Article
Biotechnology & Applied Microbiology
Huibin Shi, Taotao Li, Manchun Su, Huihui Wang, Qiao Li, Xia Lang, Youji Ma
Summary: In this study, the distribution characteristics of copy number variations (CNVs) in Tibetan sheep were investigated using whole-genome resequencing. The results showed a large number of CNV events in Tibetan sheep, which were associated with their adaptability and complex traits. Functional enrichment analysis revealed that these CNV regions were related to organ development, neural regulation, immune regulation, digestion, and metabolism. In addition, some CNV regions overlapped with quantitative trait loci (QTLs) associated with body weight and growth traits in sheep. Furthermore, significant differences were observed between different breeds, indicating that CNVs may play an important role in population differences in sheep.
Article
Biotechnology & Applied Microbiology
Chao Yuan, Zengkui Lu, Tingting Guo, Yaojing Yue, Xijun Wang, Tianxiang Wang, Yajun Zhang, Fujun Hou, Chune Niu, Xiaopin Sun, Hongchang Zhao, Shaohua Zhu, Jianbin Liu, Bohui Yang
Summary: This study identified a large number of CNVs in 32 fine-wool sheep, with CNVRs mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Functional enrichment analysis showed overlap with previously reported sheep CNVRs, with 1855 CNVRs associated with 166 quantitative trait loci.
Article
Genetics & Heredity
Linyong Hu, Liangzhi Zhang, Qi Li, Hongjin Liu, Tianwei Xu, Na Zhao, Xueping Han, Shixiao Xu, Xinquan Zhao, Cunfang Zhang
Summary: This study characterized copy number variations (CNVs) in Tibetan sheep using resequencing data and found a large number of CNVs that are associated with genetic structure, dosage regulation, and expression in the sheep genome. The shared CNV regions (CNVRs) were found to be significantly enriched in various pathways and GO terms related to transporters, sensory perception, and oxygen transport. Several CNVRs were also found to overlap with quantitative trait loci (QTLs) related to growth, body weight, and other traits. Vst analysis revealed significant divergence of certain genes between different ecotypic populations of Tibetan sheep. These findings provide valuable genetic variation resources for further elucidating the genetic basis of distinct phenotypic traits and local adaptation in Tibetan sheep.
FRONTIERS IN GENETICS
(2022)
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Genetics & Heredity
Xiaolong Li, Qingmin Wu, Xiaoxue Zhang, Chong Li, Deyin Zhang, Guoze Li, Yukun Zhang, Yuan Zhao, Zhaoguo Shi, Weimin Wang, Fadi Li
Summary: This study identified candidate genes associated with brucellosis resistance in sheep through whole-genome sequencing, revealing enrichment of these genes in specific pathways. This provides valuable molecular markers for breeding brucellosis-resistant sheep and enhances our understanding of the genetic mechanism of brucellosis resistance.
FRONTIERS IN GENETICS
(2021)
Article
Environmental Sciences
Gustavo Nunez-Acuna, Constanza Saez-Vera, Diego Valenzuela-Miranda, Valentina Valenzuela-Munoz, Cristian Gallardo-Escarate
Summary: This study used genome resequencing and transcriptome analysis to investigate structural genomic variations and gene expression in sea lice strains with different sensitivity to pesticides. It was found that duplications or copy number variants were present in transposable elements and genes related to drug response, with a higher frequency of duplications in genes associated with cuticle proteins. The study suggests that the intensive use of pesticides increases the frequency of gene duplications and expands the molecular elements involved in drug response.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Teruaki Tozaki, Aoi Ohnuma, Masaki Takasu, Kotono Nakamura, Mio Kikuchi, Taichiro Ishige, Hironaga Kakoi, Kei-ichi Hirora, Norihisa Tamura, Kanichi Kusano, Shun-ichi Nagata
Summary: This study aimed to detect genetically engineered animals for gene-doping control using whole-genome resequencing techniques, successfully identifying transgenes as intron deletions. By conducting genome-wide screening, artificially introduced single-nucleotide polymorphisms and insertions/deletions in transgenes were identified.
Article
Agriculture, Dairy & Animal Science
Wentao Zhang, Meilin Jin, Taotao Li, Zengkui Lu, Huihua Wang, Zehu Yuan, Caihong Wei
Summary: This study identifies candidate genes associated with wool fineness in sheep and reveals selection signals related to this trait. The findings provide valuable genomic information and pave the way for further investigations.
Article
Agriculture, Dairy & Animal Science
Wentao Zhang, Meilin Jin, Zengkui Lu, Taotao Li, Huihua Wang, Zehu Yuan, Caihong Wei
Summary: Wool color in sheep is regulated by various genes. This study used whole genome resequencing data to analyze different sheep populations and identified candidate genes and pathways associated with non-white and white wool coloration. The findings contribute to our understanding of wool color genetics and have implications for breeding purposes.
Article
Biotechnology & Applied Microbiology
Deyin Zhang, Xiaoxue Zhang, Fadi Li, Teng Liu, Zhihong Hu, Ning Gao, Lvfeng Yuan, Xiaolong Li, Yuan Zhao, Liming Zhao, Yukun Zhang, Dan Xu, Qizhi Song, Jiangbo Cheng, Weimin Wang
Summary: This study identified important candidate genes affecting the increase in rib number in sheep through whole-genome resequencing and analysis. Genes such as CPOX, KCNH1, and CPQ were found to have a combined effect on rib number, providing valuable molecular markers for sheep breeding in relation to rib number.
Article
Agriculture, Dairy & Animal Science
Chunna Cao, Yuxin Kang, Qian Zhou, Hojjat Asadollahpour Nanaei, Didi Bo, Peiyao Liu, Yangyang Bai, Ran Li, Yu Jiang, Xianyong Lan, Chuanying Pan
Summary: This study identified candidate genes associated with the unique grey color and environmental adaptation in Romanov sheep through whole-genome sequencing. Understanding the genetic background and signatures of Romanov sheep is of great value for its conservation and utilization.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang, Jun Zhang
Summary: This study conducted genome resequencing of transgenic poplar 741 line Pb29, identifying two T-DNA insertion sites without chromosomal rearrangement. It was found that Pb29 genome only contains the BtCry1AC gene, with minimal impact on the expression levels of surrounding genes.
Article
Genetics & Heredity
E. Guang-Xin, Dong-Ke Zhou, Zhu-Qing Zheng, Bai-Gao Yang, Xiang-Long Li, Lan-Hui Li, Rong-Yan Zhou, Wen-Hui Nai, Xun-Ping Jiang, Jia-Hua Zhang, Qiong-Hua Hong, Yue-Hui Ma, Ming-Xing Chu, Hui-Jiang Gao, Yong-Ju Zhao, Xing-Hai Duan, Yong-Meng He, Ri-Su Na, Yan-Guo Han, Yan Zeng, Yu Jiang, Yong-Fu Huang
Summary: The study used whole-genome next-generation sequencing technology to investigate the selective sweep of intersex goats from China, revealing candidate genes related to the intersexuality phenotype. It was confirmed that a duplicated fragment downstream of the PIS region was inserted into the PIS locus in intersex Chinese goats. The study suggested that this novel complex PIS variant genome could serve as a clinical diagnostic marker for XX intersexuality in goats from Europe and China.
FRONTIERS IN GENETICS
(2021)