Article
Cell Biology
Young-Sup Lee, Seungwoo Son, Hak-Kyo Lee, Ra Ham Lee, Donghyun Shin
Summary: Although conserving native pig breeds is important in Korea, there is limited research on the genomic aspects of identifying breed-specific variations. This study used whole genome sequencing data to identify breed-specific SNPs in native pig breeds, aiming to understand their unique characteristics, such as meat quality and disease resistance. Gene ontology analysis revealed specific biological processes associated with breed-specific SNPs, providing insights into the reasons behind the unique characteristics of native pig breeds.
ANIMAL CELLS AND SYSTEMS
(2022)
Article
Agriculture, Dairy & Animal Science
Futao Mo, Weibo Sun, Liping Zhang, Xiaoyan Zhang, Yongfu La, Fan Xiao, Jianlei Jia, Jipeng Jin
Summary: The study identified two single nucleotide polymorphisms, rs427897187 G > A and rs403555643 A > G, in the BMPRIB gene which could serve as potential molecular markers for improving the reproductive performance of Chinese indigenous sheep. These markers offer a new direction for breeding programs focusing on increasing litter size in indigenous sheep populations.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dan Wang, Liu Yang, Chao Ning, Jian-Feng Liu, Xingbo Zhao
Summary: This study compared the accuracy of mitogenome alignment and SNP calling using three different types of reference sequences for mitochondrial DNA analyses. The results showed that breed-specific reference sequences were optimal for mitogenome analyses, providing a refined processing perspective for NGS data.
Article
Biotechnology & Applied Microbiology
Yifu Wang, Jinhua Cheng, Chao Xu, Jian Jin, Wenbin Bao, Shenglong Wu, Zhengchang Wu
Summary: This study provides an extensive overview of circRNA expression profiles during spleen development in Meishan pigs. Through analysis, thousands of circRNAs and their host genes were identified. Additionally, circRNAs were found to interact with immune-related genes through miRNA sponges. These findings demonstrate the differential expression of circRNAs during different stages of spleen development and their interaction with immune-related genes.
Article
Agriculture, Dairy & Animal Science
Chaoqun Gao, Wenping Du, Kaiyuan Tian, Kejun Wang, Chunxiu Wang, Guirong Sun, Xiangtao Kang, Wenting Li
Summary: Abundant animal genetic resources ensure the sustainable development of animal husbandry, but the lack of appropriate conservation programs leads to a reduction in genetic diversity in indigenous breeds. Using genomic data, we investigated the population structure and genetic distance of eight Chinese indigenous chicken breeds. Our analysis identified the top three breeds for conservation priority and revealed selection signals associated with meat production traits. Effective conservation of genetic resources is crucial for the poultry industry's sustainable development.
Article
Veterinary Sciences
Chao Li, Xueyan Zhao, Guisheng Zhao, Haipeng Xue, Yanping Wang, Yifan Ren, Jingxuan Li, Huaizhong Wang, Jiying Wang, Qinye Song
Summary: This study characterized and compared the biogeography of intestinal microbiota in two pig breeds, Laiwu pigs and DLY pigs. The results showed that there were significant differences in microbial structure and abundance between the small and large intestines, and specific bacterial taxa and pathways were found to be related to the phenotypic traits of each breed. This study provides insights into the potential influence of host genetics on intestinal microbiota composition and diversity.
VETERINARY SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Neelam A. Topno, Veerbhan Kesarwani, Sandeep Kumar Kushwaha, Sarwar Azam, Mohammad Kadivella, Ravi Kumar Gandham, Subeer S. Majumdar
Summary: This study explores the variations in milk fat content among cattle breeds at the genetic and transcriptional level. The effect of breed on milk components and the presence of fixed SNP patterns in key genes were identified. Pyrosequencing validated the differences in fat QTLs between high- and low-milk-yielding breeds.
Article
Agriculture, Dairy & Animal Science
Wei Wang, Yi Shi, Fang He, Donghui Fang, Jia Gan, Fuqiu Wu, Yueda Ag, Xiaodong Deng, Qi Cao, Chu Duo, Wangdeng Rz, Maozhong Fu, Jun Yi
Summary: This study investigated the genetic diversity and population structures of Xieka cattle using genomic information. The results showed that this indigenous breed still maintains a high degree of genetic diversity and has not been affected by inbreeding. Additionally, several candidate genomic regions and genes associated with production traits in cattle were identified.
Article
Genetics & Heredity
Emily E. Binversie, Mehdi Momen, Guilherme J. M. Rosa, Brian W. Davis, Peter Muir
Summary: This study conducted a genome-wide association study (GWAS) on canine whole-genome sequencing (WGS) repository data using breed phenotypes. By applying categorical GWAS, the study identified candidate loci and genes associated with canine spontaneous complex orthopedic diseases. The findings contribute to the understanding of these diseases and provide insights into the optimal approach for conducting GWAS without individual phenotypes.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Changheng Zhao, Dan Wang, Jun Teng, Cheng Yang, Xinyi Zhang, Xianming Wei, Qin Zhang
Summary: This study compared different methods for breed-informative SNP detection and breed assignment, and proposed the combination of DFI and KSR as the optimal strategy. The results showed that using chip data for breed identification had similar accuracy to using sequence data, making chip data a cost-effective option.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Kejun Wang, Lige Zhang, Dongdong Duan, Ruimin Qiao, Xiuling Li, Xinjian Li, Xuelei Han
Summary: The introduction of genetic traits from European pigs into Chinese indigenous pigs, especially in Henan indigenous pigs, has potentially improved pig body size and feed conversion efficiency. This suggests that human-mediated introgression and selection have reshaped the genome of Henan pigs and enhanced their desired traits.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Giovanna Carpi, Lev Gorenstein, Timothy T. Harkins, Mehrzad Samadi, Pankaj Vats
Summary: The study introduces an accelerated, scalable, reproducible, and cost-effective framework for pathogen genomic variant identification. The evaluation on benchmark datasets of malaria genomes demonstrates superior performance and accuracy compared to standard pipelines.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Wasfi Fares, Anissa Chouikha, Kais Ghedira, Meriam Gdoura, Dorra Rezig, Sondes Haddad Boubaker, Imen Ben Dhifallah, Henda Touzi, Walid Hammami, Zina Meddeb, Amel Sadraoui, Nahed Hogga, Imen Abouda, Aurelia Kwasiborski, Veronique Hourdel, Guillain Mikaty, Valerie Caro, Jean-Claude Manuguerra, Nissaf Ben Alaya, Henda Triki
Summary: This preliminary study in Tunisia aimed to understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses. Through whole genome sequencing of six highly positive samples, it was found that Tunisian sequences clustered into 6 different clades with 3 major genotypes identified based on SNP mutations. Multiple introductions of the virus in Tunisia were indicated, adding new genomic data on SARS-CoV-2 at the international level.
Article
Agriculture, Dairy & Animal Science
Hao Chen, Youjiang Diao, Xiaolong Sun, Yixin Wang
Summary: In this study, an ALV-K strain SD20LH01 was isolated from Chinese indigenous chickens. The full-length genomic sequence of SD20LH01 showed high homology with ALV-K reference strains GDFX0601, GDFX0602, and GDFX0603, with nucleotide differences mainly in the gp85 gene and U3 sequence. The pathogenicity of SD20LH01 was investigated using yolk sac and intraperitoneal inoculation methods, which induced different levels of viremia and immune response in chicken embryos and 1-day-old chickens. No tumors were found in infected chickens. This study contributes to the understanding of ALV-K in Chinese indigenous chickens and provides a foundation for further research on its pathogenesis and prevention.
Article
Gastroenterology & Hepatology
Guang Li, Bowen Zhang, Jianyu Hao, Xiaojing Chu, Miriam Wiestler, Markus Cornberg, Cheng-Jian Xu, Xinjuan Liu, Yang Li
Summary: This study identified two novel plasma cell subsets in colon mucosa of UC patients through single-cell RNA sequencing analysis, as well as significant differences in five epithelial/stromal and three immune cell subsets between inflamed and non-inflamed samples. UC risk genes show consistent expression alteration in immune cells, while specific immune dysfunction signals like IgA defect are observed only in the inflamed area. Th17-driven immune activities changes were observed in both epithelial and immune cell lineages of UC patients compared to controls. The enriched UC risk genes in progenitors, glial cells, and immune cells, along with differential expression of drug-target genes in antigen presenting cells, were also noted.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
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
Genetics & Heredity
Wei Zhao, Xueshuang Lai, Dengying Liu, Zhenyang Zhang, Peipei Ma, Qishan Wang, Zhe Zhang, 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
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)