Integrated Use of Molecular and Omics Approaches for Breeding High Yield and Stress Resistance Chili Peppers

Abstract

In a rapidly changing environment along with the growing population, crop production and improvement are the most sought-after sectors in the world. Pepper (Capsicum spp.) is a highly consumed plant species in the form of spice or whole fruit and is widely popular for its pungent flavour and vibrant colours worldwide. Like other crop plants, pepper is also severely affected by environmental and genetic constraints and reflects a massive loss in yield, quality and production rate. Therefore, it is imperative to immediately change our focus towards the development of stress-resilient and high-yielding Capsicum varieties. This chapter discusses the integrated use of conventional, molecular and multi-omics tools towards meeting the end goal of Capsicum trait improvement. Conventional breeding programmes have utilized natural sources of genes and QTLs attributed to biotic and abiotic stress tolerance and other important horticultural traits in pepper improvement which involve time-consuming multiple and tedious crossing cycles followed by selection. The development of reliable molecular markers like SSRs, SNPs, InDels etc. have enabled genetic and biparental QTL mapping, and genome-wide association studies which all have not only helped in the rapid identification of significant QTLs governing important traits but also marker-assisted selection of desired phenotypes. Several candidate genes for Capsicum plant and fruit morphology, metabolite content, disease resistance and stress tolerance have been identified and are available for introgression via marker-assisted breeding and genetic engineering into elite genetic backgrounds. Further, genome and transcriptome sequencing projects have changed the tides for advancement in Capsicum research and provided new insights into Capsicum genome structure, size, features and function. Other omics approaches like epigenomics, proteomics and metabolomics are rapidly evolving to reveal transcriptional, post-transcriptional and post-translational modifications in Capsicum genes and proteins. In brief, established breeding strategies combined with new technological hues can be successfully exploited for breeding high-quality, better performing, stress-resistant and sturdy Capsicum varieties to meet the needs of the growing human population.