Sustainable Livestock Production LINK Programme

Project LK0656: Marker Assisted Selection Applied to Commercial Sheep

Start Date: 01/06/2004 End Date: 30/09/2007

Executive summary report

The project addressed issues related to the use of molecular markers as a selection tool in British commercial sheep flocks, in three terminal sire reference schemes (i.e. Texel, Suffolk and Charollais). The three main objectives of the project were:(i) To determine optimal procedures and develop infrastructure for the use of

combined quantitative trait loci (QTL) and performance data in commercial sheep breeding programmes, i.e. MAS

(ii) To demonstrate the implementation of one known QTL into MAS programmes in Suffolk, Texel and Charollais sire reference schemes

(iii) To detect/verify at least one new QTL so that it can readily be implemented as with the first QTL.

For objective (i) we (1) put in place sampling logistics, (2) established the infrastructure needed to evaluate (genotype) the markers linked to our QTL of interest and (3) adapted and developed software enabling us to compute QTL breeding values (EBVs). Combined QTL and background polygenic EBVs provide the information required to perform marker assisted selection (MAS). It must be noted that the software we currently have is not able to handle pedigree structures above 100 000 animals, for the calculation of the ‘identity-by-descent’ coefficients that are essential in the estimation of breeding values.

The presence of commercially viable QTL associated with muscle depth was successfully verified in all three breeds (Texel on chromosome 18, Suffolk and Charollais on chromosome 1) using three breed-and-location-specific multiplex microsatellite marker panels.

Additional QTL for nematode resistance on chromosome 3 and 14 were found to be segregating in Texel and Suffolk families, where adequate animal numbers allowed us to carry out analyses. These may potentially allow MAS for nematode resistance without a requirement for nematode challenge. An additional single nucleotide polymorphism (SNP) associated with muscle depth on chromosome 2 was verified to be segregating in the Charollais flocks. This can be easily genotyped with a SNP test we had developed; through an independent genotyping company the cost is 8 pence per DNA sample.

In summary, we have put in place infrastructure to perform MAS, and successfully verified all targeted QTL. The chromosome 2 SNP test can be directly used by the industry, the other QTL (for muscle depth and nematode resistance) are linked to microsatellite markers and can be used in structured evaluation procedures. However, the technology is currently limited to population sizes of less than 100 000 animals, requiring technical modification of some breed evaluation procedures in the larger breeds. Unfortunately, due to problems associated with obtaining accurate genotypes according to our schedule, we were not able to feed QTL EBVs back to breeders in a timely fashion. The vast DNA pool collected in this project will also be available for future use with high density SNP chips when they become available.

In terms of utilisation, all software, infrastructural resources (including physical items such as the mould for plastic vacutainer trays) results and procedures are available for future use. The currently extensively sampled half-sib families are spread widely through the three breeds and form the basis for implementing MAS. However, we are sceptical about the use of microsatellite markers in MAS: (1) they are prone to genotyping errors, (2) the genotyping turn-around time is longer than what is commercially acceptable, (3) the costs are still relatively high per marker and (4) few companies are investing in this technology. Future marker data are likely to be SNP based, and appropriate strategies have to be devised for handling this data, depending upon the context within which the data are being used (e.g. single SNP assisted selection, SNP-region assisted selection or genomic selection).

CONTACTDr Stephen BishopThe Roslin Institute

Roslin Midlothian EH25 9PS

stephen.bishop@roslin.ed.ac.uk

Meat and Livestock CommissionBritish Texel Sheep Society Ltd

Suffolk Sire Referencing Scheme LtdCharollais Sire Reference Scheme

GOVERNMENT SPONSORSDefra

Scottish Government