Biology subjects

Ogunpaimo, K.

Publications and source records attributed to Ogunpaimo, K..

3 recordsLinked to original sources

bioRxiv2026

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

genetics↗

bioRxiv2021

Low-cost, handheld near-infrared spectroscopy for root dry matter content prediction in cassava

Over 800 million people across the tropics rely on cassava as a major source of calories. While the root dry matter content (RDMC) of this starchy root crop is important for both producers and consumers, characterization of RDMC by traditional methods is time-consuming and laborious for breeding programs. Alternate phenotyping methods have been proposed but lack the accuracy, cost, or speed ultimately needed for cassava breeding programs. For this reason, we investigated the use of a low-cost, handheld NIR spectrometer for field-based RDMC prediction in cassava. Oven-dried measurements of RDMC were paired with 21,044 scans of roots of 376 diverse clones from 10 field trials in Nigeria and grouped into training and test sets based on cross-validation schemes relevant to plant breeding programs. Mean partial least squares regression model performance ranged from R2p = 0.62 - 0.89 for within-trial predictions, which is within the range achieved with laboratory-grade spectrometers in previous studies. Relative to other factors, model performance was highly impacted by the inclusion of samples from the same environment in both the training and test sets. Random forest variable importance analysis of root spectra revealed increased importance in a region previously identified as predictive of water content in plants (~950 - 990 nm). With appropriate model calibration, the tested spectrometer will allow for field-based collection of spectral data with a smartphone for accurate RDMC prediction and potentially other quality traits, a step that could be easily integrated into existing harvesting workflows of cassava breeding programs. CORE IDEASO_LIA low-cost, handheld near-infrared spectrometer was tested for phenotyping of cassava roots C_LIO_LIPlant breeding-relevant cross-validation schemes were used for predictions C_LIO_LIHigh prediction accuracies were achieved for cassava root dry matter content C_LIO_LIA spectral region predictive of plant water content was identified as important C_LI

plant biology↗

bioRxiv2020

Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava

Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5,310 clones developed at the International Institute of Tropical Agriculture - Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type). We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

genetics↗