**4.2 De novo domestication for future crops**

Considering the risks of introducing foreign alleles into cultivars, other potential technique for developing climate-friendly crops is de novo domestication [33]. As most staple crops are grown majorly in the regions other than where they were originally domesticated with different climatic regimes. Nevertheless, their wild relatives and landraces exhibit better adaptation to local climate in the native regions. In the scenario of climatic change, there is chance to leverage this opportunity to use those underutilized or orphan crops e.g. rise in *Sinapis alba* (white mustard) acreage replacing the *B. napus* in Europe for biofuel production [34]. A pipeline strategy has been proposed for domestication of wild germplasm in some orphan crops such as quinoa [35]. In addition to direct planting of nondomesticated crop plants, relatively advance methodology of CRISPR/Cas9 boosts the wild germplasm domestication by editing of domesticated genes e.g. editing in wild tomatoes (*Solanum pimpinellifolium*) and ground cherry (*Physalis pruinosa*) mainly focused on flower improvement, plant architecture improvement, fruit size, fruit number and nutritional content [36–38]. It is evident from such a few successful introgressions of domesticated genes that use of wild germplasm in regular plant breeding is quite promising in countering the effects of climate change on agriculture and hence, food security.

#### **4.3 Introgressiomics approach for adaptation to climate change**

The actual potential of the CWR in plant breeding largely remains underexploited due to linkage drag and frequent breeding barriers with the crops.

Introgressiomics approach allows mass scale development of plant material and populations with introgression lines from CWR into the genetic background of crops [39]. This pre-emptive breeding technique could be focused or unfocused depending upon the objective. Besides genetic analysis of traits present in CWR, MAS driven generation of chromosome substitution lines (CSL), introgression lines (IL) or MAGIC populations allow the development of genetically characterized elite material. Genomic tools like high throughput molecular markers facilitate the characterization and development of Introgressiomics populations, which can be easily incorporated into major breeding programs for coping with the accelerating environmental challenges.

#### **4.4 Some other techniques for CWR use**

After the introgression into domesticated background from CWR, populations such as backcross populations (BC), recombinant inbred lines (RILs), doubled haploids (DH), near isogenic lines (NILs), multiparent advance generation intercross (MAGIC) populations as well as nested association mapping (NAM) populations are developed to study the introgressed gene(s). After mapping their locations on to the genome and it genotypic validation with molecular markers, they are further deployed using Marker assisted selection (MAS). Systematic screening of the huge number of progenies with MAS enhances the efficiency of breeding program (van de Weil 2010). Desirable recombinants can be developed at early generations using larger populations e.g. using marker-assisted backcrossing (MABC), an important QTL was introduced into a new lowland rice background in just 2 rounds of backcrossing [40].

Genomic scans can also reveal candidate domestication and improvement loci as well as post-domestication introgression using CWR [41, 42] to be further harnessed in the scenario of climatic challenges. In case of CWR, high throughput sequencing offers a cheap and rapid way to deploy thousands to millions of markers for mapping purposes [43]. Reduced representation techniques as genotyping by sequencing (GBS) or even nimble exom capture have been exploited to this effect in several CWR species already [42, 44, 45]. These technologies offer rapid marker density as required for rapid fine mapping and can saturate mapping populations in terms of capturing all of the recombinants.

The availability of a reference genome sequence in CWR during recent times greatly boosts the use of high-throughput sequence data. Some large scale genomic sequencing and re-sequencing programs are well underway [27, 46] often with reduced representation methods. Whole genome shotgun sequencing (WGS) techniques can also be utilized to characterize CWR germplasm for climate resilience breeding in major staple crops. E.g. Rice having smaller genome size (430 mb) long with its wild relatives has been re-sequenced using WGS [47–49]. Already sequenced germplasm collections including Chickpea [50], Rice [48], Soybean [51] and Wheat [52] etc. will provide insights into these diverse gene pools to be exploited in combating various biotic and abiotic challenges during this era of climate change. More recently, a massive scale genomic study of almost 80000 accessions from CIMMYT and ICARDA unraveled unprecedented amount of genetic diversity in 29 wheat species comprising cultivated wheats, CWRs and landraces to be exploited in wheat improvement for range of climate related plant traits [53].

Potentially revolutionary technology in modern plant breeding like genome editing has enabled scientists to alter genome of any organism with unprecedented precision without involvement of any foreign DNA [54]. CWR and their sequence information may serve as a reference library for all kind of diversity. This information on allelic diversity and its phenotype is a vital requirement for many genome

editing approaches. In fact, these approaches will allow the use of this information from more distantly related, cross-incompatible CWR and domesticated species to be further utilized in crop improvement [55, 56].
