Biology subjects

Parkes, E. Y.

Publications and source records attributed to Parkes, E. Y..

4 recordsLinked to original sources

bioRxiv2025

Partitioning Genotypic and Environmental Variance of Fresh Root Yield in Provitamin A Cassava Genotypes Using Mixed Models

This study employed a multi-model statistical approach to evaluate the yield performance and environmental responsiveness of 42 provitamin A cassava genotypes across two contrasting cropping seasons. Four linear mixed models spanning BLUP-based random effects, fixed-effect genotype comparisons, genotype-by-environment interaction analysis, and variance partitioning were used to dissect phenotypic variation in fresh root yield. Months After Planting (MAP) emerged as the most influential factor, accounting for 19.82% of total variance, while genotypic effects were modest (H{superscript 2} = 4.4%) and seasonal effects reached statistical significance when accessions were treated as fixed. Residual variance dominated (70.98%), suggesting the influence of unmeasured factors such as soil properties, pest pressure, and microclimatic variation. Rainfall data revealed a stark contrast between seasons-127.38 mm in 2019/2020 versus 8.45 mm in 2020/2021 highlighting an environmental stress pattern that shaped genotype performance. Accessions IITA-TMS-IBA980581(WChk-White Check), IITA-TMS-IBA180017, and IITA-TMS-IBA180146 maintained high yields across both seasons, indicating broad adaptability, while IITA-TMS-IBA180182 and IITA-TMS-IBA180065 performed better under low-moisture conditions, suggesting drought responsiveness. These findings underscore the importance of integrating rainfall patterns and genotype-specific environmental sensitivity into cassava breeding pipelines. Future multilevel models incorporating locations and climatic data could enhance selection precision and support the development of resilient varieties for variable agroecologies.

plant biology↗

bioRxiv2025

Bivariate genome-wide association study reveals polygenic contributions to covariance between total carotenoid and dry matter contents in yellow-fleshed cassava (Manihot esculenta)

Cassava breeders aim to increase the provitamin A carotenoid content of storage roots to help combat vitamin A deficiency in sub-Saharan Africa, but a negative genetic correlation between total carotenoid (TC) and dry matter (DM) contents hinders breeding efforts. Genetic linkage between a major-effect variant in the phytoene synthase 2 (PSY2) gene and nearby candidate gene(s) has been thought to drive this correlation. Evidence from molecular experiments, however, suggest there may be a metabolic relationship between TC and DM, which we predicted would create genome-wide mediated pleiotropy. Bivariate genome-wide associations were used to test the hypothesis of pleiotropy and examine the genetic architecture of the negative covariance between TC and DM. A population of 378 accessions in the yellow-fleshed cassava breeding program at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria was genotyped with DArTseqLD. TC measured by iCheck spectrometer and DM data were available from field trials over ten years across three locations in Nigeria. Mixed linear models controlling for the previously-identified PSY2 causal variant were used to identify multiple new quantitative trait loci (QTL) jointly associated with both traits. The majority of 17 jointly-associated loci identified at a relaxed significance threshold affected TC and DM in opposite directions, although this pattern did not reach statistical significance in a binomial test. Even after accounting for the effects of these 17 loci as covariates, there was significantly negative polygenic covariance between TC and DM remaining. These findings support the hypothesis that mediated pleiotropy rather than genetic linkage drives the negative genetic correlation between TC and DM in cassava and demonstrate a new application of multivariate GWAS for interrogating the genetic architecture of correlated traits. Plain language summaryIncreasing provitamin A in cassava roots has reduced their dry matter content, making vitamin-enriched cassava varieties less desirable. This study used multi-trait models to identify shared genetic factors, most of which had opposing effects on the two traits. The negative relationship was distributed across the genome, suggesting an inherent physiological trade-off. These findings will guide breeders in developing selection strategies for vitamin-enriched cassava and other starchy crops. More broadly, this study demonstrates the use of multi-trait associations to help distinguish whether traits are associated due to separate, nearby genes (genetic linkage) or if the same genes affect multiple traits (pleiotropy).

genetics↗

bioRxiv2022

Validation of SNP markers for marker-assisted selection of genotypes with increased carotenoid and dry matter contents in cassava

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness in developing countries. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. SNP markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for marker-assisted selection (MAS). Assessment of marker performance in diverse genetic backgrounds is an important step towards their deployment for routine MAS. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific PCR assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r < 0.40) due to the more quantitative nature of the trait. This work confirmed marker effectiveness in multiple backgrounds, therefore, further strengthening its value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker development, thus leading to more routine use of markers in MAS in cassava improvement programs.

genomics↗

bioRxiv2017

Genome-wide association mapping of correlated traits in cassava: dry matter and total carotenoid content

Cassava (Manihot esculenta (L.) Crantz) is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and micronutrient density, particularly of provitamin A - traits that are negatively correlated - are among the primary selection objectives in cassava breeding. This study aimed at identifying genetic markers associated with these traits and uncovering the potential underlying cause of their negative correlation - whether linkage and/or pleiotropy. A genome-wide association mapping using 672 clones genotyped at 72,279 SNP loci was carried out. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness was identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that co-located with the 24.1 Mbp peak for carotenoid content was identified. Haplotypes at these loci explained a large proportion of the phenotypic variability. Evidence of mega-base-scale linkage disequilibrium around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid (phytoene synthase) and starch biosynthesis (UDP-glucose pyrophosphorylase and sucrose synthase) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate on the genetic architecture of carotenoids and dry matter in cassava and provides an opportunity to accelerate genetic improvement of these traits.\n\nCORE IDEASO_LICassava, a starchy root crop, is a major source of dietary calories in the tropics.\nC_LIO_LIMost varieties consumed are poor in micronutrients, including pro-vitamin A.\nC_LIO_LIThese two traits are governed by few major loci on chromosome one.\nC_LIO_LIGenetic linkage, rather than pleiotropy, is the most likely cause of their negative correlation.\nC_LI

genetics↗