Abstract
Simple SummaryEvaluating population genetic background and genomic selection signatures can provide important insights into the uniqueness and the genetic relationship among breeds. In this study, we analyzed the genetic diversity, population structure, and phylogenetic relationships between Huaxi cattle and its ancestors. The results showed that Huaxi cattle has formed its own unique genetic structure features, which could be clearly distinguished from its ancestors and similar populations. Moreover, some genes associated with important economic traits, including growth and development, reproduction, milk quality, and immune response, were identified by scanning potentially selected genomic regions, which may play an essential role in the excellent environmental adaptability and growth performance of Huaxi cattle. Our study will contribute to the genetic evaluation and rational breeding strategy, and give an extensive reference for understanding the genetic basis of economically important traits in Huaxi cattle.Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
Highlights
Cattle are vital agricultural economy species worldwide, providing meat, milk, and labor for humans
We calculated the average minor allele frequency (MAF), average observed heterozygosity (Ho), average expected heterozygosity (He), and inbreeding coefficient based on ROH (FROH ) to assess polymorphism of nine cattle populations
The He of Huaxi cattle was 0.34, which was between Canadian Simmental cattle and Montbeliard cattle
Summary
Cattle are vital agricultural economy species worldwide, providing meat, milk, and labor for humans. China has abundant cattle genetic resources, with rough feeding tolerance, excellent meat quality, and strong adaptability [1]. Chinese native cattle have been used as draft animals, ignoring the utilization of meat performance, and cattlebeef have been usedperformance as draft animals, ignoring utilization of meat performance, and resulting in lower production compared to the commercial cattle breeds. In lowermethod beef production performance compared to commercial. Hybridization resulting is an important for improving the desirable performance and cattle breeds. Is anbreeds important method for improving the desirable performance and overoverall geneticHybridization variation of cattle [2]. Crossbreeding breeds combine the beneficial genetic variation of cattle breeds combine traits/genes of all their purebred parental breeds, and [2]
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