Abstract
Wandong (WD) cattle has recently been identified as a new Chinese native cattle breed by the National Commission for Livestock and Poultry Genetic Resources. The population size of this breed is less than 10,000. WD cattle and Dabieshan (DB) cattle are sympatric but are raised in different ecological environments, on mountains and plains, respectively, and the body sizes of these two breeds are markedly different. Blood samples were obtained from 8 adult female WD cattle and 7 adult female DB cattle (24 months old). The total RNA was extracted from leukocyte cells, and sequencing experiments were conducted on the Illumina HiSeqTM 4000 platform. After the removal of one outlier sample from the WD cattle breed as determined by principal component analysis (PCA), phylogenetic and population structure analyses indicated that WD and DB cattle formed a distinct Central China cattle group and showed evidence of hybridization between Bos. taurus and Bos. indicus. The immune-regulator CD48 (P = 1.3E-6) was associated with breed-specific traits according to loss-of-function variant enrichment analysis. In addition, 113 differentially expressed genes were identified between the two breeds, many of which are associated with the regulation of body growth, which is the major difference between the two breeds. This study showed that WD cattle belong to the group of hybrids between Bos. Taurus and Bos. indicus, and one novel gene associated with breed traits and multiple differentially expressed genes between these two closely related breeds was identified. The results provide insights into the genetic mechanisms that underlie economically important traits, such as body size, in cattle.
Highlights
As key providers of milk, meat, leather and labor, cattle are one of the most important livestock species worldwide and have been domesticated since the early Neolithic period (Loftus et al, 1994, 1999; Beja-Pereira et al, 2006)
By combining the obtained whole-genome RNA sequence data and whole-genome sequence data from 11 additional representative taurine and indicine breeds, we explored the taxonomic status of the WD cattle breed in more detail
Variants (SNPs or insertions and deletions (InDels)) with >90% call rates where each variant was uniquely located in one particular gene were retained
Summary
As key providers of milk, meat, leather and labor, cattle are one of the most important livestock species worldwide and have been domesticated since the early Neolithic period (Loftus et al, 1994, 1999; Beja-Pereira et al, 2006). Transcriptome Diversity of Native Cattle in China, as described in the State Catalog of Livestock and Poultry Genetic Resource 2008. Recent studies have indicated that cattle breeds from Central China show reliable evidence of having originated from hybridization between Bos. taurus and Bos. indicus (Lai et al, 2006; Lei et al, 2006; Mei et al, 2017; Chen et al, 2018). An interesting example is provided by the Wandong (WD) cattle breed, which was recently identified in Fengyang county, Anhui Province, by the National Commission for Livestock and Poultry Genetic Resources. WD is one of the best breeds reared in China; it is characterized by a medium size and high-quality meat production that can reach the level of “3A plus” identified by the National Committee on Livestock and Poultry Genetic Resources. There is an urgent need to protect this precious genetic resource
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