Search bioRxiv⌕ Search

bioRxiv · 10.64898/2026.01.21.700123

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

Abstract

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.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Oyebode, O. G., Ogwuche, T. O.. 2026-01-23. Optimizing multi environment cowpea yield trial by appraising the fitness and similarities among test sites: a case study of IITA cowpea breeding program. https://doi.org/10.64898/2026.01.21.700123

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Generation of a transgenic cephalopod

Coleoid cephalopods (cuttlefish, octopus, and squid) are marine mollusks with elaborate nervous systems that support a diverse repertoire of complex behaviors. These include the neural control of the color, pattern, and texture of the skin, facilitating both adaptive camouflage and innate patterning that may reflect internal state. The development of transgenic cephalopods expressing fluorescent proteins, optogenetic actuators, and reporters of neural activity would contribute a new and important technology to cephalopod biology. The generation of transgenic cephalopods, however, has remained a major challenge. Here, we report the development of stable transgenic dwarf cuttlefish (Ascarosepion bandense) expressing ubiquitous nuclear-localized mScarlet, a red fluorescent protein. We evaluated multiple strategies for transgenesis, and established cuttlefish lines using both CRISPR and the transposons Sleeping Beauty and Minos. The stable expression of transgenes enabled live imaging of cell dynamics during embryonic development. The Minos transposon emerged as the most efficient transgenesis strategy and is adaptable to promoters and transgenes of choice. These strategies now enable the generation of diverse genetic tools for mechanistic studies of cephalopod biology.

genetics↗

Large language model-based bibliometric evaluation of population descriptors in human genetics

As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. Most notably, in 2023, the National Academies of Science, Engineering, and Medicine (NASEM) published a report titled Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field, which included eight specific and actionable recommendations for researchers to implement the ethical and accurate use of population descriptors in genetic research. Here, we use the 2023 NASEM report as a benchmark to analyze the use of population descriptors in genome-wide association studies (GWAS). We develop a general toolkit for large language model-based bibliometrics, operationalize the report's recommendations into an evaluation framework, and apply this framework to evaluate all 4,007 papers from the GWAS Catalog published between 2007 and 2025 with full text available on PubMedCentral. We find significant improvements in adherence to NASEM report recommendations over time. However, most improvements predate the publication of the NASEM report itself, suggesting the report functioned primarily as a synthesis of existing best practices rather than a catalyst for change. We conclude by highlighting opportunities for growth in the field of human genetics.

genetics↗

Mitigating biases of rescaling in forward-in-time population genetic simulations

Forward-in-time population genetic simulations are widely used in evolutionary analyses, but simulating large populations and long genomic regions remains computationally demanding. To reduce this cost, parameter rescaling is widely employed, in which the original evolutionary process is approximated by one with a smaller population size and fewer generations. Recently, several studies using the SLiM simulator have raised concerns about the accuracy of this rescaling approach. In this study, we show that many of the biases reported in these studies can be mitigated by using a different simulation algorithm. These results reveal that the accuracy of parameter rescaling depends on how well the simulation algorithm preserves diffusion-limit properties under rescaling.

genetics↗