. Exploring and utilization of the genetic variation within the gene pool of modern crop species is a critical step in maintaining and improving crop productivity. The genetic variation ranging from SNPs to large structural variation can result in variation in the gene content between individuals of the same species. The Pangenome concept was proposed to better capture this variation; as single reference genome is insufficient to capture the complete genetic diversity of a species. By combining genomic data from multiple accessions, pangenome allows detecting of dispensable genes. Dispensable genes contains both accessory genes (present in some but not in all the strains of a species) and unique genes. Structural variants present in dispensable genome includes Copy Number Variations (CNV), Presence or Absence Variation (PAV), inversions and translocations. The dispensable genome analysis evaluates genetic diversity and enables breeding for climate resilience and re-domestication, linking environmental adaptation traits with crop productivity. Pan-genome construction in major crop species like rice, maize, brassica, and soybean has led to the discovery of dispensable genes associated with disease resistance and yield. High-quality pan-genomes with phenotypic information aid in identifying variant dispensable alleles and delimiting CRISPR-Cas9 target sites to improve editing efficiency1.

Pan-genome analysis has been used to explore genetic diversity of dispensable genome across several crop species. For instance, the Chickpea pan-genome was constructed to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. By constructing a divergence tree based on genes present in approximately 80% of individuals in one species, the researchers identified 1582 novel genes which were not reported earlier. They found that chromosomal segments and genes of dispensable genome showed signatures of selection during domestication, migration, and improvement4.

Development of pan-genome-scale genomic resources for rice provided access to genomic variations within the dispensable genome, including 171,072 structural variations (SVs) and 25,549 gene copy number variations (gCNVs). An Oryza glaberrima assembly was also used to infer the derived states of SVs in the Oryza sativa population. These pan-genome analyses not only provide a better understanding of the genomic diversity of crop species but also reveal valuable dispensable genes associated with important traits, such as disease resistance and yield components3.

Constructing a pangenome for identification of dispensable genes poses significant challenges due to the high costs involved, potential assembly errors, and the complexity of dealing with polyploidy and heterozygosity.The development of new tools to facilitate pangenome construction and visualization is essential. An integrated pangenome browser capable of representing SNPs and SVs in a multi-reference coordinate system for dispensable genome analysis needs to be developed. Expanding the pangenome beyond species can increase the utilization of wild dispensable gene diversity in crop improvement. As more pangenomes become available for diverse species, we can gain a better understanding of how species and higher taxa are defined at the genome level, which can provide insights into plant evolution and domestication2.

References:

1.

FERNANDEZ, T. C. G., NESTOR, B. J., DANILEVICZ, M. F., MARSH, J. I., PETEREIT, J., BAYER, P. E., BATLEY, J. and EDWARDS, D., 2022, Expanding gene-editing potential in crop improvement with pangenomes. Int. J. Mol. Sci., 23(4): 2276.

2.

GAO, L., GONDA, I., SUN, H., MA, Q., BAO, K., TIEMAN, D. M., BURZYNSKI-CHANG, E. A., FISH, T. L., STROMBERG, K. A., SACKS, G. L. and THANNHAUSER, T. W., 2019, Pan-genome uncovers new dispensable genes and a rare allele regulating beneficial traits. Nat. Genet., 51(6): 1044-1051.

3.

QIN, P., LU, H., DU, H., WANG, H., CHEN, W., CHEN, Z., HE, Q., OU, S., ZHANG, H., LI, X. and LI, X., 2021, Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell J., 184(13): 3542-3558.

4.

VARSHNEY, R. K., ROORKIWAL, M., SUN, S., BAJAJ, P., CHITIKINENI, A., THUDI, M., SINGH, N. P., DU, X., UPADHYAYA, H. D., KHAN, A.W. and WANG, Y., 2021, A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nat., 599(7886): 622-627.