Chapter 7 - Application of Genomic, Transcriptomic, and Metabolomic Technologies in Arachis Species

Abstract

Peanut genetic improvement is approaching the cusp of rapidly accelerating gains due to application of genomic, transcriptomic, and metabolomic technologies. Yield is a primary target trait for improvement but is impacted by biotic and abiotic stresses, and quality traits specific to different cultural and industrial sectors that must be taken into account. Arachis genomic and transcriptomic resources, both for cultivated tetraploid peanut, Arachis hypogaea L., and its diploid ancestors, Arachis duranensis (A genome) and Arachis ipaënsis (B genome), have been greatly enriched since their status was documented in 2012, leading to an in-depth understanding of genomic architecture based on comparative sequence analyses. Identifying genes underlying important disease resistance or quality traits requires knowledge of gene action at the level of phenotypic response as well as genetic markers within (direct) or near (indirect) genes. Once direct or indirect marker–trait linkages have been validated, markers can be used as surrogates to select for a trait. The efficacy of a marker for selection of a trait is greatest when the marker is within an identified gene; therefore, targeting gene regions for development of high-density molecular maps is desirable. The density of molecular maps in cultivated peanut has been constrained by low molecular polymorphism rates among genotypes and the limited amount of sequence data from which polymorphisms could be mined, although in spite of these limitations considerable progress has been made to develop and integrate genetic maps. The peanut genome project has generated sequence and phenotype data that vastly improve our ability to create dense genetic maps encompassing traits of interest, thereby positioning markers in or near genes with functional significance for peanut growth, productivity, and sustainability.