Characterization analysis of Rongchang pig population based on the Zhongxin-1 Porcine Breeding Array PLUS

Abstract

Objective: To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population.Methods: We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual.Results: Firstly, the results of genetic diversity analysis showed that the effective population size (N<sub>e</sub>) of this population was 3.2, proportion of polymorphic markers (P<sub>N</sub>) was 0.515, desired heterozygosity (H<sub>e</sub>) and observed heterozygosity (H<sub>o</sub>) were 0.315 and 0.335. H<sub>o</sub> was higher than H<sub>e</sub>, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09.Conclusion: Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.

Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs

“…First, we used chips for the SNP genotyping, which may have missed SNPs that were detected by whole-genome sequencing. Nevertheless, previous studies have shown that the Zhongxin-1 Porcine Breeding Array PLUS chip provided reliable estimates of genomic diversity and selection signatures in a comparative analysis between pig breeds [11]. Second, low-altitude Chinese indigenous pig breeds have considerable phenotype diversity due to the thousands of years of domestication and are therefore more genetically differentiated than the high-altitude Tibetan pigs.…”

Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China’s Native Pig Breeds via Whole-Genome Resequencing

“…However, this homogenized breeding strategy has overshadowed local pig breeds, such as the Rongchang pig (RC), Tibetan pig (T), and Wuzhishan pig (WZS). Despite slower growth and lower yields, these local breeds demonstrate unique advantages in disease resistance, reproductive efficiency, and adaptability to harsh environments, and their meat also boasts distinctive flavors [ 14 , 15 , 16 ]. Additionally, local pig breeds hold considerable advantages as experimental models due to their genetic diversity and adaptability, which are vital for researching disease models relevant to humans [ 17 ].…”