Genomics-Assisted Breeding for Biotic Stress Syndrome Resistance in Cotton

The final goal of almost all plant breeding programs is to improve the economic yield—a trait that is almost always hampered by biotic and abiotic stresses. Cotton (Gossypium spp.) is the most important natural fiber producing crop globally, and cash crop for many developed and developing countries. Albeit possessing high yield potential, the on-field yield is underrepresented mainly due to biotic and abiotic stresses. A host of diseases through numerous pathways cause biotic stress and, therefore, in this chapter, we call them cotton biotic stress (CBS) syndrome. Here, we give a general overview of (1) the CBS syndrome and (2) the yield losses incurred upon cotton by the CBS. The primary focus is, however, on (1) the prospects and challenges of marker-assisted breeding via introgression of large-effect marker alleles into the breeding lines to provide resistance against the CBS syndrome and (2) the utility of the whole-genome sequencing and production of dense marker genotypes to predict the genetic value of CBS syndrome traits. We also discuss some breeding improvement targets in the context of CBS syndrome resistance. In the end, we discuss the future perspectives on the use of genomic technologies which may help cotton breeders and geneticists to improve and realize the actual yield potential of cotton varieties—a crop whose dividend provision is severely hampered by the use of extensive nongenetic agrochemical applications.