Introgression from the wild relative Manihot glaziovii on cassava (M. esculenta) chromosome 1 exhibits segregation distortion and no direct effect on dry matter

The cassava (Manihot esculenta) genome has two large introgressions from its wild relative M. glaziovii on chromosomes 1 and 4 that originate from historical hybridization efforts. The 10 Mbp chromosome 1 introgression has been increasing in frequency in African breeding populations due to its statistical association with higher dry matter content and root number. However, the region also exhibits suppressed recombination, hindering breeders ability to combine favorable glaziovii alleles with the cultivated esculenta background. Since homozygous introgressed lines are rarely selected for advanced trials, dominance effects have not been well-characterized. To analyze the effects of the introgression with higher resolution, we generated a population of over 5000 seedlings from crosses between heterozygous introgressed parents and screened for recombinants using ten KASP markers tagging glaziovii-specific alleles. An optimized subset of 453 lines was then selected and evaluated over two years for yield and vigor traits. Unlike previous studies, composite interval mapping and mixed linear models showed no significant associations between glaziovii alleles and dry matter content or root number. Small, opposing effects on clonal vigor were observed at different ends of the introgression. The region showed significant segregation distortion and enrichment of putative deleterious alleles. Genome alignment of M. esculenta and M. glaziovii assemblies did not show any major structural variants in the introgression region, suggesting that suppressed recombination is likely driven by sequence-level divergence rather than structural rearrangements. These results indicate that the glaziovii introgression does not directly contribute to dry matter, supporting the need for recombination and purging of the glaziovii introgression to aid cassava improvement. Plain language summaryA large chromosome segment from a wild relative of cassava is an important structural aspect in the cassava genome. Since the chromosome segment tends to be inherited as one block, its effects on cassava traits were not well resolved. Through genetic mapping at higher resolution, we identified that the wild segment impacts early vigor and does not appear to impact dry yield, as was previously thought. While there are no major structural differences between the wild and cultivated chromosome segments, their overall divergence seems to suppress the wild chromosome segment from pairing with the cultivated chromosome segment during reproduction. In the apparent absence of any major benefits from the wild segment, removing it from the breeding population may be beneficial. Core ideasO_LIA set of glaziovii allele-specific markers were designed to track the chromosome 1 introgression haplotype. C_LIO_LISegregation distortion suggests the presence of recessive deleterious or lethal alleles in the introgression. C_LIO_LIIncreased recombination is needed to purge deleterious alleles enriched in introgression region. C_LIO_LIThe glaziovii introgression was associated with slightly lower vigor rating and stem diameter. C_LIO_LIThe effects of the previously-identified glaziovii DM QTL were not detected in this population. C_LI