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Identification of QTL affecting main milk production traits in RP3 that are identical by descent, according to origin and effect

Most of QTL mapping experiments were performed in dairy cattle and thereof most studies focus on QTL in the highly selected purebred Holstein cattle. According to experiences with other domesticated animal and plant species the QTL mapped in one highly selected cosmopolitan breed or line presents only the smaller part of variability of complex traits. In spite of their inferiority for most of yield traits, the local cattle breeds can contribute positively to improve important yield and fitness traits in cosmopolitan breeds and inversely the cosmopolitan breeds can be used for targeted improvement (not replacement) of local breed.

The advanced backcross QTL strategy (AB-QTL) is one of the approaches to map and introgress distinct QTL between lines or breeds of domesticated species. Due to a long generation interval, there are limited possibilities to create a powerful QTL mapping or QTL introgression design in cattle. Over the last 30 years German-Austrian Fleckvieh breeders designed a large advanced backcross population, which is embedded within the Fleckvieh breed.

Our goal was to use this large advanced backcross population for learning about the feasibility of marker assisted introgression between cattle breeds and for retrospective use of collected mapping results for marker assisted accumulation of positive alleles and selection against negative alleles already introgressed by donor Red Holstein (RH) founder. Our mapping design has gone beyond traditional half-sib design to support the following requirements.

QTL mapping design should have high statistical power: large daughter design with more then 40000 sampled daughters.

The genotyping costs in large half-sib design should be acceptable: selective milk DNA pooling. " The origin of active QTL variants should be traceable: synchronic mapping in purebred Fleckvieh (FV, recipient) and advanced backcross Fleckvieh × Red Holstein (ABFV) families combined with haplotyping of all family-sires, all available ancestors including donor founder as well as most important founders of recipient population. By genome wide QTL mapping for Milk Yield (MY) and milk Protein Percentage (PP) in both FV and ABFV we detected 31 QTL distributed across 26 chromosomes. The genome wide genotyping and haplotyping of 69 animals including family-sires in both FV and ABFV, ancestors of family-sires and founder of both resource populations we made most QTL alleles traceable.

Most of QTL alleles are of FV origin: QTL segregate only in FV families or in FV and ABFV families but segregating ABFV families receive no or not detectable portion of appropriate chromosomal region from their RH founder.

Four QTL segregate most possibly in both resource populations: QTL segregate in both FV and ABFV families but all segregating ABFV families receive appropriate chromosomal region from their RH founder (BTA01, BTA05, BTA19 and BTA28).

One QTL was introgressed by RH founder into FV population (BTA10 proximal): QTL segregates only in three ABFV families, all three segregating ABFV families receive the most proximal chromosomal region of 35cM from their RH founder. The FV families as well as other ABFV families receiving no or other parts of BTA10 from the RH founder show also no QTL effect.

There can be other chromosomal regions with possible introgression but not detected by the used design: The most critical handicap of the used design is the low mapping resolution achieved by selective DNA pooling. Thus distinct QTL segregating on the same chromosome in two resource populations can appear as one QTL.

To test our ability to distinguish QTL alleles according to their breed origin we chose two QTL regions (BTA19 and BTA28) for fine mapping in a complex pedigree composed of 11 grand daughter design families of FV and ABFV origin. Using individual genotypes of 35 microsatellite markers across BTA19 and 20 microsatellite markers across BTA28 we want to resolve one-QTL versus two-QTL hypotheses. At the moment, it seems to us that this will be not a trivial challenge because of the necessity to account for complex relationships within a stratified population, to account for two or more QTL and for, possibly, not simply additive inheritance at one or two QTL.

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