Periodic Reporting for period 1 - Yamnomics (Phylogenomics, evolution, biogeography and key traits for breeders in yams (Dioscorea, Dioscoreaceae))
Reporting period: 2017-01-09 to 2019-01-08
Biodiversity conservation has become a priority concern for both science and society due to its key role in driving human wellbeing. The increased focus on understanding biodiversity and its sustainable use has evolved concurrently with new genomic (next-generation sequencing, NGS) and bioinformatic techniques that have revolutionized the availability of DNA sequence data for comparative biodiversity studies and lead to the emergence of Phylogenomics, in which evolutionary relationships are recovered based on comparative analyses of genome-scale data.
The underground organs make some species of Dioscorea essential economic sources as crops or for pharmacological purposes. Dioscorea contains 625 species distributed primarily in the tropics but with representation in temperate regions. Various Dioscorea species are critical carbohydrate and nutrient sources in many tropical regions due to their starch-rich annual tubers. Two crops, the guinea and winged yams, feed over 100 million people in Africa alone, with an annual global production of 68 MT. Its economic importance is complemented by other species which accumulate secondary steroidal compounds of pharmacological interest, and potentially for new applications like cosmetics or biofuel.
Yams are resilient plants adapted for seasonal tropical climates whose diversity holds considerable potential for coping with environmental instability and have considerable untapped potential to develop human livelihoods especially among those living in the greatest poverty. Traits of interest include the mechanisms of twining direction and dwarfism (in order to avoid the need for staking cultivated yams); sex expression, flowering and incompatibility to facilitate crossing breeding lines (yams are a clonal crop and poor flowerers); the pathways that led to the synthesis of key economic secondary metabolites; and fungal (especially anthracnose)/virus disease resistance.
Identifying the crop wild relatives (CWR) is essential for crop breeding, because CWR can offer genetically similar pools and their traits can be incorporated into crops. Orphan crops like yams have remained little studied at a worldwide scale, despite millions of people in less economically developed regions relying on them. The scale of molecular resources for yams to support fundamental and applied science supporting enhanced exploitation are far below those available for more mainstream crops.
The main objective of YAMNOMICS was investigating the evolutionary relationships and biogeographical patterns of the genus Dioscorea based on a richly sampled NGS-based phylogenetic tree.
The underground organs make some species of Dioscorea essential economic sources as crops or for pharmacological purposes. Dioscorea contains 625 species distributed primarily in the tropics but with representation in temperate regions. Various Dioscorea species are critical carbohydrate and nutrient sources in many tropical regions due to their starch-rich annual tubers. Two crops, the guinea and winged yams, feed over 100 million people in Africa alone, with an annual global production of 68 MT. Its economic importance is complemented by other species which accumulate secondary steroidal compounds of pharmacological interest, and potentially for new applications like cosmetics or biofuel.
Yams are resilient plants adapted for seasonal tropical climates whose diversity holds considerable potential for coping with environmental instability and have considerable untapped potential to develop human livelihoods especially among those living in the greatest poverty. Traits of interest include the mechanisms of twining direction and dwarfism (in order to avoid the need for staking cultivated yams); sex expression, flowering and incompatibility to facilitate crossing breeding lines (yams are a clonal crop and poor flowerers); the pathways that led to the synthesis of key economic secondary metabolites; and fungal (especially anthracnose)/virus disease resistance.
Identifying the crop wild relatives (CWR) is essential for crop breeding, because CWR can offer genetically similar pools and their traits can be incorporated into crops. Orphan crops like yams have remained little studied at a worldwide scale, despite millions of people in less economically developed regions relying on them. The scale of molecular resources for yams to support fundamental and applied science supporting enhanced exploitation are far below those available for more mainstream crops.
The main objective of YAMNOMICS was investigating the evolutionary relationships and biogeographical patterns of the genus Dioscorea based on a richly sampled NGS-based phylogenetic tree.
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.
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.
The outcomes produced in YAMNOMICS inform both applied and fundamental science. We have produced a vast amount of genomic data for triple the number of species in previous phylogenetic studies number of yams, that will enable the activities of yam breeders and the biodiversity science community. Previous studies in yams developed phylogenetic studies based on one to four genes and including up to 150 species. YAMNOMICS has produced phylogenomic trees based on 300 nuclear genes, and plastomes, for over 400 species and 48 related taxa.
The genomic methods developed in this project have the potential to be applied in other plants and organisms. For example, we have produced a bioinformatic method that estimates the ploidy level of herbarium samples, which has a direct application in agriculture because the capacity of two plant species to cross depends directly on the ploidy compatibility between them. Also, the genes associated to traits of interest have the potential to offer novel genetic variants for the crop genetic variability.
To identify the closest wild relatives of crop species, sampling efforts are required to be extensive. In addition to the broad sampling of wild species, we have studied 27 accessions from cultivated species and CWRs of seven species in collaboration with Ranjana Bhattacharjee from The International Institute of Tropical Agriculture (IITA, Nigeria). The outcomes of our studies will feed in to on yam breeding programmes regarding these species. Our genomic data resources are now available to improve crops that feed 100s of millions of people worldwide.
The genomic methods developed in this project have the potential to be applied in other plants and organisms. For example, we have produced a bioinformatic method that estimates the ploidy level of herbarium samples, which has a direct application in agriculture because the capacity of two plant species to cross depends directly on the ploidy compatibility between them. Also, the genes associated to traits of interest have the potential to offer novel genetic variants for the crop genetic variability.
To identify the closest wild relatives of crop species, sampling efforts are required to be extensive. In addition to the broad sampling of wild species, we have studied 27 accessions from cultivated species and CWRs of seven species in collaboration with Ranjana Bhattacharjee from The International Institute of Tropical Agriculture (IITA, Nigeria). The outcomes of our studies will feed in to on yam breeding programmes regarding these species. Our genomic data resources are now available to improve crops that feed 100s of millions of people worldwide.