**6. Acronyms**

The ultrahigh-throughput capacity of NGS platforms and the commercial scale of automated pipelines make it cheaper to outsource genotyping services such as GBS and RAD. Capital investment in state-of-the-art genomics facilities in all laboratories is not prudent for several reasons. However, establishment of shared resources at regional and subregional center of excellence, such as BECA, is fully recognized by stakeholders. The West Africa Biotechnology Initiative (WABI), copromoted by IITA and subregional organizations such as CORAF/ WECARD (West and Central African Council for Agricultural Research and Development), is promoting such an idea and mobilizing resources toward this goal. This is likely to reduce

Mainstreaming this highly promising but complex and rapidly evolving next-generation breeding scheme entails continuous training and effective information sharing. Although recent scientific progress heralded the era of molecular breeding, most public sector research‐

Reasons for this range from limited awareness of the technological advances to lack of adequate infrastructure, knowledge, and limited resources that are required to make use of markers in crop breeding. In recent times, that trend is changing as research institutions operating in Africa (international, regional, and national systems) strive relentlessly to accelerate the adoption and application of advanced biosciences tools in support of the region's agricultural transformation. WABI is striving to establish a center of excellence to promote the adoption of biotechnology to enable innovative approaches, resulting in increased crop yield. Availability of training and service platforms in various subregions of Africa (e.g., West and Central, East and South) will not only make it more affordable and accessible to the users and trainees in the continent but also focus more on the needs that are specific to the region's research.

Developing in-house capacity for GBS data analysis pipeline, NGS library construction, and automated DNA extraction is fundamental for routine applications of GS/MAS in breeding programs. The spectacular diffusion of ICT throughout Africa, particularly mobile phone technology and smart devices, paves the way for access to web-based education and genomic resources. Given the poor connectivity in developing countries, however, developing Internet-

Efficient data management systems are a prerequisite for applying genomic information by international, national, and private sectors involved in improving the rate of genetic gain in crops. WGS and assembly require advanced instruments, skilled personnel, and strong computational capacities. It also requires improvement of assembly and continual annotation of genes as more and more information is generated by whole-genome re-sequencing or functional genomics. Integration of genomics information with other phenotypic and envi‐ ronment data also requires strong skill in programming and database development. Moreover, processing of big data requires basic programming skills in order to automate routine data manipulation and processing needs. Thorough knowledge in bioinformatics will afford the ability to apply comparative genomics with the aim of extending the power of genomics to

turnaround times for GBS samples, and raise the quality of cDNA libraries.

306 Next Generation Sequencing - Advances, Applications and Challenges

ers in Africa are far from harvesting the fruit of the technological advances.

free databases and tools is necessary in the interim.

orphan crops with little DNA sequence information.

AOCC; African Orphan Crops Consortium BMS; Breeding management system BS; Bisulfide Cas9; CRISPR-associated protein 9 CBSD; Cassava brown streak disease CBSV; Cassava brown streak virus CGIAR; The Consortium of International Agricultural Research CORAF/ WECARD; West and Central African Council for Agricultural Research and Development CRISPR; Clustered regularly interspaced short palindromic repeat CRP; Consortium research programs DArT; Diversity Array Technology DSB; Double-strand breaks GBS; Genotyping by sequencing

GDF; Genomic Diversity Facility GEBV; Genomic-estimated breeding value GS; Genome selection GWAS; Genome-wide association study IBP; Integrated breeding platform ICT; Information and communication technology IITA; International Institute of Tropical Agriculture KASP; Kompetitive Allele-Specific PCR MAS; Marker-assisted selection NARS; National agricultural research systems ncRNA; Noncoding RNA NGS; Next-generation sequencing NHEJ; Nonhomologous end joining PDA; Personal digital assistant QTL; Quantitative trait loci R4D; Research for development RAD; Restriction-site-associated DNA RGN; RNA-guided nucleases RRS; Reduced representation sequencing RTB; Root, tuber, and banana siRNA; small interfering RNA SNP; Single nucleotide polymorphism TALENs; Transcription activator–like effector nucleases TILLING; Targeting Induced Local Lesions in Genomes WGS; Whole-genome sequencing ZFN; Zinc finger nuclease WABI; The West Africa Biotechnology Initiative (WABI),
