Measuring genetic connectedness between herds based on high density SNP markers.

The accuracy of genetic evaluations in different herds is affected by the degree of genetic connectedness among herds. In this study, we explored the application of high density SNP markers in the assessment of genetic connectedness by comparing the genetic connectedness based on pedigree data and genomic data. Six methods, including PEVD (prediction error variance of differences between estimated breeding values), PEVD (x), VED (variance of estimated difference between the herd effects), CD (generalized coefficient of determination), r (prediction error correlation) and CR (connectedness rating), were implemented to measure the genetic connectedness based on different relationship matrices (A, G, G, G and H). Our results from both simulated data and SNP chip data indicated that, except for the PEVD (x) and VED methods, the genetic connectedness obtained by PEVD, CD, r and CR based on G. G and G matrices (using genome information only) were superior to those based on A matrix (using pedigree information only). Generally, for most approaches, the genetic connectedness based on H matrix (using both pedigree and genome information) was somewhere between A matrix and G matrices. CD could overestimate the degree of genetic connectedness as it was still very high when CR and r were close to 0. The method r could not accurately reflect the true genetic connectedness of the populations. It generated 0.01 of genetic connectedness for all three pig breeding farms, which were actually genetically different with each other. With increasing of heritability, the degree of genetic connectedness obtained by all methods were increased as well. However, in the case of heritability 0.1, PEVD based on A matrix performed better than based on G matrix, suggesting that traits with medium and high heritability are more suitable for the assessment of genetic connectedness compared to traits with low heritability. Our findings indicated that high-density SNP markers have advantages over pedigree analysis for the measurement of genetic connectedness, and CR is a robust and reliable method to assess genetic connectedness. Further, CR is easily calculated and less affected by heritability of trait. PEVD is good supplement to quantify the prediction errors of estimated breeding values under the specific genetic connectedness. In comparison, G matrix can reflect genetic connectedness better than its extensions G and G matrix.