Potatoes are an economically important crop owing to food importance world widely. During the development and growth process potato faced various stresses (Quandahor et al., 2021; Zaynab et al., 2021c). The DUF4228 proteins belong to the DUF superfamily. The current study illustrated that the DUF4228 family proteins played a vital role in abiotic stress response in plants (Leng et al., 2021)(Qi et al., 2019). Sequence analysis of plant genomes has revealed the presence of DUF4228 genes in Medicago truncatula (Albornos et al., 2017). In Arabidopsis thaliana three DUF4228 family members for example, AT1G21010, ATIG28190, and ATIG10530, are important in drought stress (Yang et al., 2020). The CiDUF4228 (Caragana intermedia DUF4228) genes member Expression of the Caragana intermedia DUF4228-3 (CiDUF4228-3) genes were significantly up-regulated in low temperature, drought, and dehydration indicating its response in stress condition (Na et al., 2016). However, little information is available for the potato MAPKgene members. In this article, a total of 10 StDUF4228 genes were observed from the genome sequence of potatoes.
All identified StDUF4228 genes were classified into six groups, e.g., Group 1, Group 2, Group 3, Group 4, Group 5, and Group 6. The comparative phylogenetic analysis revealed that the organization of St, Sl, and At proteins was relatively similar in groups 1, 2, 3, 4, 5, and 6., indicating that all StDUF4228 genes in these groups may have descended from a common ancestor. The StDUF4228 protein structural analysis will provide functional analysis significance. The evolutionary relic illustrated the arrangement of exon-intron that shaped the gene family evolution (Flagel and Wendel, 2009; Moore and Purugganan, 2005). This is associated with prior scientific findings, so as too few genes are subjected to be retained in plants, during evolution, some may not show introns and may show short introns (Mattick and Gagen, 2001). Without or with few introns, the gene expression level is lowered in plants (Mattick and Gagen, 2001). Furthermore, a complex gene structure may represent a quick response against endogenous and exogenous stimuli. (Jeffares et al., 2008). Structural gene analysis results reported that sequences of StDUF4228 genes showed equal numbers and similar functional characters of introns-exons because they originated during duplication events in the course of evolution (Bari et al., 2018; Waqas et al., 2019). Cis-element studies provide vital foundations for further functional analysis of StMAPK genes. We observed that each StDUF4228 promoters restrain more than one or one stress-responsive cis-elements, including light, anaerobic induction, low-temperature response elements, MeJA response element, SA response element (SARE), and ABA response element (ABRE). Furthermore, these mentioned Cis-elements play an important function through regulating stress-responsive genes in stress conditions (Wu et al., 2014). Thus, in StDUF4228, these significant Cis-acting sites suggest their response in different environmental stresses (Maruyama-Nakashita et al., 2007; Osakabe et al., 2014).
Over the past few years, abundant miRNAs have been recognized through genome-wide examination in rapeseed to participate in diverse environmental factors (Buhtz et al., 2008; Fu et al., 2019). The present study identified 53 miRNAs from different families targeting 25 StDUF4228 genes (Fig. 6a; Table S6). Numerous genomic and proteomic studies have elucidated that plants’ response to saline and other stresses comprises a broad spectrum of processes, such as protein biosynthesis, membrane trafficking, and signal transduction (Bej and Basak, 2014), and it has been well established that miRNAs and their targets influence directly on plant stress tolerance (Li, 2015; Villanueva et al., 2016). In this context, in Arabidopsis, maize, and cowpea an upregulation of miR156, of their corresponding targets such as SBPs/SPLs, TCP family transcription factor, ARFs, RNaseIII CAF protein, AGO1, and CBF during salinity stress has been documented (Ding et al., 2009; Liu et al., 2008). Similarly, it has been widely reported that miR156 has a significant role during abiotic stress conditions in many plants (Cui et al., 2014; Kohli et al., 2014). Similarly, a microarray experiment on cotton revealed that miR827 has a crucial role of salt stress responses (Covarrubias and Reyes, 2010). miR167 was previously reported to have key roles in abiotic stress responses (Khraiwesh et al., 2012). Shortly, these reports support our results and recommend that bna-miRNAs might play pivotal roles against several stresses by altering the transcript levels of StDUF4228 genes in rapeseed.
The genome duplications, distribution of genes, and genome size are the chief feature of genetic diversity between land plants. Genetic duplication has long been observed in the above factors during gene families’ evolutionary origins, complexity, and expression. Some duplication events were also discovered in StDUF4228, which play an important function in amplifying the StDUF4228 genes. As gene duplication has been an important factor in diversification, expansion, and neofunctionalization of gene families (Lavin et al., 2005), similarly the StDUF4228 gene mapping and distribution at a chromosomal level will provide the potato breeders through desired traits to develop novel varieties of potatoes.
The function of DUF4228 genes has been suggested in different abiotic stress factors of plants (Wang et al., 2018). Therefore, the DUF4228 gene function has not yet been observed in potato. Earlier studies reported a total of 25 DUF4228 genes in Arabidopsis, 52 in Populus trichocarpa, 22 in Aquilegia coerulea, and 29 in Medicago truncatula (Yang et al., 2020). Therefore, StDUF4228 expression profiling and their validation are helpful for a deep understanding of the potato genome. The recent study illustrated higher transcript abundances of StDUF4228 in the roots; such indication was also identified in earlier studies (Yang et al., 2020) and supported our data where StDUF4228-20, StDUF4228-21, and StDUF4228-28, show a high expression in root tissues. Our RT-qPCR results show that StDUF4228-3,StDUF4228-4,and StDUF4228-30 were specifically upregulated in stem,leaf and root tissues. This illustrates that potato DUF4228 genes have a significant role in abiotic response against various stresses.
Thus, more studies on the DUF4228 gene family revealed its significant role in abiotic stress response (Leng et al., 2021). In potato, StDUF4228-21, and StDUF4228-4 are upregulated in response to heat and salt stress. Various signal transduction hormones may affect plants' biochemical and physiological processes (Fatima et al., 2021; Zaynab et al., 2017). Such as, ABA and IAA are considered essential immune responsible hormones in plants. A variety of studies reported that DUF4228 is responsible for stress control and is also involved in hormonal signaling and developmental signaling. Moreover,to find whether the DUF4228 were expressed through hormonal signaling in potato, the leaves of the potato were treated by ABA, IAA and examined the gene expression. After IAA and ABA treatment, genes were induced, showed different functions of different StDUF4228 gene members in IAA- and ABA-induced immune responses. Total 18StDUF4228 genes under ABA and 23 StDUF4228 genes under IAA and GA3 treatment, upregulation illustrated that IAA and ABA perform a vital role in this immune response. Phytohormones were identified to play a role in the ATDUF4228 genes that support our results (Yang et al., 2020). The expression of genes and their clusters also mentioned a powerful correlation of gene clusters and gene expression in different tissues under different stress factors. This co-expression and co-occurrence show their putative function in the adaptation of plants under diverse environmental stress factors.