Integrated genomics implicates a dynamin-like gene in unreduced gamete formation and yields a predictive marker for breeding in Lantana strigocamara

Abstract

Unreduced female gamete (UFG) production in the invasive ornamental Lantana strigocamara complicates breeding efforts to develop sterile triploid cultivars. To uncover the genetic basis of this trait and develop a diagnostic tool, an integrated genomic and transcriptomic approach was employed. This study combined RNA sequencing of ovary tissue from UFG-producing and non-producing diploid genotypes, DNA skim sequencing of a diverse 20-genotype panel, and the assembly of a new, chromosome-scale reference genome for the non-UFG cultivar ‘Lola’. Differential expression analysis identified over 1000 candidate genes, which were subsequently filtered using genome-wide variant data to pinpoint a high-confidence locus on chromosome 2B. This locus contains a dynamin-like gene (g29092), homologous to Arabidopsis DRP1 proteins, which carries high-impact InDels that segregate with the UFG phenotype. A high-resolution melting-based marker targeting a 36 bp InDel within this gene accurately genotyped 34 diverse cultivars and breeding lines using crude DNA extracts, demonstrating its utility as a rapid, low-cost screening tool. The identification of a dynamin-like gene provides a strong mechanistic hypothesis for UFG formation based on defects in meiotic cytokinesis. The validated HRM marker and the new ‘Lola’ reference genome represent significant advancements, offering practical tools for breeding programs and a robust foundation for future functional genomics research in lantana.