It replaced by the modern methodologies in this

Itis always mandatory to employ better breeding practices and management tocounter and eradicate major diseases in plants in order to reduce total yieldloss. The major issue in plantbreeding programs has been the identification of genes which control resistanceto various diseases. Plant breeders are always in need of sophisticated andreliable techniques and tools to capture and target disease resistance genes,and also to understand the association among resistance and desired traits pertinentto breeding applications.However, there are some major issuesassociated with some plant species such as very high mark of heterozygosity andalso the polyploidy hampered the breeding approaches needed to provide resistance.Traditional approaches for breeding resistance are quite laborious and timeconsuming which needs to be replaced by the modern methodologies in this era ofgenomics.

Genome mapping is a novel approach which is being used extensively inthe modern world by the researchers to identify genes and other molecular cues directlylinked with various phenotypes and traits of interest in plants. Genome mappingenables the identification of genes simply on quantification of their effectson the phenotype and does not require biochemical function of genes involved.For numerous plants, mapping of the important genes relevant to major importanttraits including the disease resistance have been performed in the recent past.Initially, the isolation and identification of R (resistance) genes was relyingon challenging and complex procedures and protocols of map based cloning. Now adays with advent of modern techniques like next-generation sequencing, it hasbecome more feasible to identify and map the genes related to major traits likediseases resistance with genome and transcriptome wide mapping.9.2 Architecture of R Genes Resistance to various pathogens and pests inplants have been conferred due to the existence of disease resistance geneswhich encode pathogen protective proteins (Chauhan and Sood, 2013).

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The evolutionof R genes in the plants is due to the presence of proteins involved inendogenous recognition and signaling vital for usual growth and development.Many R genes have been cloned and identified from numerous plants, conferringresistance  to a wide-ranging plantpathogens together with various bacteria, viruses and fungi (DeYoung and Innes,2006; McHale et al., 2006). Though the mechanisms underlying infection ofvarious pathogens including microorganisms vary considerably, R genes are verymuch conserved in nature i.e.

possesses similarity among themselves.R genes in plants are majorly from thenucleotide binding site-leucine rich repeat (NBS-LRR) family which providesresistance against abundance of pathogens like parasites, bacteria, fungi,viruses and insects (Dangl and Jones, 2001; Martin et al., 2003; Tarr andAlexander, 2009). These NBS-LRR proteins are further categorized in two sub divisionsbased upon the occurrence of domains and motifs N-terminal region.

One categoryis comprised of proteins having TOLL/interleukin-1 receptor (TIR) and are termedas TNL proteins (TIR-NBS-LRR). The other one non TIR-NBS-LRR group is known asCNL (CC-NBS-LRR), as most of proteins in this category encode a coiled-coil(CC) N-terminal domain. The major role of NBS domain is ATP binding whereasC-terminal leucine rich repeat (LRR) is involved in binding of pathogens,regulation of signal transduction. Also, both the domains i.e. TIR and CC arehaving major role in signaling regulation and downstream specificity (DeYoungand Innes, 2006).

The N-terminal NBS domains are associated to TIR as well asnon-TIR proteins and having motifs such as Kinase-1 (P-loop), Kinase-2,Kinase-3, and other supplementary short motifs with undefined functions (van derBiezen and Jones, 1998). These regions are generally conserved in plantkingdom. The occurrence of conserved regions of resistance genes deliver prospectsto design degenerate markers and identification of resistance gene analogues(RGAs) from plant genomes.