Groundnut (Arachis hypogaea L.) or peanut (2n = 4x = 40) (AABB) is an annual grain legume and oil crop with a primarily self-pollinated mating system [125]. As it was formed after a hybridization between diploid species, A. duranensis (AA) and A. ipaensis (BB), followed by chromosome doubling [126], it has a wide gene pool [122,125]. Cultivated groundnut genome size is approximately 2.7 Gb, very similar to the sum of its two wild progenitors, A. duranensis (1.25 Gb) and A. ipaensis (1.56 Gb) [127]. Crop wild relatives of groundnut constitute a valuable but underutilized genetic source due to difficulties in introgression of genes into the cultivated species, owing to ploidy discrepancy among groundnut (allotetraploid species) and the wild relatives (mainly diploid species) [125,128] as well as sterility barriers [129]. Drought and high temperatures constitute the major abiotic stress factors for groundnut, whereas salinity tolerance is important in many areas [125].

Plant heat shock factors (HSFs) play a key role in groundnut response to various environmental stresses by regulating the expression of stress responsive genes, such as heat shock proteins (HSPs), dehydration responsive element-binding proteins (DREBs), late embryogenesis abundant proteins (LEA), and abscisic acid response element-binding proteins AREB [130]. CRT element-binding factors (CBFs) were also found to respond to various plant stresses [131,132,133,134].

Dehydration responsive element-binding protein (DREB) genes are reported to increase transpiration efficiency under water-limiting conditions (AtDREB1A, DREB1A) [135,136,137]. A DREB factor, namely PNDREB1, was also identified by Zhang et al. [138] to respond to low temperatures and osmotic stress. However, no response of this gene to salinity has been observed. An ABA synthesis gene, AhNCED1, and three dehydration-induced transcription factor genes were also found to be differentially regulated in groundnut under drought conditions [139].

Ethylene-responsive factor (ERF) regulates gene expression associated with abiotic stress tolerance [140] through the activation of ABA [141]. In groundnut, ERF genes were found to be induced after the application of abiotic stresses, such as drought, cold, heat, and salinity [140]. Additionally, AhLea-3 has been reported to be related to salt tolerance [142]. AtNHX1, a vacuolar Na+/H+ antiporter in Arabidopsis thaliana, mediates the transport of Na+ and K+ into the vacuole, enhancing salt tolerance [143]. Overexpression of the AtNHX1 gene was also found to improve salt and drought tolerance in transgenic groundnut [144]. Moreover, stress-inducible expression of AtHDG11 in transgenic peanut lines resulted in up-regulation of various stress responsive genes (LEA, HSP70, Cu/Zn SOD, APX, P5CS, NCED1, RRS5, ERF1, NAC4, MIPS, Aquaporin, TIP, ELIP) leading to improved drought and salt tolerance [145].

Wild groundnut species genes that are drought stress involved are discriminated into two groups: (i) genes that are plant cell protectors and act as upstream regulators and (ii) regulatory genes, such as transcription factors, implicated in the ABA pathways [146]. Tolerance to abiotic stresses has been recorded in A. stenosperma [128], while Guimarães et al. [147] identified a remarkable number of transcription factors and genes related to drought stress in a peanut ancestor, A. duranencis. In the same wild species, a great number of differentially expressed genes were recorded under drought stress treatment [148]. Arachis duranensis tolerance to drought is based on restricted plant transpiration behavior upon stress implementation. Several characteristics associated with drought response were detected in A. dardani, such as leaf angle adjustment [48], and in A. duranensis high photosynthetic rate, stomatal conductance, transpiration rate, lower leaf temperature, and vapor pressure [50]. Drought-responsive candidate genes, such as Expansin, Nitrilase, NAC, and bZIP transcription factors, displaying significant levels of differential expression during stress application in A. duranensis and A. magna were identified, while they possess drought response mechanisms, including signal transduction, primary metabolism, hormone homeostasis, and protection of cellular structures [53]. More recently, genes encoding the drought-responding fatty acid, desaturase, were also identified in groundnut progenitors and presented to be homologous to peanut [149].

A heat-tolerant genotype of the wild species A. glabrata (A. glabrata 11824) and a cold tolerant genotype of A. paraguariensis (A. paraguariensis 120142) were identified by [55] through screening of thirty-six different wild genotypes. A total number of sixteen and seventeen heat shock transcription factors were found in A. duranensis and A. ipaensis, respectively, that are commonly known to protect plants from abiotic stresses [54]. Non-specific lipid transfer proteins (nsLTPs) that are known to transfer various lipid molecules between lipid bilayers in plants were identified in A. duranensis that respond to salinity and low-temperature conditions [51]. Tolerance assessed in Arachis wild species is presented in Table 1.

Genes and transcription factors identified in Arachis wild species were in many cases responding to a complex of abiotic stresses. In wild groundnut A. diogoi, the expression of gene AdDjSKI was induced under heat, salinity, drought, and osmotic stresses and seems to be related to the photosynthetic mechanism of plants [49]. Recently, NAC transcription factor genes that are implicated in salt and drought responses of many plant species were identified in A. hypogaea as well its progenitors [56]. Valine-glutamine sequences that are related to environmental changes were also assessed in wild species, A. duranensis, A. ipaensis, and A. monticola. Genes of the mTERF family that mediate acclimation of plants to adverse environmental conditions were also identified in A. duranensis and A. ipaensis that were distributed over their ten chromosomes [150]. Transcriptomic analyses on the wild and highly adaptable A. glabrata revealed a plethora of transcript factors to be expressed under drought, salt, and cold stress implementation [52]. Finally, a great number (4513) of differentiated expressed genes (DEGs) was also recorded to be expressed under UV exposure and dehydration in A. stenosperma by Martins et al. [57], mainly associated with cell signaling, protein dynamics, hormonal and transcriptional regulation, and secondary metabolic pathways. These genomic findings provide useful tools for the further improvement of the species in abiotic stresses.

Synthetic amphidiploid and autotetraploid groundnuts were created to overcome genetic barriers of groundnut breeding [151]. Synthetic groundnut germplasm was mainly screened for biotic stress tolerance [152,153,154,155,156] and introgressed into cultivated material [157,158]. The variability that synthetics often express could possess hidden alleviation for abiotic stress tolerance that remains mostly unexploited. Stress tolerance of the tetraploid groundnut species is not always expressed in the same way as their wild diploid relatives [154]. Bera et al. [159] found two interspecific derivatives, (NRCGCS-296 (J11 x A. duranensis)) and (NRCGCS-241 (GG 2 x A. cardenasii)), that presented high germination tolerant index and promptness index while applying 250 mM NaCl and therefore were characterized as tolerant to salinity. WRKY and Na+/H+ genes were also assessed as responsible for inducing tolerance in the synthetic hybrids.

2.3. Alfalfa
Legume plants make up one-third of the world’s major agricultural yield and are significant sources for human and animal consumption [84]. Medicago sativa (alfalfa), the most significant legume fodder, has been cultivated in more than 80 countries with a total surface area of 32 million hectares available globally [85]. Alfalfa is regularly exposed to harsh environments in the major regions of the world, including drought in Argentina and northern China, cold temperatures in Russia and Canada, and saline/alkaline soils in California, America, and Australia. Environmental stress in these places has had a significant impact on alfalfa productivity and quality [86–89]. Long-term domestication of cultivated alfalfa may have resulted in decreased tolerance for severe abiotic and biotic stressors because of the emphasis placed on features linked to high production. The key to accelerating M. sativa’s breeding is the use of genetic variants underlying agronomic features in wild relatives close to the cultivated Medicago [90]. Therefore, genomic data from wild species might offer important insights for enhancing features linked to the adaptability to stressful situations in legume forages. For breeding alfalfa varieties with great tolerance to environmental challenges, genetic resources rich in alleles adaptable to severe environments are highly needed. The genus Medicago includes wild species that are closely related to M. sativa, including Medicago truncatula (a model plant for legumes) [34], Medicago ruthenica [36], Medicago polymorpha [91], and Medicago falcata [38]. In the present study, emphasis was given to one of the most promising wild species. Medicago ruthenica (L.) Trautv. is a natural grassland plant that is widely distributed in hillsides, mixed grass steppes, and meadows in Siberia, Mongolia, and northern China [92]. It is an allogamous diploid (2n = 2x = 16) perennial legume fodder with re-assembled genome of 904.13 Mb [93]. It is very closely related to alfalfa [93]. Long, chilly winters and dry, saline soils limit M. ruthenica’s distribution area [94]. As a result, M. ruthenica must have developed powerful defenses to withstand the harsh conditions, such as drought, subfreezing temperatures, and saline soil. M. ruthenica is thought to be a rather uncommon species among Medicago species that is highly adapted to stressful conditions, and whose prospective applicability is favorably assessed in low input environments. The roles of differently abiotic stress-related expressed genes, such as AP2/ERF family, MYB/MYB-related family, bZIP, bHLH, and WRKY from M. ruthenica in stress resistance have not been fully elucidated [95,96]. These genes play important roles in many different regulation mechanisms of diverse abiotic stresses. Numerous studies have demonstrated the transcription factors, bZIP, WRKY, and AP2/ERF, have a role in the transduction of the ABA signal and stress responses in plants through their interaction [97].
2.3.1. Drought Stress Tolerance
In addition to being a close relative of alfalfa, M. ruthenica is a perennial species with a similar genome size, life cycle, and pollination system. More importantly, because it is a wild species with numerous accessions that is found widely in arid and/or semi-arid areas, it is highly tolerant to drought stress. As a result, it has been used as parental material to breed alfalfa cultivars that are tolerant to environmental stress, which has improved alfalfa tolerance to adverse environments [35,93]. M. ruthenica’s drought tolerance was compared to that of M. truncatula, M. varia, M. falcata, and two cultivars of alfalfa byWang et al. [36]. Among the tested legume species, M. ruthenica seedlings showed the greatest resilience to drought stress. The strongest resistance of M. ruthenica to drought stress among the examined legume forages was demonstrated by the fact that while exposure to drought significantly reduced the survival rates of other legume forages, the same treatment had little impact on the survival rates of M. ruthenica seedlings. Additionally, it was found M. ruthenica and M. truncatula, respectively, have 37 and 23 of the AP2/ERF family, drought-responsive TF genes. Twenty-one and ten drought-responsive TFs from the MYB/MYB-related family in M. ruthenica and M. truncatula, respectively, were discovered [35]. The knowledge of M. ruthenica’s genome and the discovery of its resistance genes can help to improve agronomic traits linked to high yield and exceptional tolerance to environmental stress using a molecular breeding strategy.
2.3.2. Salt Stress Tolerance
Abiotic stresses, such as salt stress, have an impact on plant productivity and growth. Medicago ruthenica exhibits exceptional stress resistance, making it a valuable gene resource
for enhancing other plants’ stress tolerance. Two differentially expressed genes (DEGs) (MrERF, MrbZIP) from M. ruthenica have not yet been thoroughly characterized in terms of their functions in salt tolerance. Wu et al. [95] demonstrated the transgenic lines of tobacco over-expressing these genes grew more successfully than wild types exhibiting greater height, more branches, and earlier flowering. Additionally, compared to wild type tobacco, the seed yield of transgenic tobacco was considerably higher. Furthermore, it was demonstrated MrERF or MrbZIP may be rapidly expressed in leaves by NaCl since three transgenic tobacco lines outgrew wild in terms of leaf growth, with MrERF and MrbZIP having the best growth. Thus, MrERF and MrbZIP can increase the germination rate of Medicago under salt stress because they greatly increased the germination rate of transgenic
tobacco lines. Plant height, biomass, and the root-to-shoot ratio of transgenic tobacco expressing MrERF or MrbZIP all significantly increased when exposed to NaCl. Lastly, under salt stress, MrERF and MrbZIP transgenic lines’ roots length grew by approximately 2.03 and 2.19 fold of wild type, respectively [96].
2.3.3. Cold Stress Tolerance
M. ruthenica is also an important resource for the genetic improvement of alfalfa in response to cold stress. Shu et al. [94] performed an RNA-Seq analysis of the M. ruthenica transcriptome in response to cold stress using high-throughput nucleotide sequencing. A total of 894 genes were identified that responded to cold stress. Expressions of MrUN10866, MrUN33504, MrUN37588, and MrUN40182 were induced by cold stress [95]. Numerous transcription factors (TFs) have been identified, and they all play crucial roles in how plants react to abiotic stressors, such as cold, including AP2/ERF, bHLH, MYB, WRKY, C2H2, and NAC. The AP2/ERF TF family, whose members have been extensively characterized for their involvement in cold tolerance, was the largest. This finding suggests these genes play a crucial role in the abiotic stress response, and they may be utilized in breeding alfalfa [95].
The wild Medicago species that presented tolerance in the above-mentioned abiotic stresses are presented in Table 1.

2.4. Woody Perennial Crops
Climate changes leading to temperature alterations (increased heat or cold), extreme weather phenomena (e.g., dry spells, heat waves, heavy rainfalls), and water availability (drought or flooding conditions) pose threats to the cultivation of woody perennial crops. Changes in weather patterns subsequently exacerbate biotic stresses and the spread of diseases. Ultimately, these adverse abiotic and biotic effects significantly compromise yield and quality of the final product. In recent years, numerous efforts have been undertaken to expand the genetic pool of woody perennial crops by exploiting the genetic diversity of wild relatives and introgressing new desirable climate-resilient traits into cultivated varieties [160,161].

2.4.1. Apple
The cultivated apple, Malus domestica Borkh., is a diploid or triploid species with a haploid set of 17 chromosomes and a genome size of approximately 600 Mb [162]. Apple cultivation and production constitute one of the major fruit-producing industries addressing markets worldwide. However, climatic changes introduce a series of environmental stressors which challenge apple yield and fruit quality. Apple breeding could greatly benefit from apple wild relatives to face the challenge from adverse environmental conditions and biotic and abiotic stressors [161]. For example, wild relatives, Malus floribunda, Malus baccata, and Malus micromalus, have been used to pyramid apple scab and powdery mildew resistance genes into progeny [163]. Assessment of a broad range of wild Malus germplasm over the last 30 years has revealed ample potential sources of resistance to a multitude of diseases. Similarly, apple wild relatives in Malus collections have been evaluated and shown to possess traits related to fruit quality as well as abiotic stress resilience, such as cold hardiness and drought tolerance [59]. In addition, investigations on the molecular basis of stress tolerance have indicated a key role for a DREB2 (dehydration-responsive element-binding factor 2) homologue in response to drought, cold, and heat in two highly drought-tolerant wild apple relatives, Malus sieversii and Malus prunifolia [60,61]. Likewise, Diacylglycerol kinase (DGK) genes were found to exhibit marked upregulation in response to drought and salt stress in M. prunifolia [58]. Comparative analyses between two widely used apple rootstocks (M. sieversii and R3) under water deficit conditions demonstrated M. sieversii is more tolerant to drought. Transcriptomic analysis of root tissue showed differential expression of stress-responsive genes associated with oxidative stress, signaling pathways in hormone biosynthesis, and transcriptional regulation between the two genotypes, suggesting these genes play a crucial role in root processes that provide drought tolerance [164]. Moreover, the deciphering of the cold-tolerant wild apple Malus baccata
genome identified cold-responsive genes (COR) that will be useful in marker-assisted selection in breeding programs [62]. Collectively, the Malus wild relatives provide an important
genetic resource for incorporating resilience in cultivated apple varieties.
2.4.2. Cranberry
Research focusing on wild cranberry is another example of targeted use of genetic variation in perennial wild populations toward the benefit of breeding resilient varieties [63,165]. Cranberry (Vaccinium macrocarpon Ait.), a fruit crop of high economic value in North America, Northern Europe, and Asia, often encounters a series of abiotic and biotic challenges, such as frost damage, high temperatures, drought, flooding, and fungal diseases, which lead to severe production losses. Recently, a collection of many wild cranberry (Vaccinium macrocarpon Aiton) accessions from the northern U.S. and Canada was assessed through environmental association analysis and revealed genomic regions linked to potential abiotic stress tolerance. One hundred twenty-six significant associations between SNP marker loci (many of which tagged genes with functional annotations) and environmental variables of temperature, precipitation, and soil attributes were uncovered [166].
2.4.3. Grapevine
Although the Vitis genus is composed of 60 species, the species used predominately for grapevine cultivation is Vitis vinifera L. Nevertheless, wild Vitis relatives exhibit important traits not found in V. vinifera, such as resistance to the devastating ‘Pierce’s disease’ (PD) caused by the bacterium Xyllela fastidiosa. Breeding programs focused on a PD-resistant grapevine wild relative, Vitis arizonica, to generate PD-resistant lines. Over the years, using V. arizonica x V. vinifera crosses, repeated backcrosses with V. vinifera and marker assisted selection (MAS) techniques, breeders managed to develop breeding grapevine lines with PD resistance and 97% V. vinifera ancestry [167]. Similarly, to confront two major grapevine fungal diseases, downy mildew (Plasmopara viticola) and powdery mildew (Erysiphe necator), the wild relative Muscadinia rotundifolia was utilized. Crosses with Vitis vinifera and subsequent crosses with other Vitis hybrids resulted in progeny containing genes implicated in resistance to both powdery and downy mildew [168,169]. On the other hand, molecular studies have begun to elucidate the genetic basis of abiotic stress tolerance displayed by wild Vitis relatives. Overexpression of a stress-related gene from the Chinese wild grape Vitis yeshanensis encoding a universal stress protein, VyUSPA3, was shown to confer drought tolerance to transgenic V. vinifera cv. ‘Thompson Seedless’ [64] (Table 1). In addition, comparative transcriptomic analysis performed between a coastline wild grapevine (Vitis vinifera L. ssp. sylvestris) accession which is tolerant to high-salinity levels and the commercial rootstock, Richter 110, a salt-sensitive cultivar, revealed differential gene expression profiles upon salinity stress [65] (Table 1). These findings facilitate the investigation of gene pathways that play key roles in survival under stress conditions and highlight the potential of such grapevine wild relatives as breeding material both for scion and rootstock improvement. In view of the gloomy projections of 56 to 73% loss of suitable land for viticulture in major wine-producing regions by 2050 [170,171], studies have been focusing on grapevine wild relatives with resilience to climate risk [172]. Recently, associations of wild species SNPs (single nucleotide polymorphisms) with bioclimatic variables and putative adaptation to biotic and abiotic stressors have been explored [173]. In addition, by integrating species distribution models, adaptive genetic variation, genomic load and phenotype, Aguirre-Liguori et al. [174] predicted certain accessions of the wild grapevine species, Vitis mustangensis, are well-suited for future climates and can contribute to grapevine bioclimatic adaptation. Importantly, commercial rootstocks currently used globally for grapevine grafting were derived from North American wild Vitis species. These rootstocks have been used since the second half of the nineteenth century to save European grapevines from the plague of the soil-borne aphid, phylloxera (Daktulosphaira vitifoliae) [175]. Moreover, depending on the rootstock, they confer drought, cold tolerance, and disease resistance to grafted grapevine [176]. Likewise, rootstocks have been used widely for improving other cultivated woody perennials (apple, pear, peach, mango, citrus, etc.). However, in general, relatively few rootstock genotypes are employed in grafting of woody perennial crops. Wild relatives could serve as a significant allele pool for developing new rootstock varieties with advantageous traits that would impart the grafted plant with resilience to environmental stressors [160].