Haplotype-phased genomes elucidate genetic architecture of environmental adaptation and domestication traits in Silphium

Developing native perennial crops is vital for climate-resilient agriculture, yet their domestication is often hindered by a lack of cost-effective genomic resources. To build a framework for genomics-accelerated domestication of perennials with large, complex genomes, we generated chromosome-scale, haplotype-phased assemblies for Silphium integrifolium Michx. and Silphium perfoliatum L., two deep-rooted native North American prairie species valued for drought tolerance and oil production. The genomes are characterized by the presence of a putative helical structure preserved during interphase with a loop circumference of 43 Mb. Using targeted sequencing of 14 Silphium species, we first refined the phylogeny of the genus, recovering the Composita and Silphium subgenera while identifying taxonomic discrepancies. We used a combination of low-coverage short-read sequencing and target-sequencing to characterize a 258-accession diversity panel to define ancestral populations and perform genome-wide association studies (GWAS) on several traits. We identified 81 loci associated with environmental adaptation and domestication traits; notably, variants in a MATE transporter, Alpha-Beta hydrolase and a ACR4 -related protein explained significant variance in seed number and floral architecture. These findings establish the genomic framework necessary to accelerate the domestication of Silphium and provide a model for unlocking the potential of other complex wild genomes.