Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Abstract

The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

Underutilized legumes: nutrient status and advanced breeding approaches for qualitative and quantitative enhancement

“…In terms of architecture, length of maturation, yield, and nutritional content, genetic and breeding efforts to improve the underutilized and neglected legume crops have not achieved the expected degree of success ( 92 ). Although traditional hybridization and other breeding methods have been attempted for some desired objectives, the expected results have not yet been obtained.…”

Next-Generation Sequencing Accelerates Crop Gene Discovery

“…Therefore, QTL-seq combined with differential expression profiling and diversity analysis proved to be efficient not only in scaling-down QTL size, but also in rapidly enabling potential candidate gene identification. The same approach has been successfully used in other crops, such as foxtail millet (Setaria italica) [45] and rice [49].…”

“…NGS-assisted expression profiling identifies candidate genes having transcripts linked with the phenotype of interest. The availability of NGS-based transcriptome-wide tools provides precise information about the abundances of gene transcripts [45]. Gene expression analysis is a method that has been frequently used to screen among candidate genes underlying a QTL in different crops, e.g., chickpea, potato, and rice [46][47][48].…”

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

“…In species where WGS are available, NGS technologies allow re-sequencing of the genome rapidly by using already available genome sequence as a reference to guide the alignment of the reads. The re-sequencing facilitates identification of minor sequence variations such as SNPs and insertions/deletions (InDels) between the reference genomes and the sample of interest by comparing the consensus sequence, leading to rapid mapping and identification of desirable mutations [ 85 , 86 ].…”