**10. Key challenges**

Wheat is an allopolyploid resulted from interspecific or intergeneric hybridization of two or more genomes from different species. Being one of the most consumed and cultivated crop globally, it is under continuous exposure to a large variety of parasite species and strains, many of which have the ability to move around the globe. Longterm co-evolution between plants and their pathogens has equipped plants with a sophisticated multi-layered immune system to guard themselves against pest and pathogens [178]. Despite this, there are a few important challenges which are required to be addressed for effectively mitigating with different biotic stresses in wheat:


6.The foremost challenge in breeding against insect pests is finding sources with reasonable levels of resistance against the pest. Secondly another major hurdle is the difference between resistance at field and protected conditions, since evaluation is carried out in protected conditions, results vary when evaluation is carried out *in vivo.* Lack of efficient evaluation and selection tools against insects also hinders the insect resistance breeding. Finally, transfer of resistance is often accompanied by linkage drag which sometimes becomes cumbersome to break.

### **11. Conclusion and future prospects**

Genetic control is considered as the most effective and environmentally friendly strategy to control rust disease and involves breeding effective disease resistance genes into wheat cultivars. Many rust resistance genes have been identified genetically, and introgression into wheat lines is increasingly being facilitated by the development of robust molecular markers. However, the massive and complex genome of wheat poses major challenges for the isolation of individual genes. As revealed by the increasing number of newly available whole genome sequences and the more precise bioinformatic pipelines developed for identifying NLR genes, the number of NLR genes varies greatly between species. Based on an analysis of the IWGSC RefSeq v1.0 assembly, a total of 3,400 full-length NLR loci have been documented [180]. The approaches for identifying effective resistance genes therefore, must consider both classical R-genes (immune receptor class genes) as well as other novel classes that may operate via different mechanisms.

Cloning of the genes that controlling resistance to rust pathogens will significantly advance our understanding of the molecular basis underlying expression of disease resistance in wheat. Only a small number of rust resistance genes have been cloned and had their molecular functions studied (**Table 2**). To overcome the limitations of the map-based cloning strategy in the large genome of wheat, alternative approaches were developed and validated by the rapid cloning of several genes using Target-sequence Enrichment and Sequencing (TEnSeq) pipelines. These include MutRenSeq (Mutagenesis and the Resistance gene Enrichment and Sequencing), AgRenSeq (Association genetics with R gene enrichment Sequencing), MutChromSeq (Mutgenesis Chromosome flow sorting and short-read Sequencing), and TACCA (Targeted Chromosome based Cloning via long-range Assembly). The common component among all these approaches is the intent to reduce the genome complexity prior to the use of next generation sequencing (NGS). Such insight into the molecular mechanisms will be the foremost step towards the functional characterization of the wheat-rust interaction and allow engineering of new resistance by exploiting novel techniques like allele mining and genome editing. Also, approaches like TILLING (Targeting Induced Local Lesions IN Genomes) can be adopted for more precise and efficient characterization of the function of targeted wheat genes for different fungal and bacterial diseases.

The rich genetic diversity available in wheat is a source of numerous novel alleles for both disease resistance and tolerance to abiotic stress. However, there is still a huge gap in characterization of the available genetic resources and their utilization in breeding programs. Over the years, traditional breeding strategies have successfully incorporated novel alleles into elite germplasm, which has significant impacts on production globally. Use of advanced technologies, marker-assisted selection (MAS), genomic selection, transgenics and genome editing will help to increase the efficiency of wheat breeding for biotic stress resilience around the world.

To escape the boom and bust cycle, resistance gene stewardship and deployment strategies such as gene pyramiding, gene stacking (transfer of gene cassettes) could

#### *Breeding Wheat for Biotic Stress Resistance: Achievements, Challenges and Prospects DOI: http://dx.doi.org/10.5772/intechopen.97359*

prove to be effective against deadly diseases of wheat (rusts, blight). It is widely reported and agreed upon fact that the most effective and durable means for genetic control of wheat rusts is the use of combinations of multiple broadly effective ASR and APR genes. Using this, the desirable combinations of effective resistance genes can be combined and transformed into wheat as gene cassettes or stacks. This can result in faster improvements in disease resistance of current high-yielding varieties. Also, the advancements in R-gene cloning pipeline like TEnSeq will provide many more tools for MAS in wheat breeding as well as the raw gene sequences to pursue gene stacking (via transgenic gene cassettes). Combining with advances in identifying genetic variation in rust *Avr* genes, these new tools will lead to more effective deployment strategies to maximize resistance durability.

Genomic selection (GS) is considered one of the best strategies for selection of multiple minor-effect loci in comparison with MAS. Using GS, a training population (after phenotyping and genotyping) is used to standardize a prediction model, which is further used to predict breeding values, thus enabling selection of candidates prior to phenotyping [181]. Recent studies have reported that greater genetic gains can be obtained by using genomic selection than by using MAS [182] and phenotypic selection [183].

More recently, genome editing has emerged as a prominent new plant breeding technique, which involves targeted modification of a native DNA sequence. For instance, it has been observed that a single amino acid substitution (Arg144Gly) in a hexose transporter in wheat results in the gene *Lr67* conferring resistance. This substitution evolved recently after common wheat polyploidization. Introduction of the *Lr67* transgene into barley conferred seedling and adult plant resistance to the barley leaf rust pathogen [184, 185]. The orthologue sequence of *Lr67* exists in the barley genome; hence altering the Arg144Gly by genome editing would be expected to produce resistance to rust in barley. Similarly, a number of homologs/ orthologues of the isolated genes exist in related species. Isolating a rust resistance gene from other related species thus can provide deeper insight into rust resistance in the wheat.

Therefore, under a changing global climate, it is of paramount importance to breed for durable and broad-spectrum disease resistance in wheat at a faster pace to reduce losses from attack by rapidly evolving new virulent pathogenic races. Moreover, this would lead to reduction of the use of agrochemicals (fungicides), escaping environmental and human health hazards, an essential component of modern sustainable crop production systems.

*Current Trends in Wheat Research*
