Articles
Generation of open-source genomics resources for African orphan tree crops by African Orphan Crops Consortium (AOCC), a public-private partnership for promoting food and nutritional security in Africa
Article number
1297_80
Pages
615 – 622
Language
English
Abstract
The growing African population needs a substantial increase in food production along with nutritious food options to address hunger, malnutrition and stunting.
The indigenous or naturalized African fruit tree species are inherently nutritious, fortified with minerals, vitamins and antioxidants with high potential to improve the resilience of African food systems.
The African orphan crops consortium (AOCC, http://africanorphancrops.org
) has prioritized 50 undomesticated or semi-domesticated perennial fruit species and 51 annual species through stakeholder consultations to improve their productivity as well as markets and value chains.
The next-generation breeding technologies based on genomics assisted selection holds immense promise to improve their domestication, yield and nutrition traits.
It involves the generation of the reference genome sequence, re-sequencing of 100 diverse accessions and using transcriptome sequencing for genome annotation.
At present the AOCC has completed sequencing of six tree genomes; Faidherbia albida (Fa), Artocarpus heterophyllus (Ah), Artocarpus altilis (Aa), Moringa oleifera (Mo), Sclerocarya birrea (Sb), and Annona senegalensis (As), three multi-purpose species genomes; Lablab purpureus (Lp), Vigna subterranea (Vs) and Solanum aethiopicum (Sa), while other 18 are under various stages of sequencing.
The AOCC is using Illuminas Hiseq2500, Hiseq4000, BGISEQ500 and customized assembly and annotation pipelines for reference genome sequencing.
Other technologies such as 10x and PacBio sequencing are also applied if deemed necessary.
Among the assembled genomes, the highest scaffold N50 was found to be around 1.54 Mb for Aa, whereas the smallest was for Sb, 0.34 Mb, whereas the majority of them ranged from 0.5 to 1 Mb.
The initial gene prediction used an electronic annotation pipeline, which is now being confirmed using a high-quality transcriptome sequence from at least 10-12 different tissues per species.
Following this, re-sequencing will provide information about the single nucleotide polymorphisms (SNPs), and will aid in trait tagging and genomics assisted breeding.
The indigenous or naturalized African fruit tree species are inherently nutritious, fortified with minerals, vitamins and antioxidants with high potential to improve the resilience of African food systems.
The African orphan crops consortium (AOCC, http://africanorphancrops.org
) has prioritized 50 undomesticated or semi-domesticated perennial fruit species and 51 annual species through stakeholder consultations to improve their productivity as well as markets and value chains.
The next-generation breeding technologies based on genomics assisted selection holds immense promise to improve their domestication, yield and nutrition traits.
It involves the generation of the reference genome sequence, re-sequencing of 100 diverse accessions and using transcriptome sequencing for genome annotation.
At present the AOCC has completed sequencing of six tree genomes; Faidherbia albida (Fa), Artocarpus heterophyllus (Ah), Artocarpus altilis (Aa), Moringa oleifera (Mo), Sclerocarya birrea (Sb), and Annona senegalensis (As), three multi-purpose species genomes; Lablab purpureus (Lp), Vigna subterranea (Vs) and Solanum aethiopicum (Sa), while other 18 are under various stages of sequencing.
The AOCC is using Illuminas Hiseq2500, Hiseq4000, BGISEQ500 and customized assembly and annotation pipelines for reference genome sequencing.
Other technologies such as 10x and PacBio sequencing are also applied if deemed necessary.
Among the assembled genomes, the highest scaffold N50 was found to be around 1.54 Mb for Aa, whereas the smallest was for Sb, 0.34 Mb, whereas the majority of them ranged from 0.5 to 1 Mb.
The initial gene prediction used an electronic annotation pipeline, which is now being confirmed using a high-quality transcriptome sequence from at least 10-12 different tissues per species.
Following this, re-sequencing will provide information about the single nucleotide polymorphisms (SNPs), and will aid in trait tagging and genomics assisted breeding.
Authors
P.S. Hendre, A. Muchugi, Y. Chang, Y. Fu, Y. Song, M. Liu, X. Liao, H. Liu, B. Song, X. Xu, S. Cheng, X. Liu, D.A. Odney, W. Kuan Ho, S. Mayes, S. Muthemba, R. Kariba, J. Featherston, C. Hefer, J. Rees, Y. Van de Peer, A. Van Deynze, R. Jamnadass
Keywords
genomics, next-generation breeding, next-generation sequencing, orphan crops
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