Allele Mining for the Improvement of Tomatoes

Traditional breeding, along with genomics, has identified valuable genes for tomato improvement, which led to the development of climate-resilient, high-yielding varieties resistant to biotic and abiotic stresses. The demand-driven research and various challenges in tomato crop have encouraged breeders to exploit desirable genes from cultivated and wild species, as well as identify the genomic variations associated with the traits. The advanced sequencing techniques have led to the identification of single-nucleotide polymorphisms (SNPs) and single-sequence repeats (SSRs) for desirable traits. In this chapter, we provide an overview of the current status of tomato genome, genetic diversity, and tomato gene bank. The chapter reviewed the significance of tomato reference genome and its use in gene discovery. Furthermore, allele mining and microRNAs for biotic stress tolerance genes, variations of genes/alleles responsible for abiotic stress tolerance, allele mining for yield component traits, nutritional traits and converting landrace diversity to breeding resources in tomato improvement are discussed. Additionally, the chapter reviewed the resistance genes and their wild species, protein class, miRNAs, disease involved, and their putative targets, QTLs, and transcription factor promoters associated with biotic, abiotic, and heat/drought tolerance in tomato, among others, are covered. Further, an analysis of future prospects and challenges of allele mining in tomato for gene discovery is given. The information will be highly useful for the tomato breeders, geneticists, and policymakers for the exploitation of genetic and genomic resources in the tomato gene pool to address the challenges of demand-driven research and better opportunities in future.