further identified from these genes. RT-qPCR analysis showed that most of PHTs and PHOs displayed specific expression patterns with respect to phosphate status, fourteen transporters were up regulated in leaves and 11 transporters were up regulated in roots under phosphate deprivation. StPHT2;1 was found to be expressed both in potato leaf and root after phosphate starvation. Most cis-regulatory elements in StPHTs and StPHOs were found associated with light, defense, stress and hormones responsiveness, endosperm and meristem expression, as well as circadian control. A scan of the coding sequences of 20 StPHTs and StPHOs against published miRNAs in potato predicted a total of 2 potential miRNAs, mainly targeting members located on the same chromosome. Expression of StPHTs and StPHOs was selectively induced by biotic and abiotic stresses, and phytohormone treatments, among them, heat stress exclusively caused the up-regulation of 14 StPHT and StPHO genes, in particular PHO1 members. Most of StPHTs and StPHOs do not exhibit the tissue-specific expression. StPHT1;7, StPHT3;1 and StPHTO1;1 were highly expressed in the root of S. tuberosum, especially the gene StPHT3;1 are highly expressed in 14 tissues which covering the entire life cycle of potato. Our results provide comprehensive insights into the PHT and PHO family genes involved in the growth, development, and stress response of the potato.

Genome-wide identification of the potato WRKY transcription factor family.

WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes. The expression analysis of 22 StWRKYs showed their differential expression levels under various stress conditions. Cis-element prediction showed that a large number of elements related to drought, heat and salicylic acid were present in the promotor regions of StWRKY genes. The expression analysis indicated that seven StWRKYs seemed to respond to stress (heat, drought and salinity) and salicylic acid treatment. These genes are candidates for abiotic stress signaling for further research.