**5. Conclusions: Prospects and perspectives**

Moreover, discovery research such as QTL mapping can be done on the database through

Tools for Crop information management Nursery and trial management Statistical analysis Marker-assisted breeding

Breeders toolbox; maps and markers; genes; phenotypes; genome sequences

Tomato, pepper, potato, coffee, Nicotiana, Petunia, and other solanaceous plants

Soybean breeder's toolbox and database including genome sequences, maps, markers, genetic stocks (including mutants)

Community-oriented informatics service featuring genome browser, maps, locus, gene, QTL, diversity, metabolic pathways

The Plant Comparative Genomics portal for sequenced and annotated green plant genomes and phylogenetics

SSR markers and linkage maps for 10 plant

\*BMS, hosted by IITA as a regional hub for integrated breeding platform (IBP), is a suite of interconnected software specifically designed to

Note: Other CGIAR-driven initiatives include Genomic and Open-source Breeding Informatics Initiative (GOBII), Integrated Genotyping Service and Support at Biosciences eastern and central Africa (BECA)/International Livestock Research Institute (ILRI), and Shared Indus‐ trial-Scale High-Throughput Genotyping Facility for delivering high-density genomics breeder's tools and low-cost genotyping services.

**Table 2.** Partial list of crop- or project-specific databases and breeder's toolboxes relevant to breeders in developing

Plant diseases are caused by a wide array of pathogens, including viruses, bacteria, and fungi. A combination of techniques, including microscopy, serological [e.g., enzyme-linked immu‐

and others

species

help breeders manage their day-to-day activities through all phases of their breeding programs.

**Reference**

in Asia

[160]

[162]

[158]

Current regional hubs: 4 in Africa, 3

Implemented based on SolGenomics

https://

ng.net/

http://

http://

http://

http://

www.soybase.org/

www.integratedbreedi

www.cassavabase.org/

http://solgenomics.net/ [159]

http://maizegdb.org/ [161]

phytozome.jgi.doe.gov/ pz/portal.html

marker.kazusa.or.jp

**Project/Host Database/Tool Purpose URL Remark/**

implementation of genetic mapping methods.

304 Next Generation Sequencing - Advances, Applications and Challenges

Breeding management system (BMS\*)

breeding project; Boyce Thompson Institute for Plant Research

Boyce Thompson Institute for Plant Research

Iowa State University

genetics and genomics

Joint Genome Institute

**4. Disease diagnostics and monitoring**

Cassavabase NextGen cassava

SolGenomics Sol Genomics Network,

Soybase USDA, Soybean Genetics Database

MaizeGDB USDA funded maize

database

Phytozome Department of Energy's

Kazusa Kazusa DNA Research Institute

nations that are in use or in progress.

Integrated breeding platform

> The productivity of staple food crops of hundreds of millions of people in developing countries is stagnating or diminishing as natural resources are depleted as a result of overcultivation and poor resource management, among other factors. Genetic improvement is heralded as the best option to enhance crop productivity, resilience to climate effects, and nutritional quality. The effective and efficient application of advanced biosciences tools and products holds substantial promise for enhanced agricultural productivity, improved livelihoods, and better prospects for food and nutrition security in Africa, where less-studied crops are grown as staples [114,115,158]. Genomics-enabled breeding will enable scientists to more effectively tap into the wealth of genetic variation in landraces and wild relatives for novel traits.

> Next-generation sequencing has evolved to the third generation of sequencing technology and boasts even longer read length, shorter run time, and lower cost per unit data [21]. Applications of NGS are broadening at a remarkable pace from whole-genome sequencing and re-sequenc‐ ing to transcript sequencing, metagenomics, and methylome sequencing. Thus, the application of NGS in agriculture is now vital to breeding, diagnosis, evolution, ecology, and basic functional genomics. SNP markers are already becoming the predominant marker types in modern breeding strategies [21,29]. Additional outcomes include the dissection of biochemical and genetic mechanisms or metabolic pathways underlying agronomically important traits, leading to a better understanding of how the genome and phenome are related [114].

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

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

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 Internetfree databases and tools is necessary in the interim.

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 orphan crops with little DNA sequence information.

The bioinformatics infrastructure at IITA can serve as a model for similar start-up bioinfor‐ matics units at the national program. Such platform hosts most of the standard bioinformatics tools to deal with any kind of sequence analysis, including shotgun and targeted DNA/RNA sequences. Importantly, analysis pipeline for GBS data is very essential for routine application of genomics in selection schemes.

Such an effort demands full engagement and transformation in the policy of national programs and other stakeholders. As expressed in previous views [52,159], relevant short-term and longterm training and institutional capacity building should be intensified. Academic institutions need to revise their curricula to develop expertise in NGS data analysis and bioinformatics. The participation of the fledging private sector also needs to be boosted.

It is clear that certain activities such as efficient DNA extraction and associated databases and decision-making breeding tools may need to operate at local levels; other activities such as GBS, SNP genotyping for forward breeding, NGS, and training may need to operate at regional levels; and curation of whole crop databases and development of analysis tools may operate at global levels. It is vital that communication occurs at all of these levels and across levels, including international institutes, NARS, and universities, and that the system remains responsive to the rapidly changing scientific environment, if NGS is to close the yield gap of staple crops in Africa.
