Abstract
Most indigenous pig resources are known to originate from China. Thus, establishing conservation priorities for these local breeds is very essential, especially in the case of limited conservation funds. Therefore, in this study, we analyzed 445 individuals belonging to six indigenous breeds from the Taihu Lake Region, using a total of 131,300 SNPs. In order to determine the long-term guidelines for the management of these breeds, we analyzed the level of diversity in the metapopulation following a partition of diversity within and between breed subpopulations, using both measures of genic and allelic diversity. From the study, we found that the middle Meishan (MMS) pig population contributes the most (22%) to the total gene diversity while the Jiaxing black (JX) pig population contributes the most (27%) to the gene diversity between subpopulations. Most importantly, when we consider one breed is removed from the meta-population, the first two breeds prioritized should be JX pig breed and Fengjing pig breed followed by small Meishan (SMS), Mizhu (MI), and Erhualian (EH) if we pay more attention to the gene diversity between subpopulations. However, if the priority focus is on the total gene diversity, then the first breed to be prioritized would be the Shawutou (SW) pig breed followed by JX, MI, EH, and Fengjing (FJ). Furthermore, we noted that if conservation priority is to be based on the allelic diversity between subpopulations, then the MI breed should be the most prioritized breed followed by SW, Erhuanlian, and MMS. Summarily, our data show that different breeds have different contributions to the gene and allelic diversity within subpopulations as well as between subpopulations. Our study provides a basis for setting conservation priorities for indigenous pig breeds with a focus on different priority criteria.
Highlights
Indigenous breeds are well adapted to their specific environmental conditions, and their interest in livestock is increasingly being recognized (Kim et al, 2019; Lukicet al., 2020)
Regarding the total gene diversity, we found that the removal of SW breed caused the largest reduction of about 0.906% followed by Jiaxing black (JX) (0.762%), MI (0.635%), EH (0.517%), FJ (0.438%), and small Meishan (SMS) (0.205%)
We observed that the HT was constantly reduced after the removal of any of the breeds from the metapopulation, with the exception of middle Meishan (MMS), given its low degree of genetic differentiation when compared to other breeds
Summary
Indigenous breeds are well adapted to their specific environmental conditions, and their interest in livestock is increasingly being recognized (Kim et al, 2019; Lukicet al., 2020). It is difficult or almost impossible to protect all the livestock species in the world. Determining conservation priorities is key to their effective management. Conservation Priority of Pig Breeds have been previously established using measures of genic or allelic diversity for different livestock species using a variety of genomic markers. No systematic assessment for the conservation priority of the Chinese indigenous pig breeds has been conducted. To effectively protect the indigenous pig genetic resources and to ensure the sustainable development of the pig industry in China, it is necessary to determine their conservation priorities, especially when the conservation funding is limited
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