Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.10.20.683460

Composite interval mapping and genomic prediction of nut quality traits in American hazelnuts and American-European interspecific hybrids

Brainard, S. H.·Dawson, J. C.
View original source ↗Export metadata ↓

Abstract

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern U.S. for its significant ecological benefits, as well as its high-value nut crop. Genetic improvement of perennial crops involves long-term breeding efforts, and benefits from the use of genetic data in selection to reduce breeding cycle time. In addition, high-throughput phenotyping methods are essential to the efficient and accurate screening of large breeding populations. This study reports novel advances in both of these domains, for American (C. americana) and interspecific hybrids between European (C. avellana) and American hazelnuts. Two populations of hazelnuts, one composed of C. americana and one composed of C. americana x C. avellana hybrids, were phenotyped over the course of two years in two locations using a digital imagery-based method for quantifying morphological nut and kernel traits. This data was used to perform composite interval mapping (CIM) using a recently released genetic map, and genomic prediction using a newly-available chromosome-scale reference genome for C. americana. Multiple QTL were detected for all traits analyzed, with an average total R2 of 52%. Genomic prediction exhibited high accuracy, with an average correlation coefficient between genotypic values and phenotypic observations of 0.78 across both environments. These results suggest that incorporating genetic data in selection is a tenable method for improving genetic gain for highly-polygenic traits in hazelnut breeding programs. Core ideasO_LIMorphological nut characteristics are under polygenic control in American and American- European interspecific hazelnuts. C_LIO_LIBest linear unbiased predictors allow for accurate prediction of morphological nut characteristics. C_LIO_LIMarker density and training population design must be tailored to the sample population for which predictions are being made. C_LI

Explore related subjects

geneticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Brainard, S. H., Dawson, J. C.. 2025-10-20. Composite interval mapping and genomic prediction of nut quality traits in American hazelnuts and American-European interspecific hybrids. https://doi.org/10.1101/2025.10.20.683460

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

KEEP EXPLORING

Related preprints

bioRxiv2026

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↗
bioRxiv2026

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↗
bioRxiv2026

OPA1 controls mitochondrial dysfunction-driven liver fibrosis in MASLD

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

genetics↗