摘要
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 indi- viduals of Qinchuan cattle （QC） from the nearby Shanxi Province of China. Linkage disequilibrium （LD） analysis showed the LD of YL was the lowest （~=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 N J-tree, the YL group formed an independent branch and BS, WL, ZB groups were mixed. We then used the FST 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.
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 indi- viduals of Qinchuan cattle （QC） from the nearby Shanxi Province of China. Linkage disequilibrium （LD） analysis showed the LD of YL was the lowest （~=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 N J-tree, the YL group formed an independent branch and BS, WL, ZB groups were mixed. We then used the FST 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.
基金
funded in part by the National Natural Science Foundation of China (31402039,31472079,31372294)
the Beijing Natural Science Foundation (6154032)
the Species and Breed Resources Conservation of the Ministry of Agriculture of China (2017-2019)
the Cattle Breeding Innovative Research Team of Chinese Academy of Agricultural Sciences (cxgc-ias-03)
the National Beef Cattle Industrial Technology System (CARS-37)
