Genetic background analysis and breed evaluation of Yiling yellow cattle

Abstract Traditionally, Chinese indigenous cattle is geographically widespread. The present study analyzed based on genome-wide variants to evaluate the genetic background among 157 individuals from four representative indigenous cattle breeds of Hubei Province of China: Yiling yellow cattle (YL), Bashan cattle (BS), Wuling cattle (WL), Zaobei cattle (ZB), and 21 individuals of Qinchuan cattle (QC) from the nearby Shanxi Province of China. Linkage disequilibrium (LD) analysis showed the LD of YL was the lowest ( r 2 =0.32) when the distance between markers was approximately 2 kb. Principle component analysis (PCA), and neighbor-joining (NJ)-tree revealed a separation of Yiling yellow cattle from other geographic nearby local cattle breeds. In PCA plot, the YL and QC groups were segregated as expected; moreover, YL individuals clustered together more obviously. In the NJ-tree, the YL group formed an independent branch and BS, WL, ZB groups were mixed. We then used the F ST statistic approach to reveal long-term selection sweep of YL and other 4 cattle breeds. According to the selective sweep, we identified the unique pathways of YL, associated with production traits. Based on the results, it can be proposed that YL has its unique genetic characteristics of excellence resource, and it is an indispensable cattle breed in China.