Whole-Genome Mapping of Date Palm (Phoenix Dactylifera L.)

Abstract

AbstractA genome represents an organelle’s complete DNA repertoire and it is the starting point of genetic studies and genome mapping. Since the advent of genome mapping techniques, researchers have devoted concerted efforts to link phenotype to genotype. Initially, efforts were made to accomplish genotyping by isozymes, followed by the execution of various kinds of molecular markers such as simple sequence repeats (SSR), single nucleotide polymorphism (SNP), and random amplified polymorphic DNA (RAPD). Nonetheless, genome mapping was dramatically revolutionized as next-generation sequencing (NGS) technologies emerged. NGS technologies have produced a deluge of genome sequencing. The analysis of such sequencing data is only possible through highly sophisticated computational tools. Presently, the low-cost sequencing technologies and highly sophisticated computational tools are of great significance in unraveling the complexity of plant genomes. Date palm (Phoenix dactylifera L.) is a socioeconomically important plant. Cultivar identification mostly relied on phenotypic traits rather than genotyping. Still, limited information is available on date palm genotyping and genome mapping. Nonetheless, advancements in whole-genome sequencing and genome assembly computational tools hold a substantial advantage to boost the identification of date palm cultivars, genome variants, and gene/genome annotation. In this chapter, advancements in date palm genome mapping are categorized into two main types: date palm genetic mapping in the pre-NGS and post-NGS eras. Various computational tools that hold an unparalleled advantage to conduct genome-wide association mapping, genome prediction, and selection, and with higher prediction accuracy of SNPs and other variations in date palm genomes are discussed. In addition, various databases related to date palm genomes are discussed, these databases encompass important information about the whole genome of certain date palm cultivars, molecular markers such as SNPs and SSR, and phylogenetic relationship of different date palm cultivars.KeywordsDate palmGenome mappingNuclear genomePost-NGSPre-NGSThird-generation sequencing