**5.1 Marker assisted breeding**

Recent advances in biotechnology tools have the potential to understand the function of genes/QTLs that govern the economic traits, and applying this information's to Smart breeding programs, leading to crop improvement. The advent of molecular markers such as Restriction fragment length polymorphism (RFLP), Rapid Amplified Polymorphic DNA (RAPD), Simple Sequence repeat (SSR), Kompetitive allele specific PCR (KASP), Cleaved amplified polymorphic sequence (CAPS) and especially Single Nucleotide polymorphism (SNP) have revolutionerized the field of plant genetics and facilitated molecular crop breeding [59].

The ultimate goal of crop breeding to develop super-varieties by assembling multiple desirable traits, such as yield related, superior quality, tolerance/resistance against biotic and abiotic stress and good environmental adaption. It is very challenging, difficult and time consuming to combine all traits in single genotypes by traditional breeding, so some alternates need to be compiling all important traits, into single varieties, can be done through marker assisted selection (MAS), which have become an integral component of genotypes/germplasm improvement. The potential benefits of using molecular markers linked to the genes/QTLs of interest in breeding programmes, which have shifted from phenotype-based (traditional breeding) to a combination of phenotype and genotype-based selection, are of great importance to the Smart breeding programme [60].

Breeding programme combine, with MAS strategies have major advantages compared to traditional phenotype-dependent breeding in terms of convenience and efficiency for transferring the genes/QTLs of interest to the plant genome [61]. Selection can be done selectively with the genotypes of molecular markers linked to the target traits, selection in off-season nurseries (reduce breeding cycle), making the technique more cost effective to grow for more generations per year (speed breeding), reduction of required population size because many lines can be discarded in earlier breeding generations after MAS. The most effective and usefulness of MAS approaches, for traits of simple inheritance (qualitative traits controlled by one or a few genes) have been well proven in many important crops [62].

Basically, two major MAS strategies are usually applied in breeding programme, (i) backcrossing for favorable alleles into elite germplasm, i.e. marker-assistedbackcrossing (MABC) and (ii) stacking multiple genes of different sources into elite breeding lines, i.e. marker-assisted gene pyramiding (MAGP). The success of MAS

has depends to search the important QTLs for complex traits (controlled by minor genes), which account for a large proportion of phenotypic variation (major QTLs). Successful applications of MABC and MAGP for improving yield or yield component traits by using well characterized major QTLs/genes in important crops [63]. Successful implementation of MAS breeding in broad range of crops including barley, beans, cassava, chickpea, cowpea, groundnut, maize, potato, rice, sorghum, and wheat [64]. Genetic markers associated with agronomic traits can be introgressed into elite crop genetic backgrounds via marker assisted breeding (MAB). It allows stacking of desirable traits into elite varieties to make them better adapted to climatic changes.

#### **5.2 DNA sequencing and advent of genomics assisted breeding**

With plummeting cost and greater accessibility of high throughput genome sequencing technology, the breadth of genomic data is expanding rapidly. In order to capture diversity of specific gene families within a large group, DNA samples can preferentially be enriched before sequencing. This approach can be adopted to define genetic variation in disease resistance gene repositories in Solanaceae and Triticeae (RNA seq) [65] and gluten gene families I bread wheat (GlutEn Seq) [66].

Sanger sequencing to study plant genomes is unfeasible due to low throughput and high sequencing costs. In 2005, Roche released its revolutionary 454 pyrosequencing platform [67]. Subsequently, several sequencing platforms such as developed by Illumina, ABI, Life technologies, PacBio, Oxford Nanopore and Complete genomics were released commercially, changing the scenario of genome sequencing. Depending on chemistry, second generation sequencing (SGS) approaches are classified as ligation based approaches and synthesis based approaches [68]. To rectify the problems of assembling repetitive genomic regions, long read sequencing offers solution by producing reads spanning the repeat regions [69].

Rapid cost reduction in genome wide genotyping allows large scale assessment of crop species diversity to capture climate related traits. It leverages cheaper sequencing to identify up to millions of SNPs in plant population [70]. High SNP density approach like whole genome resequencing (WGR) & low SNP density approach like reduced representation sequencing (RRS) are majorly used approaches. However, high density genotyping assay "SNP chips" enable large scale genotyping using SNP specific oligonucleotide probes rather than direct sequencing.

The variants identified by genotyping by sequencing (GBS) can be used for conventional QTL analysis and modern approach like genome wide association studies (GWAS). GWAS exploits the past recombinations in a diverse association panels to identity genes lined to phenotypic traits [71]. SNP genotyping have been widely used in many crops including wheat [72] and Maize [73]. Extensive use of GWAS is resulting in our enhanced understanding of genetics of important climate specific traits viz. drought and heat tolerance. In light of reducing sequencing cost and expensive validation of candidate genes, use of WGR to further enhance resolution of mapping studies is likely to become routine task in future [70].

The availability of reference genome assembly rewards us with information about gene content, ability to associate the traits with specific genes with subsequent insights into related biophysical and biochemical roles of gene(s) in the expression of that particular trait [74]. Resequencing of diverse crop cultivars reveals the gene content variation and DNA sequence differences between allelic variants, while sequencing of expressed gene products provides information on where and when genes are functioning. Such information when integrated within breeding pipelines, offers promise to accelerate the development of climate smart crop varieties.

*Smart Breeding for Climate Resilient Agriculture DOI: http://dx.doi.org/10.5772/intechopen.94847*

The recent explosion in genomic data is rapidly triggering a fundamental shift to genomic based breeding [75]. The ability to identify and genotype umpteen SNPs at ever reducing costs facilitated expansion of MAS in breeding to plethora of traits and across wider range of crops [76]. A major outcome of availability of high throughput genome wide markers is a move towards population based trait association and breeding i.e. NAM or MAGIC populations to ultimately enhance the trait mapping resolution by greatly increasing the number of recombinations in the population. After identification and validation of the candidate genes, there achieved the deeper understanding of biological mechanism underlying the trait, which can subsequently be improved through MAB or genetic alterations. Furthermore, precise understanding of the molecular basis of traits enables the engineering of novel alleles or mining of potentially desirable alleles from CWR, facilitating further enhancement of the trait.
