Ancient genomes reveal the genetic inheritance and recent introgression in Chinese indigenous pigs

Wen, Jia; Zheng, Zhuqing; Gong, Mian; Liu, Dong; Hu, Songmei; Cai, Yi; Wang, Yongdi; Nanaei, Hojjat Asadollahpour; Zhang, Naifan; Yu, Taiyong; Jiang, Yu

doi:10.1007/s11427-021-2066-y

Cited by 4 publications

(4 citation statements)

References 8 publications

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“…It serves as the raw material upon which the genetic variation within a species is built [ 1 , 2 , 3 , 4 ]. Both naturally occurring and artificially mediated genetic introgressions among pig breeds/populations have the potential to significantly impact and reshape a wide range of phenotypes [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. The Large White pig breed is renowned for its prolificacy, meat quality, and adaptability to various environments.…”

Section: Introductionmentioning

confidence: 99%

“…According to previous research, Chinese porcine breeds were believed to have directly descended from local stocks of pigs that were domesticated during the Neolithic period. Specifically, the indigenous pig breeds, such as Erhualian, Meishan, and Jiangquhai pigs, which originated from the lower reaches of the Yangtze River, are considered to have maintained a closer lineage inheritance to ancient pigs compared to other regional breeds [ 12 ]. Indeed, both the selection and genetic admixture from exotic breeds have significant roles in the breeding process of domestic pigs, contributing to their genetic architecture and improvements in important economic traits.…”

Section: Introductionmentioning

confidence: 99%

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Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

Li,

Liu,

Feng

et al. 2024

IJMS

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The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

Li,

Liu,

Feng

et al. 2024

IJMS

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“…China has the most genetic resources of domestic pigs [22] , [23] . Jinhua ( JH ), Chun’an ( CA ), Longyou Black ( LY ), and Shengxian Spotted ( SX ) pigs originated in eastern China and have similar characteristics to other indigenous breeds, e.g., improved meat quality, disease resistance, and high fertility in comparison with intensively-reared commercial pig breeds (e.g., Large white, Landrace, and Duroc pig breeds) [24] , [25] , [26] .…”

Section: Introductionmentioning

confidence: 99%

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs

Chen

Zhang

Wang

et al. 2022

Computational and Structural Biotechnology Journal

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“…This makes it difficult to harvest the target DNA of ancient remains through the conventional method of PCR amplification. One possible alternative to PCR amplification is target enrichment via DNA hybridization capture, a well‐tested method for obtaining DNA data from bones of ancient humans (Haak et al, 2015; Liu et al, 2021; Wang et al, 2019; Yang et al, 2020), ancient animals (Wen et al, 2022; Zhang, Sun, et al, 2020), and environmental sediments (Massilani et al, 2022; Schulte et al, 2021; Slon et al, 2017; Zhang, Xia, et al, 2020). However, to our knowledge, no studies on aDNA capture from wood remains have reported using this method so far (Orlando et al, 2021; Wagner et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Ancient plastid genomes solve the tree species mystery of the imperial wood “Nanmu” in the Forbidden City, the largest existing wooden palace complex in the world

Jiao

Zhang

et al. 2022

Plants People Planet

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Societal Impact Statement Combining natural and social science approaches to conduct archeological research on wooden cultural relics is important for exploring major aspects of ancient civilizations. The Forbidden City in Beijing, China, is the largest existing wooden palace complex in the world. We examined ancient DNA of imperial wood “Nanmu” specimens taken from representative structural components of the Forbidden City, in order to provide a new perspective on the long‐standing dispute about its species. This allowed us to accurately identify and properly restore these wooden artifacts and improved our understanding of the past interactions between plant distribution, forest resources, and human activities. Summary Exploring the life styles and production methods of past generations using plant resources can help us to improve our understanding of human civilization. Nanmu, known for its high wood quality, was exclusively used for imperial palace construction in the 15th–19th centuries in China, yet its species has been a subject of long‐standing debate. Here, we revisit this unresolved problem, using morphology and ancient DNA (aDNA) to analyze 21 centuries‐old Nanmu specimens sampled from representative palaces of the Forbidden City. Cytochemical staining demonstrated that endogenous aDNA sporadically occurs in the wood ray parenchyma cells of Nanmu specimens. High‐quality plastid genomes were retrieved from archeological woods for the first time via an aDNA capture method, with 90%–100% coverage (137,663–152,805 bp) and sequence depths of 27.05‐ to 1409.94‐fold. Utilizing these ancient genomes, our results demonstrate that Phoebe zhennan and Phoebe hui are most likely the main species of Nanmu in the Forbidden City. This finding diverges from the prevailing view that Nanmu encompasses woods from the whole genus Phoebe and even its close relative Machilus. It also shows that stringent criteria were used when selecting construction materials for the Forbidden City. By combining morphological traits with aDNA analyses, we provide a new solution for identifying the species of timber used for ancient architecture, and we increase our understanding of the way in which forest resources were recognized and utilized by our ancestors despite the lack of a plant taxonomic framework in ancient times.

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Ancient genomes reveal the genetic inheritance and recent introgression in Chinese indigenous pigs

Cited by 4 publications

References 8 publications

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs

Ancient plastid genomes solve the tree species mystery of the imperial wood “Nanmu” in the Forbidden City, the largest existing wooden palace complex in the world

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