Researchers Sequence Guinea Yam Genome
An international team of scientists from the United Kingdom,
Japan, and Germany has produced the first high-quality genomic sequence
for the white Guinea yam (Dioscorea rotundata), a staple tuber
crop that contributes enormously to the subsistence and socio-cultural
lives of millions of people, principally in West and Central Africa.
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| Woman selling yam tubers at Oje market in Ibadan, Nigeria. Image credit: International Institute of Tropical Agriculture |
This genus contains approximately 450 species which are primarily distributed in tropical and subtropical regions worldwide. Approximately ten species have been independently domesticated in West Africa, Southeast Asia, and the Pacific and Caribbean islands.
Yam cultivation is constrained by many factors. Yam is an annual climber that requires stakes for support and is highly vulnerable to a plethora of pests and diseases. Seeds are not often used as starting materials; instead, yams are commonly propagated clonally using small whole tubers or tuber pieces. Yam tubers can grow to over 1.5 m and weight 70 kg.
The white Guinea yam is the most popular species in West and Central Africa, the main region for yam production worldwide, which contributed 96% of the 63 million tons of yam produced globally in 2013.
“Having a reference sequence for the white Guinea yam gives us the unique opportunity to gain a better understanding of dioecy (plants having separate males and females), a very rare trait in flowering plants, in a species that’s very evolutionarily differentiated from most of what’s been sequenced so far,” said co-author Dr. Benjamen White, of Earlham Institute, UK.
“Understanding this trait and having a genomic resource for white Guinea yam will be invaluable in breeding a better yam, one that will improve food security in West and Central Africa, and the livelihood of smallholder farmers there.”
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| Comparative genomics of the white Guinea yam (Dioscorea rotundata) and other angiosperm species: (a) Venn diagram showing conserved and unique genes at 1:1 correspondence among the white Guinea yam, Arabidopsis thaliana, Brachypodium distachyon, and Oryza sativa; total gene counts in each genome are given below the species name; (b) maximum likelihood tree of the white Guinea yam, B. distachyon, O. sativa, Elaeis guineensis, Musa acuminata, and Phoenix dactylifera based on 2,381 orthologous protein-coding genes; the bootstrap values across 1,000 resamplings are shown; the scale bar represents the mean number of substitutions per site; (c) phylogenetic analysis of the relationships of mannose-specific bulb-type lectin proteins in the white Guinea yam (red), A. thaliana (blue), B. distachyon (green), and O. sativa (orange); arrowheads represent bulb-type lectins observed to have enriched expression in tubers; high confidence bootstrap values (1,000 replicates) are represented at the nodes of the tree as dots; thick red and blue lines show two root branches of white Guinea yam -specific expanded genes. Image credit: Tamiru et al, doi: 10.1186/s12915-017-0419-x. |
Dr. White and colleagues assembled a 594-Mb genome of the white Guinea yam and identified 26,198 genes.
They also identified the genomic region associated with sex in yams and found yam sex to be female heterogametic (male=ZZ, female=ZW).
Phylogentic analysis revealed that yam is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana).
“This is an important breakthrough. It means that yam has joined those crops with a full DNA sequence, a development which started with rice some years ago,” said co-author Dr. Robert Asiedu, R&D Director for the International Institute of Tropical Agriculture-West Africa in Ibadan, Nigeria.
“The full DNA sequence will greatly facilitate our understanding of the genetic control of key traits such as flowering, diseases, and others including quality traits, and this in turn will make the breeding of new varieties both faster and more precise.”
“This will help to overcome some of the many challenges facing yam farmers in Africa and other parts of the world,” added co-lead author Professor Ryohei Terauchi, of Kyoto University and the Iwate Biotechnology Research Centre in Japan.
“These include pests and diseases, post-harvest losses and the need to develop more sustainable systems of farming for the crop.”
The findings are published in the journal BMC Biology.
Source : sci-news.com
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