“Role of Pan-genomics in Crop Improvement: A Future Reference Paradigm”

UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE

COLLEGE OF AGRICULTURE, BANGALORE

Department of Genetics and Plant Breeding

Seminar on

“Role of Pan-genomics in Crop Improvement: A Future Reference Paradigm”

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 pan-genome concept was proposed to better capture this variation; as a single reference genome is insufficient to capture the complete genetic diversity of a species.

By combining genomic data from multiple accessions, pan-genome allows detecting the structural variants which include Copy Number Variations (CNV), Presence or Absence Variation (PAV), inversions and translocations. The pan-genomic 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 genes associated with disease resistance and yield. High-quality pan-genomes with phenotypic information aid in identifying variant alleles and delimiting CRISPR-Cas9 target sites to improve editing efficiency.

Pan-genome analysis has been used to explore genomic diversity 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, researchers estimated the divergence of Cicer over the last 21 million years. They found that chromosomal segments and genes show signatures of selection during domestication, migration, and improvement.

Similarly, the tomato pan-genome revealed 4,873 genes absent from the reference genome, and presence/absence variation analyses revealed substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Additionally, the development of pan-genome-scale genomic resources for rice provided access to genomic variations, 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 genes associated with important traits, such as disease resistance and yield components.

Constructing a pan-genome poses significant challenges due to the high costs involved, potential assembly errors, and the complexity of dealing with polyploidy and heterozygosity. However, the future prospects of pangenomics look promising. The development of new tools to facilitate pan-genome construction and visualization is essential. An integrated pan-genome browser capable of representing SNPs and SVs in a multi-reference coordinate system for genome analysis needs to be developed.

Expanding the pan-genome beyond species can increase the utilization of wild gene pool diversity in crop improvement. As more pan-genomes 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 domestication. Implementing the super-pangenome concept can boost genomic-assisted breeding and enhance the crop improvement process.

References:

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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, 184(13): 3542-3558.

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