Biology subjects

Oyebode, O. G.

Publications and source records attributed to Oyebode, O. G..

5 recordsLinked to original sources

bioRxiv2026

Breeding cassava for intercropping with cowpea: monoculture selection captures most intercrop selection gain, but targeted testing remains necessary

Intercropping dominates smallholder cassava production in sub-Saharan Africa, yet cassava breeding programs evaluate genotypes exclusively under monoculture. Despite consistently reported system-level yield advantages, cassava yield is reduced by 17 to 51% under intercropping, indicating a need to reduce this competitive disadvantage through breeding. However, the quantitative-genetic foundations of intercrop breeding remain uncharacterized for tropical root crop systems. We hypothesized that monoculture selection would capture most, but not all, genetic merit for intercropping and that a limited tester set would be sufficient if general mixing ability predominated. We evaluated 120 cassava clones previously selected under monoculture in IITA advanced yield trials, testing them under monoculture and in intercrop with two contrasting cowpea varieties across two years at Ibadan, Nigeria. Spatial mixed models quantified genetic variation, genotype by cropping system interaction, cross system genetic relationships, realized selection gain, mixing ability, tester effects, and land equivalent ratio. Intercropping reduced cassava fresh root yield by 19%, but total land equivalent ratios exceeded 1.0 for all clones, confirming a system-level land use advantage. Cassava performance under intercropping was heritable, with estimates of 0.50 to 0.75, and genotype by cropping system interaction was not significant. Genetic correlations between monoculture and intercrop performance were high and approached unity (rg = 0.92 to 0.99), and selection efficiency was 26 to 44% at 10% intensity, confirming that high genetic correlation does not guarantee effective indirect selection. Monoculture selection captured approximately two-thirds of direct intercrop gain. General mixing ability dominated, specific mixing ability was negligible, and producer effects explained 20 to 47% of intercrop variance. The two architecturally and phenologically contrasting cowpea varieties had limited influence on cassava rankings. Here, we show for the first time that cassava breeding for intercropping can retain monoculture selection during early stages while adding two representative cowpea testers at the advanced trial stage. This staged strategy aligns cassava breeding with diversified smallholder systems without creating a separate pipeline.

plant biology↗

bioRxiv2026

Near-infrared phenomic and genomic prediction for seed protein in winter legume white lupin (Lupinus albus L.): A utility comparison

White lupin (Lupinus albus L.) is a cool-season grain legume with seed crude protein of 33-47%, competitive with soybean (Glycine max L.) meal. It also fixes nitrogen and mobilizes soil phosphorus. Because soybean is a summer crop, white lupin can occupy Southeastern winter fields as a complementary protein source. Breeding for seed protein is limited by the cost and throughput of reference phenotyping. To determine how each is best deployed, we compared the utility of near-infrared spectroscopy (NIRS)-based phenomic selection with genomic selection based on 246,847 SNPs from low-pass, whole genome sequencing in a panel of Auburn University breeding lines and USDA National Plant Germplasm System germplasm. A handheld NIR calibration against Dumas reference protein reached screening-grade accuracy (R2 = 0.81). Under common cross-validation, phenomic predictive ability was 0.93 and genomic was 0.12. The low genomic value was consistent with moderate heritability (H2 = 0.33) and strong genotype-by-year interaction. Beyond predictive ability, NIRS recovered superior accessions the strictest selection intensity, and 40 to 60 reference assays sufficed to calibrate the model. Handheld NIRS is a low-cost tool for protein calibration and early-generation screening, while genomic prediction remains suited to parental selection, together supporting a complementary strategy for legume breeding Plain Language SummarySoybean meal is the main protein source for livestock and fish farms in the United States. Because soybean is a summer crop, many Southeastern fields sit idle or grow low-value cover crops in winter. White lupin, a cool-season legume whose seeds are as protein-rich as soybean meal, makes a good complementary winter crop: it yields high-protein grain while serving as a cover crop that fixes nitrogen and frees up soil phosphorus for later crops. In our early-stage lupin breeding program, measuring seed protein by standard lab methods is slow and costly. We built a calibration that lets a handheld scanner estimate protein from light, and compared it with predicting protein from the plants DNA. The scanner gave accurate, low-cost protein screening from only about 40-60 lab tests, while DNA-based prediction remains suited to guiding parent selection. Used together, these tools offer breeders a practical path to develop high-protein white lupin. Core ideasO_LIHandheld NIRS provides screening-grade prediction of white lupin seed crude protein. C_LIO_LISpectra carried more usable protein signal than markers by measuring seed chemistry directly. C_LIO_LINIRS and genomic prediction serve different stages of a white lupin breeding program. C_LIO_LIAbout 40 to 60 reference assays sufficed to calibrate NIRS to near-full accuracy. C_LI

genomics↗

bioRxiv2026

Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover (Trifolium incarnatum L.) for breeding purposes

AO_SCPLOWBSTRACTC_SCPLOWCrimson clover (Trifolium incarnatum L.) is an obligately outcrossing, cool-season annual legume valued for forage and cover cropping, yet genomic resources to support systematic improvement are limited. We performed the first and most comprehensive whole-genome resequencing (WGR) of global crimson clover germplasm to (i) characterize diversity and population structure and (ii) develop a public mid-density enrichment capture panel for breeding applications. A core set of 45 accessions sequenced at [~]50X generated 5.84 million variants, while 149 additional accessions sequenced at [~]2.54X yielded 17.05 million variants. After stringent filtering, we retained 542,790 high-confidence SNPs from the high-coverage dataset and [~]2.4 million from the low-pass cohort. Population analyses (PCA, ADMIXTURE) revealed compact clustering of cultivars, broader dispersion of wild and uncertain-status accessions, and low overall differentiation (FST = 0.0105) with excess heterozygosity (FIS = -0.0592), consistent with obligate outcrossing. Guided by these resources, we designed a 28,913-SNP TWIST hybrid-capture panel enriched for genic regions and evenly distributed across seven chromosomes. This panel is being deployed within Auburn Universitys crimson clover breeding program to support population improvement and cultivar development. The resulting genomic resources provide a reproducible, mid-density genotyping platform for trait discovery, predictive breeding, and diversity monitoring. Together, these advances bring crimson clover genomic resources on par with other legumes such as soybean (Glycine max (L.) Merr.) and alfalfa (Medicago sativa), establishing a robust foundation for genomics-assisted improvement of this key cover and forage crop in U.S. sustainable agriculture. CORE IDEASO_LIWhole-genome re-sequencing of 194 crimson clover accessions revealed >21 M variants. C_LIO_LIHigh-confidence SNP catalogs from 50X and 2X data enable cost-effective genotyping. C_LIO_LIGenetic diversity is weakly structured, with cultivars clustering narrowly by origin. C_LIO_LIA 28,913 SNP enrichment panel delivers uniform genome coverage and >75% genic content. C_LIO_LIThese genomic tools accelerate GWAS, genomic selection, and breeding innovation. C_LI

genomics↗

bioRxiv2026

Optimizing multi environment cowpea yield trial by appraising the fitness and similarities among test sites: a case study of IITA cowpea breeding program

Optimization of Multi environment trials (MET) trials require an efficient testing network consisting of ideal sites which should be highly discriminative and representative of their mega environments. Also concurrently managing sites that are similar in terms of information there give about genotype performance adds no extra utility to the breeding program. The objective of this study was to appraise the testing network of the cowpea breeding program of the International Institute of tropical Agriculture (IITA) based in Nigeria on the basis of their representativeness and discriminatory ability for grain yield, investigate the similarities among them and assess the variance components. 6 set sets of Advance yield trial with unique entries were analysed using Mixed models, best linear unbiased estimate (BLUPs) and BLUP based GGE biplot. Results showed significant means squares Genotype x Location interaction effect for all 6 sets; this justifies the to study GEI in cowpea, partitioning variance showed that Environment main effect accounted for the largest proportion of the total phenotypic variance, with a range of 58.1 (Adv 4) to 73.9% (Adv 3), Environment was followed by Genotype x Location interaction which explained between 16.1% (Adv 5) to 22.6% (Adv 4). Genotype main effect accounted for the least with a range of 9.5% (Adv 6) to 19.3% (Adv 4). Broad sense-heritability for GY was high in Advance 1-5 (ranging from 0.62-0.70) and medium in advance 6 (0.53). Shika June, Shika August and Minjibir consistently showed high discriminativeness with Minjibir been the most discriminating environment for this study. Ibadan September and Ibadan May on the other hand consistently showed poor discriminating ability while BUK was inconsistent having good discriminative ability in Sets 1 and 3 while it was poor in sets 2, 5 and 6. In terms of representativeness, no environment consistently had desirable results however, Shika August and Shika June were most representative while Minjibir was least representative. On the basis of discriminativeness and representativeness, the six environments were ranked in other of desirability as Shika August> Shika June> Minjibir > Ibadan September > BUK farm > Ibadan May. In terms of similarity among environments, both the BLUP-Based GGE biplot and genotypic correlations indicated that Ibadan May and September were consistently grouped together and highly correlated; indicating that they are similar, while, Shika August and Shika June were found to be unique. Ibadan May was therefore adjudged a redundant location and could be dropped and replaced without any loss of accuracy because it was neither discriminative nor representative in all biplots draw and it consistently fell in the same Mega environment with Ibadan September. We concluded that there is a need to sample more testing sites and validate their fitness for multi environment yield trials using methods applied in this study.

genetics↗

bioRxiv2026

Simultaneous selection for yield and stability in cassava (Manihot esculenta Crantz) under optimum condition in Nigeria

High yield and stability of performance across environments are required for success in agricultural systems. Selection of high yielding and stable genotypes is always hindered by Genotype by environment interaction (GEI). Hence plant breeders have proposed diverse methods to help increase their efficiency of selection in multi environment yield trials. The aim of this experiment was to identify and select high yielding and stable cassava genotypes using to GGE biplot and Yield selection index (YSi) techniques and to determine the efficiency of the techniques. 24 hybrids and 2 checks were tested across five locations in Nigeria using the randomized complete block design with 4 replications. ANOVA provided clear evidence of GEI (P<0.001) for dry root yield. 23 of the hybrids showed 10% to 83% economic improvement over the best check variety. GGE biplot identified genotypes TMS-IBA090574, TMS-IBA090521, TMS-IBA090590 and TMS-IBA090576 as high yielding and stable, while YSi selected 14 genotypes TMS-IBA090454, TMS-IBA090504, TMS-IBA090506, TMS-IBA090509, TMS-IBA090521, TMS-IBA090523, TMS-IBA090536, TMS-IBA090564, TMS-IBA090574, TMS-IBA090576, TMS-IBA090581, TMS-IBA090590, TMS-IBA090597 and TMS-IBA090609. Six of these genotypes (TMS-IBA090523, TMS-IBA090536, TMS-IBA090574, TMS-IBA090581, TMS-IBA090506, TMS-IBA090521) were marked as unstable by the Shuklas stability variance which indicates a weakness of YSi. The two techniques identified TMS-IBA090590 and TMS-IBA090576 as high yielding and stable genotypes. These two clones performed above average in at least four of the five locations used for evaluation. The genotypes jointly selected by both methods may therefore be released to increase the productivity of the crop in Nigeria and comparable agro ecology.

genetics↗