Utilising public resources for fundamental work in underutilised and orphan crops

Chapman, Mark and Fisher, David (2022) Utilising public resources for fundamental work in underutilised and orphan crops. In, Chapman, Mark (ed.) Underutilised Crop Genomes. 1 ed. Springer Cham, pp. 437-450. (doi:10.1007/978-3-031-00848-1_24).

Abstract

A starting point to understanding more about underutilised and orphan crops is to investigate their genetic diversity and origins. Whilst whole genome analyses will give a wealth of information in this regard, this is often impractical in terms of cost and an overkill in terms of these initial goals. Therefore, molecular markers are used to establish the partitioning of genetic variation, the location of domestication, and relationships between these crops and their wild relatives. All of this will generate information required to begin improving these crops and identify adaptive variation. A convenient and high throughput way to generate molecular marker information is to mine a genome for markers such as Simple Sequence Repeat markers (SSRs) or others. In this analysis we assembled draft genomes for three underutilised crops (slender Amaranth [Amaranthus viridis L.], lychee [Litchi chinensis Sonn.] and velvet bean [Mucuna pruriens (L.) DC.]) using publicly available data. We show that whilst the assembly could be improved considerably in terms of completeness and duplication, this can house thousands of potential SSR markers. In addition, the chloroplast DNA (cpDNA) was assembled from the same sequencing reads and housed ca. 50–60 potential SSR markers. We also identified 10–11 million potential SNP markers by comparing three genomes for lychee. The approach we use relies solely on publicly available software and can be modified or adapted by others with ease.

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Contributors

Author: Mark Chapman

Author: David Fisher

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