Biodiversity

New database of genetic markers for tropical trees

tropiTree is a new interactive open-access database that provides detailed information on genetic markers for 24 trees species that are important to smallholders in complex tropical agroforestry systems.

Source: World Agroforestry Centre

The development of the genetic markers in the database has been possible through massive cuts in sequencing costs that can now be applied to ‘non-model’ (or genetically under-researched) species such as most trees.

Ian Dawson, Associate Fellow with the World Agroforestry Centre, who was involved in the development of the database, wants researchers to know about the kind of genetic work that is now possible for tropical trees.

“With the low cost of next-generation sequencing methods, we can now design tools for studying the genetics of trees cheaply and quickly,” explains Dawson.

“In the area of tree genetics, technology has advanced considerably in recent years and with this comes major opportunities for research in the field of agroforestry.”

The tropiTree database contains, on average, more than 5,000 genetic markers per species, a massive increase in the resources available for the study of the majority of these trees. This information will be useful for scientists who are studying the breeding systems of the trees and who are working towards preventing inbreeding depression caused by a lack of genetic diversity resulting from a lack of connectivity in farm landscapes.

“Scientists can also use the database to identify genetic markers in particular regions of interest in the genome, such as in genes that may be responsible for adaptation to climate change,” says Dawson. “The data will provide a better understanding of how to manage trees productively in agroforestry systems.”

The tree species chosen for the database include nine of African origin, five from Asia or Oceania, nine from Latin America and one with a natural distribution spanning both Africa and Asia. Due to human movement of seed, the selected species are now often found growing together in various combinations of indigenous and exotic trees in agricultural landscapes.

Among the species are those which provide a range of products and services to farmers, including: fruit (the baobab, Adansonia digitata), timber (Acacia mangium), gum (Acacia senegal), fodder (Calliandra calothyrsus), fertilizer (Faidherbia albida), biofuel (Jatropha curcas) and medicine (Prunus africana and Warburgia ugandensis).

The sequencing work and development of the database has been a collaborative effort between the James Hutton Institute in Scotland, the World Agroforestry Centre, the Kenya Forestry Research Institute and other partners.

As well as wanting to rectify the absence of genetic tools, the scientists were keen to ensure the sequencing data they generated was made available in a suitable format to researchers that are not necessarily familiar with modern sequence-based molecular technologies. Hence, the database is freely available and straightforward to interpret.


Read the full article on Plos One. The database is here.

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