Published in Cell Genomics, the study was led by Peter Doris, PhD, director of the Center for Human Genetics at The Brown Foundation Institute of Molecular Medicine within McGovern Medical School at UTHealth Houston. The researchers used advanced long-read DNA sequencing to construct a telomere-to-telomere assembly of the brown rat genome. Unlike earlier genome drafts, which contained gaps and unresolved repetitive regions, the new assembly provides continuous sequences extending from one telomere—the protective DNA structure at a chromosome’s end—to the other.

The completed genome revealed that the rat’s genetic architecture is considerably more complex than previously recognized. The team identified more than 60 genes that had not been accurately captured in earlier reference genomes. Many of these genes lie in regions that are difficult to sequence because they contain repeated or nearly identical DNA segments. Some appear to be involved in immunity and other biological processes, raising the possibility that missing genetic information has contributed to incomplete or misleading interpretations of rat-based disease research.

One of the most surprising discoveries involved the rat’s X and Y chromosomes. In humans and most other mammals, these chromosomes contain a shared segment called the pseudoautosomal region, or PAR. The PAR contains genes present on both the X and Y chromosomes, allowing the two chromosomes to pair during the formation of reproductive cells and to replicate correctly. Although the X and Y chromosomes differ substantially, this shared region acts as a genetic bridge between them.

The researchers found that the brown rat has lost these PAR genes from its sex chromosomes. Instead, the genes have moved to ordinary, non-sex chromosomes. The team also identified newly organized DNA sequences that appear to allow the rat’s X and Y chromosomes to pair in a head-to-tail configuration, rather than the head-to-head arrangement seen in most other mammals. This finding suggests that the mechanics of rat reproduction have evolved along a distinct genetic pathway, despite the animal’s close relevance to human biology.

“Sexual reproduction in the rat can take place, but it’s not taking place in exactly the same way that it is in humans,” Doris said. The unusual chromosome structure would have been difficult to detect without a highly accurate genome assembly, because incomplete reference sequences can obscure rearrangements and make genes appear to be missing, misplaced, or incorrectly duplicated.

The new work also addresses a long-standing problem in genetic disease research. Researchers often compare the genomes of laboratory rats with those of other strains or with disease-associated genetic regions, but missing segments can make it difficult to determine which DNA differences are biologically meaningful. Gene duplications are especially challenging: when two copies are nearly identical, conventional sequencing methods may collapse them into a single sequence. Yet duplicated genes can acquire different functions, allowing one copy to retain an original role while the other becomes specialized.

To capture this diversity, the team assembled eight reference-quality genomes from different brown rat strains. These assemblies were combined into a pangenome—a comprehensive genetic resource that represents variation across multiple individuals rather than treating one genome as the definitive standard. The rat pangenome contains approximately 7% more sequence than the previously available reference genome, revealing genetic regions that would otherwise remain invisible. Scientists can now examine a gene across several rat strains and determine whether its sequence, copy number, or biological function varies between animals.

Such variation may have direct implications for laboratory studies. A gene involved in digestion, for example, may have been duplicated in some rats, with one copy retaining a digestive function while the other becomes involved in immune activity. If researchers use different strains without accounting for these differences, they may obtain conflicting results or fail to reproduce findings. The pangenome provides a framework for identifying these differences before they influence an experiment, potentially improving the reliability of studies that use rats to investigate human disease.

The rat genome consists of 22 chromosome pairs, and the new assembly describes each chromosome in an unbroken sequence. By filling the gaps in the genetic “map,” the study gives researchers a more precise way to locate disease-associated variants, study chromosome evolution, and compare rat biology with human biology. The resource is expected to support future research into cardiovascular and metabolic disease, kidney function, inflammation, immunity, and neurological disorders. Alongside Doris, the study included Yaming Zhu of UTHealth Houston and collaborators from the University of Kentucky, the National Institutes of Health, the University of Louisville, and The Jackson Laboratory.

Subject of Research: Genetic sequencing, genome assembly, pangenomics, chromosome biology, and biomedical rat research

Article Title: Telomere-to-telomere genome assembly and a pangenome for the rat

News Publication Date: 6-Aug-2026

Web References: https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00143-6

References: Cell Genomics, “Telomere-to-telomere genome assembly and a pangenome for the rat”

Image Credits: Photo by UTHealth Houston; Peter Doris, PhD, director of the Center for Human Genetics at The Brown Foundation Institute of Molecular Medicine within McGovern Medical School at UTHealth Houston.

Keywords: Brown rat, rat genome, telomere-to-telomere assembly, pangenome, genomics, genetics, sex chromosomes, pseudoautosomal region, gene duplication, disease research, biomedical research, long-read sequencing

The study emerges against a backdrop of divergent practices in piglet rearing between the United States and the European Union. While U.S. pork production often employs cross-fostering—transferring piglets among sows to ensure milk access—the EU is increasingly embracing artificial rearing with milk replacer. This simulation of sow lactation dynamics, common in biomedical contexts, prompted researchers to examine the nuances of feeding regimen impacts with unprecedented rigor.

Researchers led by doctoral candidate Kaitlyn Sommer assessed 85 piglets, all separated from their mothers at two days old, raised on a nutritionally complete milk replacer. These piglets were divided into two feeding groups: one allowed unrestricted access to milk (ad libitum feeding), and the other receiving measured, weight-based portions designed to mimic natural nursing frequency and quantity. Over a 15-day period, the team meticulously recorded metrics including body weight dynamics, insulin levels, behavioral tendencies, and soft tissue characteristics.

The findings compellingly demonstrate that piglets with free access to milk exhibited accelerated growth rates compared to their counterparts on a fixed feeding schedule. Surprisingly, though, the body composition measurements—specifically muscle protein and fat percentages—showed no statistically significant divergence between the two cohorts at the study’s conclusion. This suggests that while ad libitum feeding enhances growth velocity, proportional tissue development remains consistent regardless of feeding mode.

A pivotal biochemical axis in these observations is the role of insulin—a hormone integral to amino acid utilization and muscle protein synthesis. Insulin functions as a metabolic conductor, channeling amino acids from digested proteins into skeletal muscle growth. The ad libitum group’s feeding pattern, characterized by larger yet less frequent meals, led to sustained insulin concentrations surpassing the anabolic threshold necessary to maximize muscle-building processes. Conversely, piglets on the prescribed feeding schedule consumed smaller, more frequent meals that failed at times to maintain elevated insulin levels, potentially constraining maximal muscle accretion.

Behavioral analyses utilizing advanced video tracking methodologies uncovered further distinctions tied to feeding style. Piglets on prescribed feeding regimes spent notably more time in proximity to the milk bowl, exhibiting behaviors such as rooting and nosing—instinctive actions that, in a natural setting, stimulate milk production from the sow. These observations suggest that artificial feeding might stimulate inherent exploratory and suckling behaviors differently depending on how feeding is structured.

Enrichment conditions added another layer of insight. When provided with toys and cloth towels, piglets displayed clear attachments to these objects, often curling up with them and showing distress when removed. Such findings underscore the importance of environmental complexity in managing stress and promoting welfare in artificially reared animals, further complicating the nutritional and behavioral interface.

The translational value of this research reverberates beyond pig farming. Pigs serve as prominent biomedical models due to their physiological and genetic affinities with humans—particularly in studies targeting gastrointestinal function, immunology, and neurobiology. This work highlights how feeding regimens can fundamentally alter experimental outcomes, an element that must be rigorously controlled and considered in laboratory settings to enhance data fidelity.

Moreover, from an agricultural safety standpoint, the study offers practical implications. Understanding how hunger and feeding patterns influence piglet proximity to the sow may inform strategies to mitigate risks such as piglet crushing—a significant welfare and economic concern. Hungrier piglets staying closer to their mothers can inadvertently increase injury incidence, a dynamic that feeding management can potentially alleviate.

The integration of nutritional science, endocrinology, and ethology in this research creates a comprehensive framework for rethinking piglet rearing standards. It challenges the industry to balance growth optimization with behavioral needs, enhancing overall animal welfare while preserving or enhancing productivity.

Lead author Kaitlyn Sommer and senior collaborator Ryan Dilger emphasize that these findings are just the opening act in a continuing exploration to harmonize agricultural practices with biomedical needs. As nutrient intake patterns evidently influence metabolic pathways and behavioral repertoires, subsequent studies aim to expand upon these physiological markers and welfare indicators.

Such interdisciplinary endeavors also highlight the necessity of rearing protocols that acknowledge the complexity of early life nutrition and its cascading effects on lifetime health and function. In pig models, this may translate to refined interventions that better simulate natural growth trajectories, enhancing both scientific validity and applied livestock management.

The study, titled "Feeding style alters the growth and behavior of artificially-reared pigs," underscores a fundamental principle: the modality of feeding is not merely a logistical consideration but a driver of physiological and behavioral outcomes. This insight calls for a reevaluation of standard protocols in both agricultural systems and laboratory research to cultivate more resilient, healthier animals from the earliest stages of life.

As researchers continue to dissect the interactions between nutrition, metabolism, and behavior in the porcine model, the broader implications for animal welfare science and translational human medicine grow increasingly evident. The work illustrates a promising bridge between the practical challenges of food production and the controlled conditions of biomedical inquiry, offering pathways to optimized strategies that serve dual purposes.

In sum, this research eloquently demonstrates that how we feed is as consequential as what we feed—impacting growth kinetics, metabolic regulation, behavioral expression, and ultimately, the translatability of animal models to human health contexts. Through the lens of the piglet, a species sharing remarkable similarities with humans, the study invites a paradigm shift towards more nuanced and integrative rearing practices that respect both biological imperatives and scientific rigor.

Subject of Research: Effect of feeding style on growth, metabolism, and behavior in artificially reared piglets

Article Title: Feeding style alters the growth and behavior of artificially-reared pigs

Web References:
University of Illinois Urbana-Champaign: http://illinois.edu/
Journal of Animal Science: http://dx.doi.org/10.1093/jas/skaf098

References:
Sommer, K. M., Sutkus, L., Senthil, P., & Dilger, R. N. (2021). Feeding style alters the growth and behavior of artificially-reared pigs. Journal of Animal Science. https://doi.org/10.1093/jas/skaf098

Image Credits: University of Illinois Urbana-Champaign

Keywords: Nutrition, Agriculture, Animal Physiology, Feeding Regimen, Insulin, Muscle Growth, Behavior, Artificial Rearing, Piglets, Biomedical Model