Single-Step Breeding Value Estimations and Optimum Contribution Selection in Endangered Dual-Purpose German Black Pied Cattle (DSN) Using a Breed Specific SNP Chip.

The aims of the present study were to perform single-step genomic predictions in the dual-purpose German Black Pied cattle (DSN) breed considering a DSN specific SNP chip (DSN_200 K), and to use the corresponding estimated breeding values (EBV) in ongoing optimum genetic contribution (OGC) selection. All results were compared with the application of the commercial Illumina BovineSNP50 BeadChip (50 K). The traits of interest in the present study (due to the differing breeding history of these traits in the past) included 305-day lactation protein percentage (Pro%) of 9029 DSN cows, fat-to-protein ratio (FPR) from the first test-day of 8773 DSN cows, and stature (STAT) measured in cm of 4409 DSN cows. The DSN cows represented the calving years 2008-2019. Genotyping of 2797 DSN animals was conducted using both the DSN_200 K and the 50 K. From the genotyped animals, a subset of 1800 cows had phenotypic records for all three traits FPR, Pro% and STAT. Heritabilities from the single-step genetic parameter estimations were quite large for Pro% (0.69) and STAT (0.78), but small for FPR (0.11). The choice of the SNP chip only had minor effects on variance components, heritabilities and EBVs. Furthermore, genetic parameters were very similar from genetic-statistical models additionally considering a linear regression on pedigree-based inbreeding coefficients. OGC selection was applied to a pool of 1125 pre-selected bull sires (BS) and bull dams (BD). A more relaxed genetic relationship constraint was associated with favourable effects on the average EBVs for Pro%, FPR and STAT, and a declining number of selected BS. The gains in genetic merit were marginal when relaxing the constraint at 0.06 for the genetic relationships or higher. The same associations were found for an overall breeding index (I-DSN), considering the three traits with equal weights. Consequently, we suggested OGC applications with a genetic relationship constraint of 0.06, which contributed to genetic gain in I-DSN of 17.9%, and to increased diversity due to an increased number of BS, when compared to the current practical elite animal selection scheme. A large number of finally selected BS and BD was identical when either using EBV from the DSN_200 K or from the 50 K. From such perspective, we only see marginal extra value for the specific DSN SNP-chip application.