Periodic Reporting for period 1 - HOPE (Unveiling the true historical and biological origins of key phenotypes in modern domestic horses)
Berichtszeitraum: 2021-07-12 bis 2023-07-11
This document summarizes a collection of research publications that were produced under the Marie Curie project HOPE. The primary focus of this project was to (i) investigate the phenotypic evolution of horses and its broader implications for human society, and (ii) identify and contrast horse traits preferred and selected by horse herders in Western Europe and the steppes. To facilitate accurate research on phenotypic evolution, two software tools were developed to manipulate ancient DNA data, which represent the main type of data generated and available during the course of the project: mapDATAge (Liu, 2022; Bioinformatics, Figure 1) and MethylationAge (Liu, 2023; iScience, Figure 2). These software represent significant advancements in the field of ancient DNA research as they enable the prediction and identification of various phenotypes using a combination of ancient and modern DNA data. These software tools were inspired by the notable identification of a causal mutation within the TBX3 enhancer, which drives height phenotypes in Asian horses (Liu, 2022; Current Biology, Figure 3). The project's research and impact transcended its initial intentions. In particular, it engaged in an exploration of sex-specific management practices across varying historical epochs in France, unearthing socio-cultural insights (Clavel, 2021; J. Archaeol. Sci. Rep.). Additionally, the contributed to an in-depth investigation into the early dispersal of domestic horses into the South American Great Plains, unveiling insights into the colonial expansion of European horses (Taylor, 2023; Science).
Problems Being Addressed:
1. How to effectively identify positively-selected candidate loci in ancient DNA datasets? mapDATAge provides a simple solution to this complex task by facilitating the interactive visualization of ancient DNA data, providing insights across spatial and temporal dimensions.
2. Age estimation stands as a classical yet pivotal indicator of animal management practices. However, the fragmented nature of the archaeological record have limited the capacity to obtain reliable age. To address this, we developed a new method to predict the age-at-death (and castration status) of ancient horses. Our method relies on the DNA methylation profiles at key CpG loci. It provides reliable age predictions within a one-year precision range.
3. How to explain the genetic variations contribute to phenotype? We first use these tools to make an prediction. Then validated through cellular and mice experiments, exemplified by the TBX3 study. This robust validation approach enhances our understanding of the genetic underpinnings driving phenotypic evolution in horses throughout their domestication history.
Importance for Society:
Our research spans multiple domains, exerting a profound influence that resonates with animal breeding, human history, and ancient DNA analysis. Advancements in Breeding: Our identification of key markers related to height and spinal development holds critical implications. These findings can guide modern horse breeding, particularly in providing new strategies for racehorse enhancement. Advancing ancient DNA Research: Our contributions introduce a new era in ancient DNA studies, with two pivotal software tools for phenotype and age prediction. Refining Historical Understanding: Our research sheds new light into the timeline of horse domestication and its societal roles, particularly and through uncovering sex-specific management practices and which phenotypes incentivized horse selective breeding in the course of history.
Problems Being Addressed:
1. How to effectively identify positively-selected candidate loci in ancient DNA datasets? mapDATAge provides a simple solution to this complex task by facilitating the interactive visualization of ancient DNA data, providing insights across spatial and temporal dimensions.
2. Age estimation stands as a classical yet pivotal indicator of animal management practices. However, the fragmented nature of the archaeological record have limited the capacity to obtain reliable age. To address this, we developed a new method to predict the age-at-death (and castration status) of ancient horses. Our method relies on the DNA methylation profiles at key CpG loci. It provides reliable age predictions within a one-year precision range.
3. How to explain the genetic variations contribute to phenotype? We first use these tools to make an prediction. Then validated through cellular and mice experiments, exemplified by the TBX3 study. This robust validation approach enhances our understanding of the genetic underpinnings driving phenotypic evolution in horses throughout their domestication history.
Importance for Society:
Our research spans multiple domains, exerting a profound influence that resonates with animal breeding, human history, and ancient DNA analysis. Advancements in Breeding: Our identification of key markers related to height and spinal development holds critical implications. These findings can guide modern horse breeding, particularly in providing new strategies for racehorse enhancement. Advancing ancient DNA Research: Our contributions introduce a new era in ancient DNA studies, with two pivotal software tools for phenotype and age prediction. Refining Historical Understanding: Our research sheds new light into the timeline of horse domestication and its societal roles, particularly and through uncovering sex-specific management practices and which phenotypes incentivized horse selective breeding in the course of history.
The HOPE project has been steadfastly dedicated to advancing the identification and functional validation of horse phenotypes, underscoring the project's commitment to scientific progress and discovery. Throughout the project, substantial progress has been achieved across the four deliverables:
D1: mapDATAge Software Development - The mapDATAge software was successfully developed under the GNU Public License, facilitating ancient DNA data analysis by offering interactive visualizations.
D2: MethylationAge Software Development - MethylationAge, a deep learning-based software, was created to provide reliable predictions of the horse’ age-at-death from ancient DNA methylation profiles.
D3: Functional Validation – A number of key genetic variants selected by past breeders were identified, including one (TBX3) associated with horses' height. This locus was functionally validated using state-of-the-art tools in functional genomics, including at the transcriptional level and through mice models (Liu, 2022). Another locus of interest encompasses the GSDMC gene, which has represented the earliest selection target in horse domestication. Functional validation following the same strategy as with the TBX3 locus is pending, and is expected to be finalized within the next 3 months.
D4: Progress Reports - Regular monthly reports were produced, including the final report, for comprehensive documentation and effective monitoring of the project progress.
Dissemination efforts involved nine outreach activities, including international conferences (PAG, SAP) and “Fête de la Science”. Additionally, a number of lectures for M.Sc. and undergraduate students were held to share research findings and promote scientific engagement.
Beyond this:
D5: Selection Coefficients and Demographic History – The identification of candidate loci that have been positively selected by past horse breeders entains the characterization of a robust statistical model describing the demographic trajectory of horses in the last ~50,000 years. This significantly improved the models allowed us to identify a total of 10 candidates for positive selection. The corresponding article is currently under preparation, with an estimated submission timeline in September.
D1: mapDATAge Software Development - The mapDATAge software was successfully developed under the GNU Public License, facilitating ancient DNA data analysis by offering interactive visualizations.
D2: MethylationAge Software Development - MethylationAge, a deep learning-based software, was created to provide reliable predictions of the horse’ age-at-death from ancient DNA methylation profiles.
D3: Functional Validation – A number of key genetic variants selected by past breeders were identified, including one (TBX3) associated with horses' height. This locus was functionally validated using state-of-the-art tools in functional genomics, including at the transcriptional level and through mice models (Liu, 2022). Another locus of interest encompasses the GSDMC gene, which has represented the earliest selection target in horse domestication. Functional validation following the same strategy as with the TBX3 locus is pending, and is expected to be finalized within the next 3 months.
D4: Progress Reports - Regular monthly reports were produced, including the final report, for comprehensive documentation and effective monitoring of the project progress.
Dissemination efforts involved nine outreach activities, including international conferences (PAG, SAP) and “Fête de la Science”. Additionally, a number of lectures for M.Sc. and undergraduate students were held to share research findings and promote scientific engagement.
Beyond this:
D5: Selection Coefficients and Demographic History – The identification of candidate loci that have been positively selected by past horse breeders entains the characterization of a robust statistical model describing the demographic trajectory of horses in the last ~50,000 years. This significantly improved the models allowed us to identify a total of 10 candidates for positive selection. The corresponding article is currently under preparation, with an estimated submission timeline in September.
HOPE has significantly advanced the field in multiple areas. The development of mapDATAge and MethylationAge tools has revolutionized ancient DNA research, enabling interactive data visualization and accurate age prediction. These tools have applications beyond horse phenotypic evolution. Identification and functional validation of genetic variants linked to horse height and spine development have expanded our understanding of these traits. The innovative use of the GSDMC gene knockout mouse model for validation enhances our grasp of spinal development.
We foresee successful completion of ongoing research. The forthcoming article on selection coefficients and demographic history will provide a comprehensive genetic overview, shedding light on adaptations and breeding effects. The imminent publication on GSDMC variations and validation will offer crucial insights into equine spinal development.
Our research has significant societal implications. The identification of crucial genetic mutations related to horse height and spinal development provides essential guidance for horse breeding and racehorse management. Furthermore, our analysis of phenotype formation, development processes, and evolutionary patterns in ancient samples aids in predicting future prospects. This not only advances the equine industry but also directly impacts broader areas such as horse racing and leisure entertainment, benefiting a wide range of society.
Taking into account the transfer of knowledge activities, the record of publications, the milestone and the deliverable produced, the overall objectives of the project were achieved.
We foresee successful completion of ongoing research. The forthcoming article on selection coefficients and demographic history will provide a comprehensive genetic overview, shedding light on adaptations and breeding effects. The imminent publication on GSDMC variations and validation will offer crucial insights into equine spinal development.
Our research has significant societal implications. The identification of crucial genetic mutations related to horse height and spinal development provides essential guidance for horse breeding and racehorse management. Furthermore, our analysis of phenotype formation, development processes, and evolutionary patterns in ancient samples aids in predicting future prospects. This not only advances the equine industry but also directly impacts broader areas such as horse racing and leisure entertainment, benefiting a wide range of society.
Taking into account the transfer of knowledge activities, the record of publications, the milestone and the deliverable produced, the overall objectives of the project were achieved.