Pan-Genome Research to Help Solve the 10-billion People Question

Abstract: Since the world population is expected to increase to approximately 10 billion by 2060 - 2070, the rice community is searching for novel ways to help the 10-billion people question (10BPQ) by breeding new varieties that are nutritious, sustainable, and climate resilient. Thus, understanding and exploiting genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we aim to explore and study all genetic variants using a pan-genome strategy in rice. We have assembled a pan-genome Rice Population Reference Panel (RPRP) that represents the K=15 subpopulation structure of Asian rice, plus two outgroup species, i.e., O. rufipogon [AA] and O. punctata [BB]. Using this pan-genome, we identified 71,529 large structural variations (SVs, >50 bp) and generated a pan-genome inversion index (PGII) with 1,769 large inversions (>100 bp), which revealed evolutionary insights into the subpopulation structure of Asian rice. Gene annotation of the RPRP was used to develop a Rice Gene Index (v1.0), where we detected 112,658 Ortholog Gene Indices (OGI). Lastly, the RPRP was used as a template to map resequencing data from the 3K-RGP resequencing data set to identify virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. To speed up the process, we developed a high-performance computing genomic variant calling workflow (HPC-GVCW) based on GATK (v4). The workflow enables mapping 3K rice genome to a reference sequence within 4 days. Results showed an average of ~27.3 million SNPs per genome, ~2.1 M of which were novel. Using the submergence-tolerant gene Sub-1A as a test case to investigate genetic variation across the 3K-RGP, we discovered 180 accessions that possess the submergence-tolerant allele, which may be useful for accelerated breeding programs and functional genomics studies.