YAMNOMICS has generated a genomic tool that takes advantage of NGS advances to enable sequencing hundreds of nuclear and plastid genes for Dioscorea species. This set of genes include traits of agricultural and evolutionary interest (e.g. tuberization, starch biosynthesis, flowering genes, secondary compounds synthesis). The project YAMNOMICS has generated genomic data (300 nuclear genes and plastome sequences) for 800 samples that represent over 400 taxa of Dioscorea and 48 outgroups. We have doubled the number of species from the 300 samples planned. We have also included infraspecific sampling for some more variable taxa. We have also expanded the use of the genomic tools outside Dioscorea.
YAMNOMICS has increased the value of traditional dried herbarium specimens held in their millions by European institutes. We have been able to use NGS methods to extract low quality DNA for use in novel genomic approaches and sequence data collection via developing new bioinformatic pipelines. For example, we have produced a method that estimates the ploidy level of the herbarium specimen, which will have broad application across the whole of plant. A measure of this success is found in the sequencing of hundreds of genes and the plastome of historical samples.
The outcomes of YAMNOMICS possess an enormous potential for crop breeding and to identify new crops. The newly generated phylogenomic tree, representative of the biodiversity within Dioscorea, has enabled the identification of the closest wild relatives of the cultivated species, which are likely have traits of interest for their improvement. Due to the intensive sampling and the new collaborations, we have identified new crop wild relatives for the main cultivated species of Dioscorea. For example, we have received dried leaves of cultivars and CWRs (D. bulbifera, D. burkilliana, D. esculenta, D. abbysinica, D. dumetorum and D. cayenensis) from The International Institute of Tropical Agriculture (IITA, Nigeria), 27 samples in total. A PhD student of the British Columbia University in Canada is studying the domestication origin and identifying the CWRs of Dioscorea alata and D. esculenta using the outcomes from YAMNOMICS.
The outcomes of YAMNOMICS will produce at least five scientific papers of interest to the scientific community and plant breeders. Our results have already been published in one scientific paper, two that are currently under review and further papers are currently in preparation. We have initiated the transfer of knowledge through oral presentations at three international conferences: The Plant & Animal Genome Conference 2018, in San Diego, which is a forum for communication between genomic scientists and breeders; and two important scientific conferences in plant evolution: Botany Conference 2018, in Rochester; and at the 6th International Conference on Comparative Biology of Monocotyledons – Monocots VI 2018, in Natal, where the ER gave a talk and organized a symposium.
