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A map of QTL affecting milk production traits in the Bavarian and Austrian Simmental

The most important dual purpose cattle breed in Middle Europe is the Fleckvieh (Simmental) breed. So far no complete genome scan for quantitative trait loci (QTL) affecting any production trait has been performed in this Fleckvieh breed. Here we report on the first whole genome scan in the German-Austrian Fleckvieh (FV) for two milk production traits Milk Yield (MY) and Milk Protein Percentage (PP). To increase mapping power and reduce experiment costs we applied a selective DNA pooling strategy in a daughter design with ten large half-sib families. The average family size was 2341 daughters ranging from 1635 to 4043 per family. The selection criteria for DNA pooling were corrected breeding values calculated from the routinely performed, common genetic evaluation for South-Germany and Austria. The marker set consists of 220 microsatellite markers covering all 29 autosomes.

Totally 12569 pool genotypes were produced and combined into 2661 single marker linkage tests for both traits. Three families sampled in Austria by different logistic show high proportion of pool genotypes with inconsistent allele frequency patterns between two replicates and also high proportion of significant sire-by-marker tests results. Additional information (individual genotyping etc) indicated that a systematic error source in these three families cause inconsistent pool genotypes as well as highly significant mapping results at apparently consistent genotypes.

Therefore we excluded the three mentioned families from all further analysis. There were a total of 220 comparisonwise linkage tests at the individual marker level for both MY and PP. Combining false discovery rate and approximate interval mapping (AIM) thresholds we detected 29 QTL distributed across 25 chromosomes. Only four chromosomes (BTA10, BTA15, BTA17 and BTA21) are without indication for a QTL affecting PP or MY. Our pool results give consistent indications for segregation of two QTL on BTA04, BTA09, BTA13, and BTA20. Most of the detected QTL affect both PP and MY simultaneously but with higher significance for one of the two traits.

There are six PP-QTL which are partly independent from MY: BTA13 central, BTA14, BTA20 (GHR), BTA25, BTA28 and BTA29. Unlike to this, we found only a weak indication for a pure MY-QTL but there are eleven QTL affecting both traits but with higher significance for MY: BTA03, BTA04 (proximal), BTA07, BTA11, BTA12, BTA16, BTA18 (distal), BTA20 (proximal to GHR), BTA22, BTA23 and BTA26. The remaining twelve QTL showed effects for both traits too, but with higher significance for PP.

There are nine QTL (BTA02, BTA04 distal half, BTA11, BTA18 distal, BTA19, BTA22, BTA24, BTA25, and BTA28) which are possibly mapped for the first time in cattle and thus present novel information for genetic dissection of quantitative traits. Some recent crossing experiments in plant breeding indicated the local and global importance of genetic variability in presently less modern breeds or lines. The results of QTL analysis in different populations with underlying different adaptive evolution (alpine versus lowland) and different selection criteria (dual purpose versus dairy cattle) could be used to verify the role of selection in producing the observed divergence in phenotype, and may identify additional loci that underlie traits that are part of the same adaptive syndrome.

Therefore here produced QTL mapping results in Fleckvieh, as important dual purpose cattle breed from the alpine region, are valuable not only locally for implementation of marker assisted selection in this breed but also globally for molecular dissection of a major gene effect on a quantitative trait under natural and artificial selection.

The estimated positions of mapped QTL is rather inaccurate but provide valuable starting information for running studies aiming at the confirmation by interval mapping, fine mapping and use for MAS. Seven of the QTL detected here present starting points for ongoing fine mapping attempts with the ultimate goal to infer the genetic basis of traits under artificial selection in the Fleckvieh breed and to increase the sustainability of the European dual purpose cattle populations. Four of the QTL regions detected by this and other project have been selected as first choice for ongoing implementation of marker assisted selection in German-Austrian Fleckvieh cattle.

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