Abstract
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.
Highlights
The world’s population is predicted to increase to nearly 10 billion people by 2050 [1], coupled with a predicted increase of average surface temperature of 2 ◦ C by 2043 [2] and more variable weather patterns
There is significant genome variation present between individuals, and this genomic variation can be associated with important functional traits [21–26], such as nucleotide deletions linked with embryo sac fertility and presence/absence variation of genes (PAV) linked with submergence tolerance, yield, and phosphorus deficiency tolerance in rice (Oryza sativa) [26]; PAV linked with silique length, seed weight, and flowering time in Brassica napus [27]; PAV associated with disease resistance, acyl lipid metabolism, and glucosinolate metabolism in B. napus [28]; and SNPs linked with number of branches, number of seeds per pod, number of pods per plant, plant height, seed weight, and seed yield in pigeon pea (Cajanus cajan) [29]
Gene editing to improve agronomically-significant traits is challenging if the target gene is not present in the reference genome sequence and the sequence cannot be used to tailor the genome editing experiment, and so single reference genomes are often inadequate for designing editing target sites
Summary
The world’s population is predicted to increase to nearly 10 billion people by 2050 [1], coupled with a predicted increase of average surface temperature of 2 ◦ C by 2043 [2] and more variable weather patterns. Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), Zinc finger nucleases (ZFNs) [5–7], and transcription activator-like effectorbased nucleases (TALEN) [8–11] have already demonstrated their capacity in supporting crop resilience and yield improvements in several species [12–16], but the lack of knowledge of genome diversity and the polyploid nature of some crop genomes complicates the targeting of gene editing sites, leading to inefficiency in the traits that could be improved and the potential for adverse off-target effects from gene-editing experiments [12,17]. Gene editing to improve agronomically-significant traits is challenging if the target gene is not present in the reference genome sequence and the sequence cannot be used to tailor the genome editing experiment, and so single reference genomes are often inadequate for designing editing target sites.
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