Pan-genome and Haplotype Map of Cultivars and Their Wild Ancestors Provides Insights into Selective Evolution of Cassava (Manihot esculentaCrantz)

Abstract

SUMMARYCassava is the most important starch sources, a tropical model crop. We constructed nearly T2T genomes of cultivar AM560, wild ancestors FLA4047 and W14, pan-genome of 24 representatives and a clarified evolutionary tree with 486 accessions. Comparison of SVs and SNVs between the ancestors and cultivated cassavas revealed predominant expansion, contraction of genes and gene families. Significantly selective sweeping occurred in the cassava genomes in 122 footprints with 1,519 candidate domestication genes. We identified selective mutations inMeCSKandMeFNR3promoting photoreaction associated withMeNADP-MEof C4assimilation in modern cassava. Co-evolved retardation of floral primordia and initiation of storage roots arose fromMeCOL5mutants with altered bindings toMeFT1, MeFT2andMeTFL2. MebHLHsevolved to regulate the biosynthesis, transport and endogenous remobilization of cyanogenic glucosides, with new functionalities ofMeMATE1, MeGTRin selected sweet cassava. These findings enhanced comprehensive knowledge and database on the evolution and breeding of cassava.HIGHLIGHTSThree nearly T2T cassava genomes of cultivar AM560 and its wild ancestors FLA4047 and W14.A species-level cassava panSV haplotype map across 346,322 structural variations over 31,362 gene families and 96,032,008 SNPs and InDels variations globally and a clarified evolutionary tree with 486 accessions.Selective mutations inMeCSKandMeFNR3promoted photoreaction associated withMeNADP-MEof C4assimilation shaped the C3-C4intermediate photosynthesis of modern cassava.Coevolution of floral primordia contrary to initiated storage root is pivotal for the domestication of cassava, and arose fromMeCOL5mutants altered the binding withMeFT1, MeFT2(SP6A), andMeTFL2.