The jigsaw puzzle of pedigree: whole-genome resequencing reveals genetic diversity and ancestral lineage in Sunong black pigs

文献类型： 外文期刊

第一作者： Ye, X. W.

作者： Ye, X. W.;Gu, J. M.;Cao, C. Y.;Zhang, Z. Y.;Cheng, H.;Zhang, Z.;Wang, Q. S.;Pan, Y. C.;Wang, Z.;Chen, Z.;Fang, X. M.

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关键词： Genomic analysis; Hybrid pigs; Local ancestry inference; Pig breeding; Population structure

期刊名称：ANIMAL （ 影响因子：3.6； 五年影响因子：3.7 ）

ISSN： 1751-7311

年卷期： 2023 年 17 卷 11 期

页码：

收录情况： SCI

摘要： The Sunong black pig is a new composite breed under development generated from Chinese indigenous pig breeds (i.e., Taihu and Huai) and intensive pig breeds (i.e., Landrace and Berkshire), which is an important genetic material for studying breeding mechanisms. However, there is currently limited knowledge about the genetic structure and germplasm characteristics of Sunong black pigs. To comprehensively understand their genetic composition and ancestry proportions, we performed population structure and local ancestry inference analysis based on whole-genome sequencing information. The results showed that Sunong black pigs could be clustered independently into a group, whose pedigree was intermediate between indigenous and commercial pig breeds, but closer to commercial pigs. Furthermore, local ancestry inference analysis revealed that Sunong black pigs inherited immune and reproductive traits from indigenous pig breeds, including CC and CXC chemokine family, Toll-like receptor family, IFN gene family, ESR1, AREG and EREG gene, while growth and development-related traits were inherited from commercial pig breeds, including IGF1 and GSY2 gene. Overall, Sunong black pigs have formed a relatively stable genome structure with some advantageous traits inherited from their ancestral breeds. This study deepened the understanding of the breeding mechanism of Sunong black pigs and provided a reference for cross-breeding programmes in livestock. (c) 2023 The Author(s). Published by Elsevier B.V. on behalf of The Animal Consortium. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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