Genetic variation within the gene pool of modern crop species is the result of a continuum of changes ranging from single-nucleotide polymorphisms (SNPs), through indels, to large structural variants (SVs). This variation provides the raw material on which both human and natural selection acts. Understanding the processes that cause this variation, exploring its extent, and exploiting it are critical to maintain and improve crop productivity in the face of increasing demands imposed by a growing world population under the impact of climate change (Tao et al., 2019).

The availability of reference genomes for the majority of modern crops has allowed genome-wide surveys of SNPs and subsequent marker–trait association studies to link genetic variation with phenotypic variation. However, until recently our understanding of genetic variation has been constrained by the dependency on resequencing approaches based on a single reference genome. Such approaches have limited capacity to identify SVs. Nevertheless, mounting evidence demonstrates that SVs are prevalent in crops and play key roles in the genetic determination of agronomical traits. To better capture this structural variation, the concept of the ‘‘pan-genome’’ was proposed. The idea centers on the investigation of the entire gene repertoire of a species by sequencing multiple individuals of the species (Tao et al., 2019).

Pangenome concept was first introduced by Tettelin in 2005 and it has been defined as full complement of genes of a biological clade, such as a species, which can be partitioned into a set of core genes that are shared by all individuals and a set of dispensable genes that are partially shared or individual specific. There are two types of pangenome: open and closed, which help to determine the number of genomes to be sequenced to obtain the complete gene repertoire of a given species or related organisms ((Danilevicz et al., 2020).

Availability of high throughput next generation sequencing technology enabled sequencing multiple individuals of the same species to develop pangenome. Mainly three different approaches have been used so far for plant pangenome development viz., De Novo Assembly, Iterative Mapping and Assembly and De Bruijn Graph. Recently, pangenomes have been developed for several crops such as rice, wheat, maize, soybean, sesamum, tomato, B. napus and B. oleracea (Khan et al., 2020).

 A pangenome study can identify SVs and eliminates single-sample bias and has the capacity to present a nearly full view of the diversity present in a species. However, as the crop’s gene pool comprises many species, especially wild relatives with diverse genetic stock, it is suggested to use accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which has been referred  as  super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement (Khan et al., 2020).

Gao et al., 2019, developed tomato pangenome from 725 geographically and phylogenetically diverse accessions. The ‘map-to-pan’ strategy resulted in the identification of 351 Mbp of sequences (comprising 4873 novel genes) missing in the reference genome. The modelling of the tomato pangenome indicated it to be a closed pangenome with finite numbers of core and dispensable genes. The pangenome analysis resulted in the identification of a 4-bp substitution in the regulatory region of the TomLoxC gene modifying the tomato fruit flavor.

Song et al., 2020, constructed pangenome by using eight B. napus accessions and its analysis identified millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs). More than 9.4 percent of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length and seed weight in a nested association mapping population, which were not detected by SNP-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits.

Pangenome development is imperative for in-depth dissection of dispensable as well as species-specific genes. It could help to identify genes involved in adaptation and help in the formulation of strategies for the introduction or cultivation of environmentally stable varieties. The variations identified through pangenome analysis can be used as markers for marker-assisted selection, by which desirable traits present in crop wild relatives can be incorporated into domesticated cultivars. The implementation of the super-pangenome concept will definitely boost genomic assisted breeding and will enhance the crop improvement process. However, future research requires new tools to support De Bruijn graph assembly, pangenome construction and visualisation.

 

References:

 

Danilevicz, M. F., Fernandez, C. G. T., Marsh, J. I., Bayer, P. E. and Edwards, D., 2020, Plant pan-genomics: Approaches, applications and advancements. Current Opinion Pl. Bio., 54: 18-25.

 

Gao , L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., Chang, E. A. B., Fish, T. L., Stromberg, K. A., Sacks, G. L., Thannhauser, T. W., Foolad, M. R., Diez, M. J., Blanca, J., Canizares, J., Knaap, E. V. D., Huang , S., Klee, H. J., Giovannoni , J. J. and Fei, Z.,  2019, The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavour. Nature Gent., 51: 1044–1051.

 

Khan, A. W., Garg, V., Roorkiwal, M., Golicz, A. A., Edwards, D. and Varshney, R. K., 2020, Super-Pangenome by integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci., 25(2): 148-158.

 

Song, J. M., Guan, Z., Hu, J., Guo , C., Yang, Z., Wang, S., Liu, D., Wang, B., Lu, S., Zhou, R., Xie, W. Z., Cheng, Y., Zhang, Y., Liu , K., Yang , Q. Y., Chen, L. L. and Guo, L., 2020, Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6: 34–45.

 

Tao, Y., Zhao, X., Mace, E., Henry, R. and Jordan, D., 2019, Exploring and exploiting pangenomics for crop improvement. Mol. Plant., 12: 156–169.