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Genetics & Heredity
Fen Wu, Hao Sun, Shaoxiong Lu, Xiao Gou, Dawei Yan, Zhong Xu, Zhenyang Zhang, Qamar Raza Qadri, Zhe Zhang, Zhen Wang, Qiang Chen, Mingli Li, Xiaoyi Wang, Xinxing Dong, Qishan Wang, Yuchun Pan
FRONTIERS IN GENETICS
(2020)
Article
Agriculture, Dairy & Animal Science
Z. Zhang, Z. Zhang, F. O. Oyelami, H. Sun, Z. Xu, P. Ma, Q. Wang, Y. Pan
Summary: The study conducted a single-step GWAS on 950 Duroc pigs and identified genomic loci that may affect intramuscular fat (IMF) without changing backfat thickness (BF). Specific genetic variants were found to potentially improve IMF without altering BF, indicating valuable targets for molecular breeding of IMF in Duroc pigs.
Article
Genetics & Heredity
Favour Oluwapelumi Oyelami, Qingbo Zhao, Zhong Xu, Zhe Zhang, Hao Sun, Zhenyang Zhang, Peipei Ma, Qishan Wang, Yuchun Pan
FRONTIERS IN GENETICS
(2020)
Article
Biotechnology & Applied Microbiology
Qing-bo Zhao, Favour Oluwapelumi Oyelami, Qamar Raza Qadri, Hao Sun, Zhong Xu, Qi-shan Wang, Yu-chun Pan
Summary: This study identified significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds using the partial least squares method. The results showed that Chinese local pig breeds like Hongdenglong, Huaibei, and others have significant specific SNPs, while Western pig breeds are more related to growth rate. The study provides insights into genetic differences among local Chinese and Western pig breeds for better conservation strategies in the future.
Article
Genetics & Heredity
Qing-bo Zhao, Eugenio Lopez-Cortegano, Favour Oluwapelumi Oyelami, Zhe Zhang, Pei-pei Ma, Qi-shan Wang, Yu-chun Pan
Summary: The study found that different indigenous pig breeds contribute differently to the gene and allelic diversity within and between subpopulations. Different conservation priorities can be set for these breeds based on different priority criteria.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Zhe Zhang, Peipei Ma, Zhenyang Zhang, Zhen Wang, Qishan Wang, Yuchun Pan
Summary: The study utilized extremely low coverage whole genome sequencing (lcWGS) to construct a haplotype reference panel (lcHRP) for pigs, which significantly improved the accuracy of genomic prediction and identified more signals in genome-wide association study (GWAS) compared to traditional methods like SNP arrays.
Article
Multidisciplinary Sciences
Zhen Wang, Zhenyang Zhang, Zitao Chen, Jiabao Sun, Caiyun Cao, Fen Wu, Zhong Xu, Wei Zhao, Hao Sun, Longyu Guo, Zhe Zhang, Qishan Wang, Yuchun Pan
Summary: Pigs are not only a major meat source but also an important animal model for studying human traits. However, the lack of high-quality pig reference panels limits the application of genotype imputation. In response, the pig Haplotype Reference Panel (PHARP) database has been constructed, providing a large number of pig haplotypes and web-based tools.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Qamar Raza Qadri, Qingbo Zhao, Xueshuang Lai, Zhenyang Zhang, Wei Zhao, Yuchun Pan, Qishan Wang
Summary: This study examines the application of holo-omics framework in breeding programs and demonstrates the effectiveness of holo-omics interaction models through comparisons with real data, providing important insights into the structure of complex traits.
Article
Genetics & Heredity
Rui Cao, Jian Feng, Yuejin Xu, Yifei Fang, Wei Zhao, Zhenyang Zhang, Zhe Zhang, Meng Li, Qishan Wang, Yuchun Pan
Summary: This study investigated the genetic differences and introgression between Lulai pigs, Laiwu pigs, and Yorkshires, identifying significantly different genes and genomic regions. The findings reveal the genetic exchanges among these breeds and shed light on the molecular background of synthesized Lulai pig breeds.
Article
Biochemical Research Methods
Wei Zhao, Qamar Raza Qadri, Zhenyang Zhang, Zhen Wang, Yuchun Pan, Qishan Wang, Zhe Zhang
Summary: This study developed a fast and user-friendly Python package, PyAGH, for calculating kinship matrices using pedigree, genotype, microbiome, and transcriptome data. It also provides functions for processing, analyzing, and visualizing the data and results. PyAGH integrates multiple methods for calculating kinship matrices and has advantages in terms of speed and data size compared to other software.
BMC BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Jiamin Gu, Jianwei Guo, Zhenyang Zhang, Yuejin Xu, Qamar Raza Qadri, Zhe Zhang, Zhen Wang, Qishan Wang, Yuchun Pan
Summary: Genomic selection techniques have improved animal breeding by enhancing the prediction accuracy of breeding values, especially for traits that are difficult to measure and have low heritability, as well as reducing generation intervals. However, the requirement to establish genetic reference populations can limit the application of GS in pig breeds with small populations. We proposed the kinship index based selection (KIS) method which overcomes this limitation and showed that it is feasible, particularly for small population sizes.
Article
Agriculture, Dairy & Animal Science
Ruifeng Zhang, Yi Zhang, Tongni Liu, Bo Jiang, Zhenyang Li, Youping Qu, Yaosheng Chen, Zhengcao Li
Summary: This study utilized three genome-wide association study methods to identify variants related to growth traits in pigs and performed genomic selection. The results showed that genomic best linear unbiased prediction (GBLUP) models with pre-selected variants significantly improved prediction accuracies compared to using 60K SNP-chip data, with improvements ranging from 4% to 46% for the four traits; and a two-kernel based GBLUP model showed improvements ranging from 5% to 27%.
Article
Agriculture, Dairy & Animal Science
Ziqi Zhong, Ziyi Wang, Xinfeng Xie, Shuaishuai Tian, Feifan Wang, Qishan Wang, Shiheng Ni, Yuchun Pan, Qian Xiao
Summary: Protection of genetic diversity is crucial for the sustainable development of the animal industry. The genetic diversity and population structure of three Chinese indigenous pig populations in Hainan Province were assessed in this study using whole-genome sequencing data. The analysis revealed that native Chinese pig populations have higher genetic diversity compared to commercial pigs, and identified candidate genes associated with certain traits such as stress resistance.
Article
Agriculture, Dairy & Animal Science
Jian Miao, Zitao Chen, Zhenyang Zhang, Zhen Wang, Qishan Wang, Zhe Zhang, Yuchun Pan
Summary: In this study, researchers demonstrated that accurate identification of different pig breeds is possible using the web tool iDIGs.
GENETICS SELECTION EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Zitao Chen, Zhenyang Zhang, Zhen Wang, Zhe Zhang, Qishan Wang, Yuchun Pan
Summary: This study investigated the effects of ROHet and ROH on reproductive traits in pigs and identified candidate genes associated with reproductive performance. Through multi-omics analysis, the roles of these genes in mammalian reproductive performance were revealed. The findings are of significant importance for genetic improvement and understanding the function of ROHet and ROH in mammals.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)