Fig. 1

The association of CNVRs with embryonic mortality in 791 Japanese Black cattle. a Schematic representation of artificial insemination (AI) breeding program in Japanese Black cattle. At each parity, female cattle were artificially inseminated (1st AI) at the onset of estrus. Second AI (2nd AI) was carried out after the cow showed estrus. The resumption of estrus after the 1st AI indicated that the fertilization or embryo development derived from the 1st AI had failed. Thus, embryonic mortality was defined by cows that received a 2nd AI at 18–29 days (D), 30–60 D, 61–90 D, 91–140 D, and 141 D–parturition after the 1st AI. b Manhattan plot of the association of 116 deleted-type CNVRs with embryonic mortality at 30–60 D in 791 Japanese Black cattle. Chromosomes are distinguished with alternating colors (blue, odd numbers; red, even numbers). Dashed line is the Bonferroni-corrected threshold for genome-wide significance (-log10 (P) = 3.365). c Manhattan plot of the association of the surrounding SNPs, which are derived from Illumina BovineHD BeadChip array, at approximately ± 400 kb distance from CNVR_322. Positions are based on the UMD3.1 assembly of the bovine genome