An Overview of all QTL-mapping Projects in Pigs

F e b u r a r y,     1 9 9 9

This is a summary of answers to my query on current mapping projects in pigs carried out via the 'Animal Genetics discussion Group' (AGDG) and the 'Animal Gene Mappers' (ANGENMAP) discussion group. Many thanks to everybody who responded. ("an overview over all QTL-mapping projects in Pigs that are currently underway or planned including a short description of the project and the stage the project is currently at.") Note that this survey does not show all projects currently carrried out on pigs. Furthermore, be aware that the survey dates back to November 1998. Please use the listed contact addresses for serious inquires only and with the appropriate 'netiquette'.

February 9, 1999, Chris Stricker

Location:  US Meat Animal Research Center, Clay Center, NE, USA
Contact: Dr. Gary Rohrer rohrer@email.marc.usda.gov
Description: Resource population based on a cross between Meishan and White composite (a four breed composite of equal contributions of Large White, Chester White, Landrace and Yorkshire) pigs. Currently litters up to the F4 generation and nearly 2,000 pigs phenotyped. However, most phenotypes only on a subset of the population. Major emphasis are traits affecting reproduction: age at puberty, ovulation rate, uterine capacity and serum hormone levels in females, and testicular size, sperm production and serum hormone levels in males. Carcass composition was measured on > 500 F2-progeny (J. Anim. Sci. 76: 2247&2255). Some initial results of female reproduction are in press in J. Anim. Sci. Currently, all resouces devoted to fine-mapping regions likely to contain QTL for reproduction.
   
 Location: Depart.of Animal Science, Iowa State University, Ames IA, USA
 Contact: Dr. Max Rothschild mfrothsc@iastate.edu
 Description: 2 projects: First is directed chromosomal search. See Wang et al., in J Anim. Sci. October or November 1998. We have also extended it to chromosome 13 and that paper was sent to Prof Pirchner for J. Animal Breeding. Second project is a completemeats study - 530 Berkshire x york cross with about 90 markers. Genotyping has started and phenotypes have been collected on 480 of the pigs so far.
   
 Location: Dept. of Animal Science and Animal Health, Royal Vet- and AgriculturalUniversity, Bülowsvej 13 DK-1870 Frederiksberg C, Denmark
 Contact: Dr. Knud Christensen, Peter Henrik Nissen PeterH.Nissen@agrsci.dk
 Description Verifying QTL, influencing fat deposition and weight gain on porcine Chr. 4. Animal material consists of an inbred line, founded by a Landrace boar and a Yorkshire sow. Inbreeding coefficient has reached a theoretical value of >0.6 and the number of generations is 7. Initially, seven MS markers spaced evenly along Chr. 4 typed, doing currently further typing with new markers in an area with indications of a QTL. By using an inbred line, it will hopefully be possible to narrow the region of the QTL, although the cross between Landrace and Yorkshire is not expected to show large effects.
   
 Location Roslin Institute (Edinburgh) Roslin Midlothian EH25 9PS Scotland
 Contact Grant Walling Grant.walling@bbsrc.ac.uk
 Description F2 population of Meishan (Ms) x Large White (LW) was set up from 2 LW boars x 2 Ms sows and 2 Ms Boars x 2LW sows. F1's were mated to other F1's from a different F0 pair i.e. no inbreeding. 390 F2 animals were produced with a full phenotype record: birth weight, weaning weight, start test wight (~30kg), end test weight (~80kg), fat depths at shoulder, midback and loin. Genotyping has now covered ~75% of the genome the areas not covered are chromosome 12 (no markers), chromosome 16 (1 marker) and the X chromosome (1 marker). With the exception of these three chromosomes the coverage and information content is good throughout (the only other gaps tend to be 'ends' of chromosomes requiring a marker to be typed at the extreme telomeric end).
The major findings (significant at a genome wide level)

Chromosome 4:
   Nearest Marker
 Growth Birth-Start of test 13.3 g/day  S0001
 Birth-End of test 33.3 g/day  S0217
 Weaning-Start of test 23.4 g/day  S0001
 Weaning-End of test 39.9 g/day  S0001
 On Test 44.2 g/day  S0217

Chromosome 7:
   Nearest Marker
 Fat Shoulder 2.18 mm  TNFB
 Mid-back 3.00 mm  TNFB
 Loin 2.90 mm  TNFB
 Mean fat 2.86 mm  TNFB

Chromosome 14:
   Nearest Marker
 Growth On Test 44.0 g/day  SW210

All effects are given as the additive effect of the large white allele so the effect of chromosome 14 explains 88g/day on test between the two breeds.

** Note that the Meishan allele on chromosome 7 DECREASES fat substantially (6mm between breeds at the mid back position). There is no logical explanation but this has been seen in other groups as well. The chromosome 4 stuff can be found in Proceeedings of 6th WCGALP 23:519-522 or Animal Genetics 29:1-10. Currently waiting for the final markers to go through (16 in total) before writing up a genome scan paper.
   
 Location: Institute for Animal Health Compton nr. Newbury Berks. RG20 7NN, UK
 Contact: Dr Ir Pauline van Diemen Pauline.vandiemen@bbsrc.ac.uk
 Description: Information upon request.
   
 Location: Roslin Institute (Edinburgh) Roslin Midlothian EH25 9PS Scotland
 Contact: G.J.C. (Deon) Goosen Gideon.Goosen@bbsrc.ac.uk
 Description: Roslin Institute in partnership with organisations in Sweden, Spain and the UK is working on a European Commission demonstration project in QTL mapping in commercial pig populations: 'Transferring QTL technology to the pig breeding industry (PigQTech) - a demonstration project'.
Currently at the 14 month mark of this 36 month project, that originated in October 1997.

Objectives: The aim is to demonstrate how the farm animal breeding industry can utilise gene mapping technology to identify and utilise Quantitative Trait Loci (QTL) controlling traits of major economical importance. Optimal strategies for detecting QTL in commercial populations will be explored. The introgression of a QTL from one breed to another will be demonstrated.

Brief description: Optimal sampling designs for detecting QTL segregating in commercial pig populations will be specified through statistical work. On the basis of this result, a total of about 5,000 pigs representing ten commercial populations will be sampled. Phenotypic data on growth and carcass traits will be collected. Genomic DNA will be isolated from all animals. Ten chromosomal regions will be evaluated in this experiment. Seven of these will be candidate QTL regions identified in previous studies and three will serve as random controls for which no QTL has yet been reported. Two microsatellites for each of the ten regions will be genotyped. The presence of segregating QTL will be investigated by statistical analysis of phenotypic and genotypic data. Marker assisted backcrossing will be used to show how a QTL allele can be introgressed from one breed to another. The work will focus on the major fatness QTL on pig chromosome 4 previously identified in a wild pig/Large White intercross. The task will be to establish whether QTL are real single entities and do not break up due to recombination during the course of introgression. It will reveal the prospects for positional cloning or positional candidate cloning of the QTL itself.
   
 Location: Department of Animal Science University of Sydney NSW 2006 Australia
 Contact: Dr. Chris Moran Chris.Moran@doolittle.vetsci.su.oz.au
 Description: Two resource pedigrees within Australian commercial pigs. The first is a two generation pedigree consisting of 4 large sire families and 473 progeny in total in sire familes ranging from 166 to 69 progeny. Dam DNA samples are available for about 80% of the progeny. The progeny have been measured for a large number of meat quality and growth traits and a low resolution genome scan is being peformed. The results of this work are confidential to protect the Intellectual Property of the Pig Research and Development Corporation (PRDC), which is funding the work, and the University of Sydney. We have some quite encouraging preliminary results.

A new two generation resource pedigree is now being bred which is being performance tested for a larger and more diverse group of traits. This will consist of 7 sire families and the aim is to produce about 500 progeny in total. Unfortunately I can't even reveal all the traits being measured due to confidentiality restrictions, but meat quality and growth as well as a number of disease related traits are being measured. This resource will be evaluated initially for the presence of previously detected QTL from published studies and our previous work and for candidate genes for which there is reasonable evidence of effects from published studies. This project is also being funded by the PRDC and the results will be confidential.

Hope this is of some help and sorry about the "secrecy" but that is how my funding now operates. Only the broadest overview of the results will be released in order to protect the possible IP. Unfortuantely that seems to be how just about everyone is operating these days. We may even have to pay licencing fees or negotiate exemptions to even evaluate some of the published candidate genes.

My lab is involved in analysis of the Hohenheim resource pedigree. We are genotyping chromosome 2 and chromosome 5 markers as part of that collaborative QTL mapping project. We have obtained some very interesting preliminary results for chromsome 2 which were reported at ISAG. Gerhard Moser from Hohenheim spent 6 months in my lab from 6WCGALP until ISAG and performed the analyses for us during his stay. Of course all these results will be in the public domain.
   
 Location: Animal Breeding and Genetics Group of Wageningen Agricultural University
 Contact: Dr. Dirk-Jan de Koning Dirk-Jan.deKoning@ALG.VF.WAU.NL
 Description: Large scale asscosiation study in pigs. The material is an F2 of Meishan x commercial lines. The F2 consists of approx. 1200 F2 animals from 256 litters (38 paternal half-sib families). Purebred Meishans, the F1 parents and the F2s are genotyped for 130 microsatellite markers, which cover ~95% of the porcine genome. Genome scans are carried out for three types of traits:

1) Meat quality traits (measured on 840 animals): Backfat thickness, Intramuscular fat content, Ph, color, drip loss, cooking loss and shear force

2) production traits like growth and untrasonically measured backfat

3) reproduction traits : #piglets born alive at first and second parity

At present we have submitted a manuscript on linkage analysis for QTL affecting Backfat thickness and Intramuscular fat content. In that study half of the population was typed and analysed. Marker density has been increased for the QTL regions from that study. Furthermore a BAC library has been screened for clones reprsenting the QTL regions and sequnecing of these clones has started.

All animals have been genotyped for the initial set of 130 markers. Currently working on the linkage analysis for the remaining slaughter traits. Subsequently the production and reproduction traits will be evaluated.

The population and segregation analyses on this population are described by Janss et al (Genetcis 145 :395-408 & JAS 75:2864-2876) Prelaminary results were presented at the 6 WCGALP and the ISAG last summer.

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