Figure 4.

Breed and region-specific variation

(A) Left panel: The breed-specific SVs for each population. Right panel: The region-specific SVs for each population. ECN: Eastern Chinese, EUD: European domestic, EW: European wild, NCN: Northern Chinese, SCN: Southern Chinese, SWCN: South West Chinese. See Table S2 for more details.

(B) The genome-wide SV frequency distribution in 1-Mbp non-overlapping windows for the 11 pigs. Circos from the outside (from A to K) to the inside present Anqingliubai, Bamamini, European wild, Jinhua, Laiwu, Meishan, Min, Rongchang, Tibetan, Wuzhishan and Yorkshire, respectively.

(C) The density of SVs per Mb on the X chromosome (averaged by the total number of SVs on the X chromosome) for each sample. The top and right panels reveal the number of SVs of each type. Nonredundant SVs represent a collection of merged SVs across all individuals. Chinese-specific SVs (CSSVs), defined as SVs, appear only in the Chinese pig group.

(D) The frequency of Southern Chinese specific (SCN-specific) and Chinese-specific SVs on the X chromosome.