Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F-NEJ), Li and Horvitz (F-L&H), Van Raden method 1 (F-VR1) and method 2 (F-VR2), and Yang (F-YAN). Inbreeding based on runs of homozygosity (F-ROH) and pedigree inbreeding (F-PED) were also computed. F-ROH, F-NEJ, and F-L&H were also adjusted for their average values in the first generation of selection and named F-ROH0, F-NEJ0, and F-L&H0. triangle F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (triangle F-PEDt) and individual increases in inbreeding (triangle F-PEDi). Moreover, individual triangle F was calculated from the different molecular inbreeding coefficients (triangle F-NEJ0, triangle F-L&H, triangle F-L&H0, triangle F-VR1, triangle F-VR2, triangle F-YAN, and triangle F-ROH0). The Ne was obtained from different triangle F, such as Ne-PEDt, Ne-PEDi, Ne-NEJ0, Ne-L&H, Ne-L&H0, Ne-VR1, Ne-VR2, Ne-YAN, and Ne-ROH0. Comparing with F-PED, F-ROH, F-NEJ and F-VR2 overestimated inbreeding while F-NEJ0, F-L&H, F-L&H0, F-VR1 and F-YAN underestimated inbreeding. Correlations between inbreeding coefficients and triangle F were calculated. F-ROH had the highest correlation with F-PED (0.89); F-YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne-PEDi was more reliable than Ne-PEDt and presented similar behaviour to Ne-L&H0 and Ne-NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne-PEDi was 42.20, Ne-L&H0 was 45.04 and Ne-NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F-ROH presented the highest correlation with F-PED, which addresses the identity by descent probability (IBD). The evolution of Ne-L&H0 and Ne-NEJ0 was the most similar to that of Ne-PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.