Population genetic diversity and genetic evaluation models reveal the maternal genetic structure and conservation priority characteristics of indigenous cattle in China

The population genetic structure of domestic animals and the protection of genetic resources are major issues of concern in the field of global biology. In this study, the mtDNA D-loop sequences of 1163 Chinese indigenous cattle (Bos taurus and Bos indicus) were used to analyze their maternal origin and population genetic structure and to prioritize conservation evaluations based on a population genetic evaluation model. The results revealed three maternal origins or domestication events among Chinese indigenous cattle and the occurrence of secondary expansions but also the phenomenon of gene penetration. The population genetic evaluation model results showed that the genetic diversity of Huangpi cattle (HHP), Mountainous cattle (CMO), Bashan cattle (SBS) and Guanling cattle (GGL)populations was highest and that the Zaosheng cattle (GZN), Qinchuan cattle (SQB) and Pingliang cattle (GPL) populations contributed most to the richness of Chinese indigenous cattle genetic resources, indicating that these populations should be protected first. Our research provides a scientific basis and effective evaluation methods for the protection of genetic resources of indigenous livestock varieties.