Graph Pangenomes Track Genetic Variants for Crop Improvement

Abstract

Global climate change and the urgency to transform crops require an exhaustive genetic evaluation. The large polyploid genomes of food crops, such as cereals, make it difficult to identify candidate genes with confirmed hereditary. Although genome-wide association studies (GWAS) have been proficient in identifying genetic variants that are associated with complex traits, the resolution of acquired heritability faces several significant bottlenecks such as incomplete detection of structural variants (SV), genetic heterogeneity, and/or locus heterogeneity. Consequently, a biased estimate is generated with respect to agronomically complex traits. The graph pangenomes have resolved this missing heritability and provide significant details in terms of specific loci segregating among individuals and evolving to variations. The graph pangenome approach facilitates crop improvements through genome-linked fast breeding.

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

“…Recently, several African orphan crops have had their genome sequenced (reviewed in Ghazal et al., 2021), which provides opportunities to perform pangenomic analyses to further understand the domestication history and support genome‐assisted breeding of these African orphan crops. With the development of more whole genome comparative algorithms (Kille et al., 2022), graph‐genome‐based mapping (Siren et al., 2021), and downstream analysis tools (Liao et al., 2022), we could soon be able to get accurate multi‐alignment results of whole genomes, identify more complex sequence variations such as transposable elements (TEs) and nested SVs, and use pan‐reference genomes to update traditional bioinformatics pipelines for different omics (for the further application of graph pangenomes in crop improvement, please also refer to Hameed et al., 2022, Wang et al., 2022b, Zanini et al., 2022). By then, pangenomic analysis could help us better understand the evolution of different plants, the origin of new genes, and the molecular basis of complex phenotype variations.…”