Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
Highlights
Such underutilized crop species (UCS) refer to neglected species cultivated mainly in their centers of origin or centers of diversity by native inhabitants where they are central to sustenance of local communities by providing special ecological, production, and consumption related roles, and underutilized species that were once widely grown but degraded to disuse because of a range of agronomic, genetic, and economic reasons [61,62,63,64,65]
Double haploid (DH) created from haploid wheat plants developed by anther culture or fertilization with maize pollen have been used for wheat genetic research and breeding, whereby maize-pollen-derived haploids have been more feasible than anther culture in durum wheat; the rate of DH plant production in the durum × maize system has been significantly improved [213]
Modern developments in genome sequencing, assembly, and annotation, coupled with sophisticated bioinformatics and computational tools have facilitated our better understanding of the structure and information contained in crop genomes
Summary
The orphan crops are envisaged as the future climate-smart crops and are gaining global recognition [44] Such UCSs refer to neglected species cultivated mainly in their centers of origin or centers of diversity by native inhabitants where they are central to sustenance of local communities by providing special ecological, production, and consumption related roles, and underutilized species that were once widely grown but degraded to disuse because of a range of agronomic, genetic, and economic reasons [61,62,63,64,65].
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