Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
Highlights
Plant breeders have continually faced the challenge of increasing crop yield, nutrition, and disease resistance as the human population increases, and regions suitable for the production of crops shift with a changing global environment [1–3]
Improving genomic resources for crop species has predominantly focused on a limited number of high-yield, popular species such as wheat (Triticum aestivum) [5], rice (Oryza sativa) [6], maize (Zea mays) [7], barley (Hordeum vulgare) [8], soybean (Glycine max) [9,10], canola (Brassica napus) [11], and sorghum (Sorghum bicolor) [12]
Genetic resources are largely limited to genetic linkage maps that can identify domestication-related traits and quantitative trait loci (QTL) not present in moth bean, but that are present in other Vigna species [54]
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Improving genomic resources for crop species has predominantly focused on a limited number of high-yield, popular species such as wheat (Triticum aestivum) [5], rice (Oryza sativa) [6], maize (Zea mays) [7], barley (Hordeum vulgare) [8], soybean (Glycine max) [9,10], canola (Brassica napus) [11], and sorghum (Sorghum bicolor) [12] These species are often referred to as major crops due to their extensive use in agriculture systems and high demand as food sources worldwide. Other pangenomes have been constructed, including one representing 3 rice individuals [31], 10 Brassica oleracea individuals [32], 18 bread wheat individuals [20], 54 Brachypodium distachyon individuals [33], 53 canola individuals [34], 5 sesame (Sesamum indicum) individuals [35], 725 tomato (Solanum lycopersicum) individuals [36], 89 pigeon pea (Cajanus cajan) individuals [37], and 1961 cotton (Gossypium spp.) individuals [38] (Table 1) These provide valuable resources for understanding genetic variation in these species [39]. This review aims to provide a foundation for further studies to construct pangenomes for under-utilised crop species and improve their traits through plant breeding based on pangenomic analyses
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