**3. Findings of novel genes in native plants from arid land areas**

The development of high-throughput next-generation sequencing technologies offers opportunities for genome-wide transcription analysis of non-model plants and especially of desert plants and discovery of novel pathways and genes related to drought tolerance. These novel genes may be useful to improve drought tolerance in cultivated plants. Even though there are not many studies in plants native to arid regions, the results of some of the research that different groups have carried out allow insights over the abundance of potential novel genes for drought tolerance.

By using the analysis of subtracted expressed sequence tags (ESTs) in horse gram (*Macrotyloma uniflorum* (Lam.) Verdc.), 531 unigenes were found as upregulated by drought. Among these unigenes 366 showed significant similarity to known sequences in the database. Approximately 30% of the ESTs had no similarity to known proteins in the GenBank database. Those are considered as novel. Also, according to the functional classification, the most abundant ESTs were those related to stress responses (12%), DNA processing and nucleotide metabolism (10%), photosynthesis and electron transport (9%), and transcription factors (5%). There was redundancy in several known stress-responsive clones in dehydrated sample. The most prominent were metallothionein, glutathione S-transferase, RabGAP/TBC domain-containing protein, lipoxygenase, translationally controlled tumor protein, chaperon, lipid transfer protein, cysteine proteinase, calmodulin, calmodulin-binding protein, and sterol 24-C-methyltransferase [79]. Moreover, a protein-protein interactome study carried out in *M. uniflorum* showed that the highest number of PIPs occurred in shoot (416) and root (2228) tissues of a droughttolerant genotype as compared to shoot (136) and root (579) tissues of a sensitive genotype. The PIPs most responsive to drought stress were kinase and transferase activities involved in signal transduction, cellular processes, nucleocytoplasmic transport, protein ubiquitination, and localization of molecules. These PIPs could be enclosed in mechanisms of drought tolerance of *M. uniflorum*. Also, they could provide new understandings of mechanisms involved in drought tolerance [80].

A transcriptomic analysis of the roots of *Ammopiptanthus mongolicus*, an endemic species to the Gobi Desert*,* allowed to identify 27 drought-responsive genes. These genes were grouped into the GO categories of response to osmotic stress, response to oxidative stress, response to hormone stimulus, and response to light stimulus. A total of 9771 (34%) out of 29,056 ESTs matched to known proteins recorded in the PlantGDB database. This means that many ESTs could be novel drought-responsive genes [81]. Another study of comprehensive transcriptome of *A. mongolicus*

**67**

involved in protein kinase [85].

*Native Plants to Arid Areas: A Genetic Reservoir for Drought-Tolerant Crops*

identified up to 6102 DEGs under drought stress at 3 points of exposure. A group of 2028 DEGs were common for the 3 points. Among them 779 DEGs were upregulated and 1185 were downregulated by drought. The upregulated DEGs included a heavy representation of genes encoding ripening-related proteins, LEA proteins, peroxidases, transporters, enzymes of flavonoid biosynthetic pathways, protein kinases, ethylene receptors, and transcription factors. About 17.2% of the common DEGs had no homology to known functional proteins [82]. Similarly, Pang et al. [83] identified

1620 DEGs, including 1106 upregulated DEGs and 514 downregulated DEGs.

pathway for this plant species protection when exposed to drought [30].

*Reaumuria soongorica* is an extreme xerophyte shrub from Gobi and marginal loess of central Asia. A transcriptomic analysis identified 123 unigenes potentially associated with drought adaptation. A total of 46 unigenes were related to drought escape mechanisms, while 40 unigenes were potentially involved in drought avoidance. Also, 32 unigenes had identity to genes involved in ABA-dependent, while 8 unigenes had homology to some genes involved in ABA-independent pathways of drought tolerance. There was a 7.96% of unigenes that did not match any homologous genes in the known plant species [84]. Another study identified 1325 DEGs, including 379 upregulated DEGs and 946 downregulated DEGs under drought stress. Among DEGs, 20 genes encoded for kinases, and 14 encoded for transcription factors such as WRKY, NAC, MYC, TCP, and bZIP. Also 13 DEGs encoding for functional proteins such as LEA proteins, small heat shock proteins, and aquaporin (AQP) and proline transporter were identified. Moreover, 14 DEGs were found encoding for low-temperature-induced protein, dehydration-induced protein, defensing precursor, resistance protein, universal stress protein, and protein

*Haloxylon ammodendron* (C.A.Mey) is a desert tree distributed in Middle and Central Asia. By doing a transcriptomic analysis in this species, up to 1060 unigenes were identified as DEGs for drought stress. Among them, 356 DEGs were upregulated and 704 DEGs were downregulated. A total of 469 (44%) of DEGs did not show homology to genes in NCBI database. Approximately 12.1% of DEGs with homology to known genes were associated with nitrogen metabolism, starch and sucrose metabolism, and fatty acid metabolism. Also, 35 DEGs encoded known or putative transcription factors such as WRKY, MYB, and ethylene-responsive [86]. The expression of drought-responsive genes may depend on the stress intensity.

A study in *Sophora moorcroftiana* revealed that more genes were differentially expressed under severe water stress than mild stress. Up to 5648 unigenes were differentially expressed between control and severe stress plants. Around 601 unigenes were common for mild and severe water stress. Eleven out of 1534 TFs were selected for expression analysis. Among these, seven were drought-responsive. Those encoding for DREB, zinc-finger protein (ZnF), zinc-finger protein kinase (ZFPK), MYB, NAC, and WRKY were upregulated, while ERB was downregulated. Three selected aquaporins (AQPs) and one sugar transporter (SUT) genes were upregulated by

In *Cynanchum komarovii*, a xerophytic plant species, up to 3134 unigenes were found as differentially expressed genes (DEGs) under drought stress. A total of 601 unigenes were induced, while 2533 unigenes were repressed. The most abundant upregulated DEGs were into the following GO groups: "oxidation-reduction process" with 120 DEGs, "single-organism metabolic process" with 185 DEGs, and "oxidoreductase activity" with 113 DEGs. The most downregulated genes were grouped into the following GO terms: "metabolic process," "cellular component organization or biogenesis," "cellular response to stimulus," "macromolecular complex," "cytoplasm,", "protein binding," and "hydrolase activity." KEGG pathway analysis allowed to identify that DEGs involved in "cutin, suberine, and wax biosynthesis" changed significantly, which may be due to the important role of this

*DOI: http://dx.doi.org/10.5772/intechopen.86485*

#### *Native Plants to Arid Areas: A Genetic Reservoir for Drought-Tolerant Crops DOI: http://dx.doi.org/10.5772/intechopen.86485*

*Drought - Detection and Solutions*

Plants native to arid lands may have antioxidant defense systems to limit the deleterious effects of ROS. For example, in *Oudneya africana*, a Saharan plant, water deficit caused variations in enzymatic and nonenzymatic antioxidants, differentially affecting the concentration of SOD and POX [76]. Transgenic poplar expressing the eukaryote translation initiation factor 5A (TaeIF5A1) from *Tamarix androssowii* showed greater superoxide dismutase (SOD) and peroxidase (POD) activities, lower electrolyte leakage, and improved tolerance to abiotic stresses [77]. Six plant species from semiarid Loess Hilly Region of China showed significant differences in SOD and POD activities when subject to drought along 3 months. Also there were significant interactions of SOD, CAT, and POD activities and MDA content between months and species [78]. A transcriptomic study under drought stress showed that *Prunus mongolica* Maxim, a species widely distributed in the Gobi Desert, increased transcription of iron superoxide dismutase and manganese

superoxide dismutase which promoted drought stress tolerance [31].

**3. Findings of novel genes in native plants from arid land areas**

The development of high-throughput next-generation sequencing technologies offers opportunities for genome-wide transcription analysis of non-model plants and especially of desert plants and discovery of novel pathways and genes related to drought tolerance. These novel genes may be useful to improve drought tolerance in cultivated plants. Even though there are not many studies in plants native to arid regions, the results of some of the research that different groups have carried out allow insights over the abundance of potential novel genes for drought tolerance. By using the analysis of subtracted expressed sequence tags (ESTs) in horse gram (*Macrotyloma uniflorum* (Lam.) Verdc.), 531 unigenes were found as upregulated by drought. Among these unigenes 366 showed significant similarity to known sequences in the database. Approximately 30% of the ESTs had no similarity to known proteins in the GenBank database. Those are considered as novel. Also, according to the functional classification, the most abundant ESTs were those related to stress responses (12%), DNA processing and nucleotide metabolism (10%), photosynthesis and electron transport (9%), and transcription factors (5%). There was redundancy in several known stress-responsive clones in dehydrated sample. The most prominent were metallothionein, glutathione S-transferase, RabGAP/TBC domain-containing protein, lipoxygenase, translationally controlled tumor protein, chaperon, lipid transfer protein, cysteine proteinase, calmodulin, calmodulin-binding protein, and sterol 24-C-methyltransferase [79]. Moreover, a protein-protein interactome study carried out in *M. uniflorum* showed that the highest number of PIPs occurred in shoot (416) and root (2228) tissues of a droughttolerant genotype as compared to shoot (136) and root (579) tissues of a sensitive genotype. The PIPs most responsive to drought stress were kinase and transferase activities involved in signal transduction, cellular processes, nucleocytoplasmic transport, protein ubiquitination, and localization of molecules. These PIPs could be enclosed in mechanisms of drought tolerance of *M. uniflorum*. Also, they could provide new understandings of mechanisms involved in drought tolerance [80].

A transcriptomic analysis of the roots of *Ammopiptanthus mongolicus*, an endemic species to the Gobi Desert*,* allowed to identify 27 drought-responsive genes. These genes were grouped into the GO categories of response to osmotic stress, response to oxidative stress, response to hormone stimulus, and response to light stimulus. A total of 9771 (34%) out of 29,056 ESTs matched to known proteins recorded in the PlantGDB database. This means that many ESTs could be novel drought-responsive

genes [81]. Another study of comprehensive transcriptome of *A. mongolicus*

**66**

identified up to 6102 DEGs under drought stress at 3 points of exposure. A group of 2028 DEGs were common for the 3 points. Among them 779 DEGs were upregulated and 1185 were downregulated by drought. The upregulated DEGs included a heavy representation of genes encoding ripening-related proteins, LEA proteins, peroxidases, transporters, enzymes of flavonoid biosynthetic pathways, protein kinases, ethylene receptors, and transcription factors. About 17.2% of the common DEGs had no homology to known functional proteins [82]. Similarly, Pang et al. [83] identified 1620 DEGs, including 1106 upregulated DEGs and 514 downregulated DEGs.

In *Cynanchum komarovii*, a xerophytic plant species, up to 3134 unigenes were found as differentially expressed genes (DEGs) under drought stress. A total of 601 unigenes were induced, while 2533 unigenes were repressed. The most abundant upregulated DEGs were into the following GO groups: "oxidation-reduction process" with 120 DEGs, "single-organism metabolic process" with 185 DEGs, and "oxidoreductase activity" with 113 DEGs. The most downregulated genes were grouped into the following GO terms: "metabolic process," "cellular component organization or biogenesis," "cellular response to stimulus," "macromolecular complex," "cytoplasm,", "protein binding," and "hydrolase activity." KEGG pathway analysis allowed to identify that DEGs involved in "cutin, suberine, and wax biosynthesis" changed significantly, which may be due to the important role of this pathway for this plant species protection when exposed to drought [30].

*Reaumuria soongorica* is an extreme xerophyte shrub from Gobi and marginal loess of central Asia. A transcriptomic analysis identified 123 unigenes potentially associated with drought adaptation. A total of 46 unigenes were related to drought escape mechanisms, while 40 unigenes were potentially involved in drought avoidance. Also, 32 unigenes had identity to genes involved in ABA-dependent, while 8 unigenes had homology to some genes involved in ABA-independent pathways of drought tolerance. There was a 7.96% of unigenes that did not match any homologous genes in the known plant species [84]. Another study identified 1325 DEGs, including 379 upregulated DEGs and 946 downregulated DEGs under drought stress. Among DEGs, 20 genes encoded for kinases, and 14 encoded for transcription factors such as WRKY, NAC, MYC, TCP, and bZIP. Also 13 DEGs encoding for functional proteins such as LEA proteins, small heat shock proteins, and aquaporin (AQP) and proline transporter were identified. Moreover, 14 DEGs were found encoding for low-temperature-induced protein, dehydration-induced protein, defensing precursor, resistance protein, universal stress protein, and protein involved in protein kinase [85].

*Haloxylon ammodendron* (C.A.Mey) is a desert tree distributed in Middle and Central Asia. By doing a transcriptomic analysis in this species, up to 1060 unigenes were identified as DEGs for drought stress. Among them, 356 DEGs were upregulated and 704 DEGs were downregulated. A total of 469 (44%) of DEGs did not show homology to genes in NCBI database. Approximately 12.1% of DEGs with homology to known genes were associated with nitrogen metabolism, starch and sucrose metabolism, and fatty acid metabolism. Also, 35 DEGs encoded known or putative transcription factors such as WRKY, MYB, and ethylene-responsive [86].

The expression of drought-responsive genes may depend on the stress intensity. A study in *Sophora moorcroftiana* revealed that more genes were differentially expressed under severe water stress than mild stress. Up to 5648 unigenes were differentially expressed between control and severe stress plants. Around 601 unigenes were common for mild and severe water stress. Eleven out of 1534 TFs were selected for expression analysis. Among these, seven were drought-responsive. Those encoding for DREB, zinc-finger protein (ZnF), zinc-finger protein kinase (ZFPK), MYB, NAC, and WRKY were upregulated, while ERB was downregulated. Three selected aquaporins (AQPs) and one sugar transporter (SUT) genes were upregulated by

drought. Genes encoding for scavenging reactive oxygen species such as POD, PRX, and GPDH were induced by drought stress [49].

*Prunus mongolica* is a plant native to the Gobi Desert. In this species a total of 3365 differentially expressed transcripts (DETs) for water stress were identified, counting 1876 transcripts upregulated and 1489 transcripts downregulated. Among these, 42 transcripts coding for 5 aquaporin subfamilies were found. Also, 15 potential plasma membrane intrinsic proteins (PIPs) were upregulated and 1 downregulated. Interestingly, 177 transcripts related to ROS scavenging were identified. Approximately 28% of them were predicted as SOD. Several significant pathways were identified to be related to drought tolerance of *P. mongolica*. These pathways included transcription factors and plant hormone signal transduction, starch and sucrose metabolism, and cysteine and methionine metabolism [31].

*Artemisia sphaerocephala* is a species found in sand dunes in the deserts of Northwest China. A transcriptomic analysis in this species identified 108 unigenes related to drought stress tolerance. These had homology to 17 kinases, 2 potential chaperones, 52 enzymes, 6 transporters and channels, and 3 aquaporins. Even though, transcription factor were not identified, 25 out of the 108 unigenes were among the 1000 most highly expressed genes [87].

*Zygophyllum xanthoxylum* is a succulent halophythe adapted to arid environments. In this plant a total of 1723 DEGs were identified as upregulated in leaves of plants under osmotic stress (−0.5 MPa) during 24 h. Up to 53 DEGs related to ROS scavenging were also identified as upregulated, most of them encoded for glutathione S-transferase (GST) and peroxidases (POD). Also, 31 DEGs homologous to transporters were upregulated in the roots under salt and osmotic stress. However, 23 DEGs related to photosynthesis were downregulated under osmotic stress [88].

*Cleistogenes songorica* is a C4 xerophyte widely distributed in the arid regions of Northwest China. A mining study for LEA genes identified at least 44 putative LEA proteins. They were named CsLEA1 to CsLEA44 and classified into eight subfamilies. These LEAs were characterized, and two unusual LEA stress-related domains, water stress and hypersensitive response (WHy), and LEA14-like desiccationrelated proteins were detected. Most LEAs within the same family showed similar structures and properties. All the CsDehydrin proteins contained the YKS segments which are essential for keeping the capacity to adjust their conformation and maintain cellular homeostasis under stress conditions. Among the cis-regulatory elements of the LEA genes, more than three G-Boxes were registered for each *dehydrin*, *LEA\_2*, and *SMP* genes and more than two MBS for *dehydrin* and *LEA\_2* subfamily gene [89].

*Prosopis juliflora* is a species native to arid lands of Mexico and widely distributed in arid and semiarid regions of Central and South America. In this species 6874 DEGs were found under salt and drought stress. Approximately 42.6% (2932 DEGs) had homology to genes with GO annotation. Among these, 1339 DEGs were upregulated, while 1596 were downregulated. More DEGs under salt and drought stress were found in roots than those of leaves. Under drought stress, there was more upregulation than downregulation in leaves, while in roots there was more downregulation. A total of 30 unigenes were recognized as exclusively responsive to drought stress. One of these genes encoding for *Arabidopsis* ortholog ABR1 was downregulated. Two upregulated genes encoded for transcription factors involved in diminishing intracellular H2O2 levels. Also, three highly upregulated DEGs encoded for "pq-loop repeat family protein transmembrane family protein" which has been assigned with a potential role in stress tolerance. Many drought-responsive genes were tissue specific. For example, 1040 genes were specifically expressed in root tissues. Up to 805 genes were commonly regulated by drought and salt stress in root tissue. Upregulated genes included those coding for dehydration-responsive

**69**

**Author details**

and Fabian García-González

provided the original work is properly cited.

*Native Plants to Arid Areas: A Genetic Reservoir for Drought-Tolerant Crops*

line-5-carboxylate synthase, and ras-related protein rabc2a [90].

protein rd22, pectinesterase-2, LEA protein, and POD. Moreover, 74 DEGs were commonly upregulated in leaf tissues and 16 were downregulated. The induced genes included pectinesterase-2, non-specific lipid-transfer protein, delta-1-pyrro-

Drought stress tolerance is a complex quantitative trait that involves several mechanisms and multiple genes to produce the defense responses of the plants for dealing with environmental conditions of drought. Studies in model plants have found some of the main mechanisms, genes, and proteins that are activated upon drought stress. However, not enough studies have been carried out in plants native to arid lands. The new sequencing technologies and bioinformatic tools applied to some plants native to desert areas have allowed to identify many of the already characterized genes and proteins involved in drought stress tolerance. The most important is that this kind of studies has shown that myriads of drought-related transcripts are not characterized and may belong to novel genes. These may be part of the already known pathways of plants responses to drought or may participate in novel ways to tolerate drought, and after further studies may be used to improve

Ricardo Trejo-Calzada\*, Aurelio Pedroza-Sandoval, Jesus G. Arreola-Avila

© 2019 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

Chapingo Autonomous University, Bermejillo, Durango, México

The authors of this work declare no conflict of interest.

\*Address all correspondence to: rtrejo@chapingo.uruza.edu.mx

*DOI: http://dx.doi.org/10.5772/intechopen.86485*

**4. Conclusions**

drought tolerance in crops.

**Conflict of interest**

protein rd22, pectinesterase-2, LEA protein, and POD. Moreover, 74 DEGs were commonly upregulated in leaf tissues and 16 were downregulated. The induced genes included pectinesterase-2, non-specific lipid-transfer protein, delta-1-pyrroline-5-carboxylate synthase, and ras-related protein rabc2a [90].
