Genome Assembly of the Green Revolution Wheat Cultivar Pavon 76 Establishes a Reference for CIMMYT-Derived Wheat

Abstract

Common wheat (Triticum aestivum L.) is a cornerstone of global food security. However, the standard reference genome, IWGSC RefSeq v2.1, is derived from wheat cultivar Chinese Spring, a historically important lineage that is not representative of modern cultivated wheat. In contrast, Pavon 76 is a CIMMYT Green Revolution wheat cultivar grown worldwide and is present in the pedigrees of numerous elite wheats, as well as in the genetic background of over 600 cytogenetic stocks used in studies ranging from recombination to male sterility. As no Pavon 76 reference has been reported, interpretation of these Pavon 76-derived stocks has relied on the genetically distant IWGSC RefSeq v2.1. To address this gap, we generated PacBio HiFi reads and Hi-C read pairs to assemble Pavon 76s genome. The final assembly comprises the expected 21 chromosomes, spans 15 Gb, and has an N50 of 710 Mb. Annotation identified 167,201 genes, of which 89.5% were functionally annotated. Comparative sequence and gene synteny analysis between Pavon 76 and IWGSC RefSeq v2.1 revealed significant structural divergence, establishing that IWGSC RefSeq v2.1 is not fully representative of modern wheats. This robust Pavon 76 assembly establishes the first chromosome-scale de novo assembly of a CIMMYT-derived wheat and provides a foundation for future genetic and genomic studies.