Dorothy Russell Havemeyer 12th International Horse Genome Workshop

About the Workshop

About the Pavia Workshop

The Dorothy Russell Havemyer Foundation is conducting a Workshop on horse genomics in Pavia, Italy from September 12-15, 2018.  The conference is hosted by Professors Elena Giulotto and Elena Raimondi of the University of Pavia.  This meeting includes two invited speakers, two workshops and research presentations by participants.  

History of Dorothy Russell Havemeyer Workshops on Horse Genomics

The First Dorothy Russell Havemeyer (DHR) Workshop in this series met in October 1995.  Since then, the DRH workshop convened every 2 years and spawned sister workshop meetings, one occurring every January at the Plant and Animal Genome Conference  in San Diego  ( and the second occurring once every two years at the Conference of the International Society for Animal Genetics (  The mission is to encourage collaboration for development and use of  genomic tools  to benefit the health and welfare of horses. (

Workshop Principles

1.  Developing tools for the horse genome is a large undertaking and greater than can be accomplished at any one laboratory. Therefore, cooperative and collaborative activities are essential to accomplish our goals.

2.  Success by any one of us is success for all of us.  Genomic tools and approaches will be accepted when the public becomes aware of their effectiveness.  We need to be mutually supportive to be successful. 


Wednesday, September 12

12:00 -19:00  Arrival, registration

18:00 - on Welcome reception at Palazzo Vistarino

Thursday Morning, September 13

8:30-8:45  Welcome/Announcements

8:45-10:00  FAANG related talks I

Chairpersons: Doug Antczak  (Cornell University, USA), Rebecca Bellone (University of California, Davis, USA)

Carrie Finno  (University of California, Davis, USA) Update on the UCD/UNL Equine FAANG initiative

Nicole Kingsley (University of California, Davis, USA) An Update on the Functional Annotation of the Equine Genome Using ChIP-seq

Erin Burns  (University of California, Davis, USA) Using the FAANG RNA-Sequencing Data to Validate the Genome Annotation

Tomasz Zabek  (National Research Institute of Animal Production, Krakowska, Poland) Methylome characteristics of eight tissue types of Thoroughbred mares

Eleonora Cappelletti  (University of Pavia, Italy) Functional Annotation of Horse Centromeres

10:00-11:00   Coffee Break and Posters

11:00-11:45  FAANG related talks II

Chairpersons: Doug Antczak  (Cornell University, USA), Rebecca Bellone (University of California, Davis, USA)

Stephen Coleman  (Colorado State University, USA) Annotation of protein-coding and non-coding genes in equine small intestine tissues to support investigations of gastrointestinal homeostasis

Anna Dahlgren  (University of California, Davis, USA) Comparison of poly-A+selection and rRNA-depletion in detection of lncRNA in horse RNA-seq

11:30-12:15   Key note speaker

Stefano Gustincich  (Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy) Transposable elements in health and disease

12:15-12:30  Discussion

12:30-14:00  Lunch at Palazzo Vistarino

Thursday Afternoon, September 13

14:00-16:00  Annotation Workshop

Ted Kalbfleisch  (University of Louisville, USA) assisted by: Pouya Dini (University of Kentucky, USA), Shavahn Loux (University of Kentucky, USA), Marco Corbo (University of Pavia, Italy), Marco Santagostino (University of Pavia, Italy)

 The workshop will be comprised of three sections:

     1. A primer on RNA-seq 

     2. Pipelines for transcriptome analysis

     3. Using these data for annotation and supporting metadata for submission to public repositories

16:00-16:30  Coffee Break and Posters

16:30-17:00  Population Genomics

 Chairpersons: Teruaki Tozaki (Japanese Racing Association, Japan), Jessica Petersen (University of Nebraska, USA)

Donald Miller (Cornell University, USA) Integrated Major Histocompatibility Complex assessment in the Horse

Tosso Leeb (University of Bern, Switzerland) A comprehensive set of equine sequence variants derived from 81 whole genome sequences

18:00   Bus to dinner

19:00- on   Dinner at Agriturismo Granai Certosa

Friday Morning, September 14

9:00-9:30  New Tools for Genomic Studies of the Horse

 Chairperson: James MacLeod (University of Kentucky, USA)

Molly McCue (University of Minnesota, USA) Annotation of EquCab 3.0 using RNAseq data and crowd-sourcing for genes of interest

Robert Schaefer  (University of Minnesota, USA) Processing tens of millions of genotypes with HapDab and analyzing tissue specific gene co-expression networks with Camoco

9:30- 9:45  Discussion 

9:45- 10:30  Key note speaker

Giulio Pavesi  (University of Milan, Italy) Opportunities and challenges in single cell transcriptomics

10:30- 10:45  Discussion

10:45- 11:15  Coffee Break and Posters

11:15-12:15  Evolution

 Chairpersons: Terje Raudsepp (Texas A&M University, USA), Donald Miller (Cornell University, USA)

Ludovic Orlando  (Faculté de Médecine de Purpan, Toulouse, France) Tracking Six Millenia of Horse Selection Admixture: Management with Complete Genome Time-Series (30 minutes)

Barbara Wallner (University of Vienna, Austria) A molecular view on the paternal ancestry of modern horse breeds

Marco Corbo  (University of Pavia, Italy) Birth, evolution and transmission of equine centromeres


12:15-12:45  Applications of Genomics I

 Chairpersons: James Mickelson (University of Minnesota, USA), Eric Barrey (INRA-Jouey-en-Josas, France)

Gabriella Farries (University College, Dublin, Ireland) Identification of expression quantitative trait loci (eQTL) in the skeletal muscle of Thoroughbreds

Stefano Capomaccio (University of Perugia, Italy)  Circulating miRNAs As Putative Biomarkers Of Exericse Adaptation In Endurance Horses

12:45-14:15  Lunch at Palazzo Vistarino

Friday Afternoon, September 14

14:15-15:30  Applications of Genomics II

 Chairpersons: Emmeline Hill (University College, Dublin, Ireland), Gabriella Lindgren (Swedish University of Agricultural Sciences, Sweden)

Julia Metzger  (University of Hannover, Germany) Detection of Copy Number Variants in Shetland ponies gives evidence for pony-specific selection signatures

Xuexue Liu  (Chinese Academy of Agricultural Sciences, Beijing, China) Whole-genome sequencing reveals the genetic mechanisms underlying the small body size in ponies and the high-altitude adaptation in Tibetan horses

Sam Beeson  (University of Minnesota, USA) Investigation of fine-scale recombination rate variability in the horse

Samantha Brooks  (University of Florida, USA) Transcriptome diversity and differential expression of supporting limb laminitis

Sofia Mikko  (Swedish University of Agricultural Sciences, Sweden) Signatures of selection in the genome of a modern equestrian sport horse breed.

15:30-18:30  Walk through medieval town, stop for ice cream, visit University History Museum, back to Palazzo Vistarino   

19:30-on  Dinner at Palazzo Vistarino

Saturday Morning, September 15

9:00-10:00   Reproduction and Genomics

Chairpersons: Petr Horin (University of Brno, Czech Republic), Monika Bugno-Poniewierska (National Research Institute of Animal Production, Krakow, Poland)

Doug Antczak  (Cornell University, USA) Global run-on and sequencing approaches to functional genome annotation in the horse

Jason Bruemmer (Colorado State University, USA) Evaluation of equine endometrium gene transcripts and circulating miRNA during maternal recognition of pregnancy utilizing RNA sequencing

Pouya Dini  (University of Kentucky, USA) Reciprocal paternal and maternal control of angiogenesis in equine chorioallantois

Shavahn Loux  (University of Kentucky, USA) A closer look at the equine feto-maternal interface via high-throughput sequencing

10:00-12:00  Discussion about upcoming workshops and plans for future workshops

Chairpersons: Ernest Bailey (University of Kentucky, USA), Jessica Petersen (University of Nebraska, USA)

Upcoming workshops

    PAG: Stephen Coleman (Colorado State University, USA) , Annette McCoy (University of Illinois, USA)

    ISAG: Ted Kalbfleisch (University of Louisville, USA), Carrie Finno (University of California, Davis, USA), Doug Antczak (Cornell University, USA)

10:00-10:45  Coffee Break 

10:45-12:00  Plans for the future workshops

    1. Resources need for FAANG

    2. Development of UMN initiative

    3. Promotion of Horse Genomics Research

    4. Other topics?

12:00-14:00  Lunch at Palazzo Vistarino

End of Conference

Invited Speakers

Stephano Gustincich

Stefano Gustincich is Deputy Director for Technologies for Life Science (LifeTech) and Director Department of Neuroscience and Brain Technologies at the Istituto Italiano di Tecnologia (IIT), Genova, Italy. He is part-time Full Professor in Applied Biology at the International School for Advanced Studies (SISSA), Trieste. His research interests concern the biology of the non-coding portion of the genome, the so-called “Junk DNA”. He recently discovered the SINEUPs, a new functional class of antisense long noncoding RNAs able to increase translation of their sense gene. 

Giulio Pavesi

Giulio Pavesi is a faculty member (Bioinformatics) at the University of Milan, Department of Biosciences where he teaches Bioinformatics and works with the Bioinformatics, Evolution and Comparative Genomics Research Group.  His research is mostly focused on the development of computational tools and algorithms for the annotation of regulatory elements in genomic sequences and their application, including the analysis of next-generation sequencing ChIP/RIP/RNA-Seq data

Additional Support

Travel to Pavia and Lodging

Travel to Pavia

Pavia is served by 3 regional airports near Milan, Linate and Malpensa, or by the airport of Orio al Serio (Bergamo). Parking is limited in Pavia so arrival by train or bus is recommended.  There is a direct bus from Linate. You can also take bus or train links to the central Train station in Milan.  Local train lines to Pavia leave the Milan Central station every 30 minutes. The total time from the airport to Pavia will be about 1 hour 40 minutes.  Travel costs can range from 10 Euros for train to 140 Euros for Taxi.  

Occasionally, trains are delayed or traffic is slower than usual.  Plan plenty of time to make connections at airports.


Participants will stay in rooms in local colleges. All accommodations are within easy walking distance to the conference site. (Links give walking directions from train station)

Cairoli College

Santa Caterina





Conference Venue -- Palazzo Vistarino

Palazzo Vistarino 

In the 18th century, the Bellisomi-Vistarino Palace was the residence of a noble family. It is situated in the heart of Pavia, facing the Ticino River. The palace is now the property of the University of Pavia and is the site of the University Foundation Alma Mater Ticinensis.

The City of Pavia

Pavia was originally known as the Roman  town of Ticinum.  Subsequently it was a capital of this rich agricultural region under the Ostrogoths, Lombards, and other peoples who lived in the region during medival, renaissance and later ages.  It was  a city of towers. Only 5 of the original 100 towers remains today.  The Ponte Coperto crosses the Ticino river just before it joins the Po River.

(Youtube about the region)

University of Pavia

The University of Pavia, founded in 1361, is one of the oldest universities in the world and enrolls up to 24,000 students. Students have the choice of over 80 undergraduate programmes, over 42 master’s programmes and around 20 doctoral programmes offered by 18 departments.  The university has been home to many distinguished faculty including the scientists Camillo Golgi (Nobel in Medicine & Physiology), Giulio Natta (Nobel in Chemistry),  Carlo Rubba(Nobel in Physics), Allesandro Volta, Lazzaro Spallanzani and Luigi Cavalli-Sforza.

Venue and Contact

12th Havemeyer International Horse Genome Workshop

Palazzo Bellisomi-Vistarino Via Sant’Ennodio, 26 – 27100 PAVIA

Get in Touch


Useful Smartphone Apps

Historical Sites of Pavia

Useful links are "Turismo" and "Pavia new Cuore".  In English.

Historical Sites of Pavia

Map with major sites and information at a touch.

Train Schedules and Booking

This site provides train schedules, allows you to purchase tickets and provides an electronic or pdf ticket on your phone.