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4 results on '"Du, Jinshi"'

1. Evaluation of the Breed Composition of Pork via Population Structure Analysis in Pigs.

Author

Lin, Qing, Diao, Shuqi, Chen, Xinyou, Du, Jinshi, Wu, Jiaxuan, Zhang, Xinshuo, Liu, Xiaohong, Li, Jiaqi, and Zhang, Zhe

Subjects
PRICES, GENEALOGY, CROSSBREEDING, SWINE, WORKFLOW, MEAT quality
Abstract

Simple Summary: The quality of pork meat is partially impacted by the breed composition, while the breed composition is difficult to deconvolute because of the lack of a reference panel and comprehensive pipeline. In this study, we established the ancestry reference panel and developed a comprehensive pipeline to identify the breed composition for purebred and crossbred pigs. In summary, the ancestry reference panel contains 3 commercial and 38 indigenous breeds for breed identification. We found that the workflow could favorably identify the breed information for pure breeds. In addition, it could also favorably deconvolute the breed composition for cross breeds in pigs. We suggest that the workflow could be utilized to identify the breed composition and evaluate the quality of pork meat from pigs. The quality of pork meat directly influences the price and consumption. The genetic improvement of pigs has mainly focused on high productive efficiency, which has resulted in poor meat quality. Crossbreeds containing commercial and indigenous breeds could improve the meat quality, but identifying breed composition was difficult because of the lack of an ancestry reference panel. Therefore, we first constructed an abundant reference panel and convenient pipeline to identify ancestry/breed composition. The ancestry reference panel consisted of 517 reliable individuals, including three commercial breeds (Duroc, Landrace, and Yorkshire) and 38 indigenous Chinese breeds. The nature of the reference panel showed that the European domestic breed (EUD) and Asian domestic breed (ASD) were distinctly divided into two clusters. The evaluation of ancestry identification revealed that the reference panel performed well in identifying EUD and ASD ancestry proportions for commercial breeds, indigenous breeds, and crossbreeds. In addition, the ancestry reference panel also performed excellently in identifying breed composition for 3 commercial and 38 indigenous breeds. Specifically, the reference panel showed the outstanding identification of breed composition for crossbred individuals. These results suggested that the ancestry reference panel and convenient pipeline played a good role in identifying breed composition for pigs. [ABSTRACT FROM AUTHOR]

Published
2024
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2. PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Author

National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, Earmarked Fund for China Agriculture Research System, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Amills, Marcel [0000-0002-8999-0770], Clop, Alex [0000-0001-9238-2728], Zeng, Haonan, Zhang, Wenjing, Lin, Qing, Gao, Yahui, Teng, Jinyan, Xu, Zhiting, Cai, Xiaodian, Zhong, Zhanming, Wu, Jun, Liu, Yuqiang, Diao, Shuqi, Wei, Chen, Gong, Wentao, Pan, Xiangchun, Li, Zedong, Huang, Xiaoyu, Chen, Xifan, Du, Jinshi, The PigGTEx Consortium, Zhao, Fuping, Zhao, Yunxiang, Ballester, María, Crespo-Piazuelo, Daniel, Amills, Marcel, Clop, Alex, Karlskov-Mortensen, Peter, Fredholm, Merete, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Liu, Xiaohong, Chen, Yaosheng, Zhang, Qin, Li, Jiaqi, Yuan, Xiaolong, Ding, Xiangdong, Fang, Lingzhao, Zhang, Zhe, National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, Earmarked Fund for China Agriculture Research System, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Amills, Marcel [0000-0002-8999-0770], Clop, Alex [0000-0001-9238-2728], Zeng, Haonan, Zhang, Wenjing, Lin, Qing, Gao, Yahui, Teng, Jinyan, Xu, Zhiting, Cai, Xiaodian, Zhong, Zhanming, Wu, Jun, Liu, Yuqiang, Diao, Shuqi, Wei, Chen, Gong, Wentao, Pan, Xiangchun, Li, Zedong, Huang, Xiaoyu, Chen, Xifan, Du, Jinshi, The PigGTEx Consortium, Zhao, Fuping, Zhao, Yunxiang, Ballester, María, Crespo-Piazuelo, Daniel, Amills, Marcel, Clop, Alex, Karlskov-Mortensen, Peter, Fredholm, Merete, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Liu, Xiaohong, Chen, Yaosheng, Zhang, Qin, Li, Jiaqi, Yuan, Xiaolong, Ding, Xiangdong, Fang, Lingzhao, and Zhang, Zhe

Abstract

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

Published
2024

3. PigBiobank:a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs

Author

Zeng, Haonan, Zhang, Wenjing, Lin, Qing, Gao, Yahui, Teng, Jinyan, Xu, Zhiting, Cai, Xiaodian, Zhong, Zhanming, Wu, Jun, Liu, Yuqiang, Diao, Shuqi, Wei, Chen, Gong, Wentao, Pan, Xiangchun, Li, Zedong, Huang, Xiaoyu, Chen, Xifan, Du, Jinshi, Zhao, Fuping, Zhao, Yunxiang, Ballester, Maria, Crespo-Piazuelo, Daniel, Amills, Marcel, Clop, Alex, Karlskov-Mortensen, Peter, Fredholm, Merete, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Liu, Xiaohong, Chen, Yaosheng, Zhang, Qin, Li, Jiaqi, Yuan, Xiaolong, Ding, Xiangdong, Fang, Lingzhao, Zhang, Zhe, Zeng, Haonan, Zhang, Wenjing, Lin, Qing, Gao, Yahui, Teng, Jinyan, Xu, Zhiting, Cai, Xiaodian, Zhong, Zhanming, Wu, Jun, Liu, Yuqiang, Diao, Shuqi, Wei, Chen, Gong, Wentao, Pan, Xiangchun, Li, Zedong, Huang, Xiaoyu, Chen, Xifan, Du, Jinshi, Zhao, Fuping, Zhao, Yunxiang, Ballester, Maria, Crespo-Piazuelo, Daniel, Amills, Marcel, Clop, Alex, Karlskov-Mortensen, Peter, Fredholm, Merete, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Liu, Xiaohong, Chen, Yaosheng, Zhang, Qin, Li, Jiaqi, Yuan, Xiaolong, Ding, Xiangdong, Fang, Lingzhao, and Zhang, Zhe

Abstract

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

Published
2024

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