Groundnut entered post-genome sequencing era: opportunities and challenges in translating genomic information from genome to field

Summary

Cultivated groundnut or peanut (Arachis hypogaea) is an allopolyploid crop with a large complex genome and genetic barrier to exchanging genetic diversity from its wild relatives due to ploidy differences. Optimum genetic and genomic resources are key to accelerating the process for trait mapping and gene discovery and deploying diagnostic markers in genomics-assisted breeding. The better utilization of different aspects of peanut biology such as genetics, genomics, transcriptomics, proteomics, epigenomics, metabolomics, and interactomics can be of great help to groundnut genetic improvement programs across the globe. The availability of a high-quality reference genome is core to all the ‘omics’ approaches, and hence optimum genomic resources are a must to fully exploit the potential of modern science by incorporating it into conventional breeding. In this context, groundnut is passing through a very critical and transformational phase with regard to the availability of the required genetic and genomic resources such as reference genomes of progenitors, resequencing of diverse lines, transcriptome resources, germplasm diversity panels, and multi-parent genetic populations for conducting high-resolution trait mapping, identifying associated markers, and developing diagnostic markers for selected traits. Lastly, available resources have been deployed in translating genomic information from genome to field by developing improved groundnut lines with enhanced resistance to root-knot nematode, rust, and late leaf spot and high oleic acid. In addition, the International Peanut Genome Initiative (IPGI) has made available a high-quality reference genome for cultivated tetraploid groundnut, which will facilitate better utilization of genetic resources in groundnut improvement. In parallel, the development of high-density genotyping platforms, such as Axiom Arachis array with 58 K SNPs, and the constitution of a training population, will initiate the deployment of genomic selection for achieving higher genetic gains in less time with more precision.