Article
Biotechnology & Applied Microbiology
Emily C. Patterson, Gurdeep Matharu Lall, Rita Neumann, Barbara Ottolini, Chiara Batini, Federico Sacchini, Aiden P. Foster, Jon H. Wetton, Mark A. Jobling
Summary: This study used Nanopore sequencing to analyze the mitochondrial genomes of 119 cats, revealing a higher number of distinct haplotypes and providing phylogenetic information. Additionally, the study discovered dynamic mutation processes through the examination of tandem repeat sequences.
Article
Genetics & Heredity
Naifan Zhang, Xinyue Shao, Yaqi Guo, Xinyu Zhang, Yawei Zhou, Jing Yuan, Zhuowei Tang, Songmei Hu, Sergey Stepanovich Minyaev, Dawei Cai
Summary: Cattle in China have played a significant role in Chinese history, but little is known about the exact route and diffusion of taurine cattle introduced to China. This study analyzed the mitochondrial genomes of ancient taurine cattle excavated from northern China and the eastern Eurasian steppe, revealing close genetic exchange between domestic taurine cattle in different regions through cultural exchange and trade. The genetic continuity of domestic cattle suggests the strong cultural influence of major capital city sites on surrounding areas. The study suggests that ancient northern Chinese taurine cattle may have contributed genetically to modern Tibetan cattle as part of the westward transmission of agricultural or painted pottery culture.
Article
Agriculture, Dairy & Animal Science
Xiaona Chen, Xinyu Duan, Qingqing Chong, Chunqing Li, Heng Xiao, Shanyuan Chen
Summary: This study analyzed the differences in DNA methylation between zebu and taurine cattle and identified pathways and candidate genes associated with disease, disease resistance, and economic traits. These findings provide a foundation for further screening of characteristic epigenetic molecular markers in zebu and support genetic improvement of domestic cattle.
Article
Biochemistry & Molecular Biology
Isaac J. Nijman, Benjamin D. Rosen, Philippe Bardou, Thomas Faraut, Tristan Cumer, Kevin G. Daly, Zhuqing Zheng, Yudong Cai, Hojjat Asadollahpour, Bengi Cinar Kul, Wei-Yi Zhang, Guangxin E, A. Ayin, Hayley Baird, Meirat Bakhtin, Valentin A. Balteanu, Diana Barfield, Beate Berger, Thor Blichfeldt, Geert Boink, Sri R. A. Bugiwati, Zexi Cai, Sean Carolan, Emily Clark, Vlatka Cubric-Curik, Muhammad I. A. Dagong, Tashi Dorji, Louise Drew, Jiazhong Guo, Jon Hallsson, Simon Horvat, Juha Kantanen, Fuki Kawaguchi, Polat Kazymbet, Negar Khayatzadeh, Namshin Kim, Manoj Kumar Shah, Yuying Liao, Amparo Martinez, Joseph S. Masangkay, Maho Masaoka, Raffaele Mazza, John McEwan, Marco Milanesi, Faruque Md Omar, Yuto Nomura, Nadjet-Amina Ouchene-Khelifi, Filipe Pereira, Goutam Sahana, Mazdak Salavati, Shinji Sasazaki, Anne Da Silva, Mojca Simcic, Johann Solkner, Alison Sutherland, Johannes Tigchelaar, Hongpin Zhang, Paolo Ajmone-Marsan, Daniel G. Bradley, Licia Colli, Cord Drogemuller, Yu Jiang, Chuzhao Lei, Hideyuki Mannen, Francois Pompanon, Gwenola Tosser-Klopp, Johannes A. Lenstra
Summary: This study analyzed the Y-chromosomal variants in domestic and wild goats, revealing the importance of paternal population history and male-mediated introgression. The findings provide insights into the evolution of goat species and the influence of migrations and crossbreeding on their genetic diversity.
Article
Genetics & Heredity
Xing Zhang, Liu Yang, Xingbo Zhao, Hai Xiang
Summary: The complete mitochondrial genome of a 4000-year-old cattle from Taosi site was determined using high throughput sequencing, revealing close genomic relationship between early taurine cattle in Northern China and modern domestic cattle.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Agriculture, Dairy & Animal Science
Selma Farah Boudali, Ahmed S. Al-Jumaili, Ameur Bouandas, Fatima Zohra Mahammi, Nacera Tabet Aoul, Olivier Hanotte, Semir Bechir Suheil Gaouar
Summary: This study assessed the genetic diversity and maternal origin of domestic chickens from five regions in western Algeria and found that Algerian chickens mainly originated from the Indian subcontinent. These findings provide important information about the origin of North-West African chicken and the historical dispersal of the first chicken populations into the African continent.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Mohammed Dashti, Hussain Alsaleh, Muthukrishnan Eaaswarkhanth, Sumi Elsa John, Rasheeba Nizam, Motasem Melhem, Prashantha Hebbar, Prem Sharma, Fahd Al-Mulla, Thangavel Alphonse Thanaraj
Summary: This study utilized whole-exome sequencing data to extract complete mitochondrial haplogroups, revealing a significant association between haplogroups R and L and obesity risk in an Arab population. The findings suggest that mitochondrial variants play a role in the pathogenesis of obesity.
FRONTIERS IN GENETICS
(2021)
Article
Neurosciences
Amber Watts, Prabhakar Chalise, Jinxiang Hu, Dongwei Hui, Judy Pa, Shea J. Andrews, Elias K. Michaelis, Russell H. Swerdlow
Summary: This study examined the role of mitochondrial DNA (mtDNA) in cognitive decline, specifically in the domain of verbal memory. The results showed that individuals carrying the J haplogroup had lower baseline performance and slower rates of improvement in verbal memory compared to those carrying the H haplogroup. No significant differences were observed in executive function or attention. Further research is needed to investigate the underlying mechanisms by which mtDNA affects cognitive performance in different domains across haplogroups.
JOURNAL OF ALZHEIMERS DISEASE
(2022)
Review
Genetics & Heredity
Samantha W. Jones, Amy L. Ball, Amy E. Chadwick, Ana Alfirevic
Summary: The triad of drug efficacy, toxicity and resistance is crucial in determining the risk-benefit balance of therapeutics. Pharmacogenomics can potentially improve this balance by stratifying patient populations based on DNA variants. Research on the impact of mitochondrial DNA variation on drug response is still inconclusive and further studies are needed to explain the variability in drug response.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
David G. Mahal
Summary: This study revealed the genetic affinities of Brahmins with foreign populations as well as with domestic non-Brahmin groups in India. By tracing Y-chromosome haplogroups and genetic markers, the deep ancient origins of Brahmins were identified, with their progenitors emerging from at least 12 different geographic regions worldwide. Additionally, the study found that 83% of Brahmins in the dataset belonged to four major haplogroups, two from Central Asia, one from the Fertile Crescent, and one of indigenous Indian origin.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Agriculture, Dairy & Animal Science
Hongfei Liu, Junjun Zhai, Hui Wu, Jingyi Wang, Shaowei Zhang, Jie Li, Zhihan Niu, Chenglong Shen, Kaijuan Zhang, Zhengqing Liu, Fugui Jiang, Enliang Song, Xiuzhu Sun, Yongsheng Wang, Xianyong Lan
Summary: By sequencing the mtDNA D-loop region of Chinese Holstein cows, abundant genetic resources and two haplogroups with different maternal origins were found, which were associated with the number of antral follicles. These distinguished mutations could be considered as important genetic markers for cattle breeding.
Article
Agriculture, Dairy & Animal Science
Yoshinori Nishita, Yosuke Amaike, Nikolai Spassov, Latinka Hristova, Dimitar Kostov, Diyana Vladova, Stanislava Peeva, Evgeniy Raichev, Radka Vlaeva, Ryuichi Masuda
Summary: The domestication of horses in the Eurasian steppe began over 5000 years ago and spread to the Thracian culture region in present-day Bulgaria starting from the second half of the 2nd millennium BCE. Analysis of horse bone remains from Thracian archaeological sites in Bulgaria revealed a close genetic relationship between ancient Thracian horses and modern horses of Southern Europe, while having less genetic similarity to horses of Central Asia. The study also identified 11 modern horse mitochondrial DNA haplogroups in the Thracian horse remains, showing high genetic diversity and close relationship with modern horse breeds.
ANIMAL SCIENCE JOURNAL
(2023)
Review
Endocrinology & Metabolism
Agnieszka H. Ludwig-Slomczynska, Markus Rehm
Summary: Cellular energy metabolism is regulated by two genomes, the nuclear genome and the mitochondrial genome, which coevolve and affect cellular processes and metabolic diseases. Variations in the mitochondrial genome can influence cellular metabolism and physiology, and are associated with the onset of metabolic diseases.
Article
Biophysics
Sana Masroor, Mohd Tanzeel Aalam, Owais Khan, Gunturu Narasimha Tanuj, Ravi Kumar Gandham, Sujoy K. Dhara, Praveen K. Gupta, Bishnu Prasad Mishra, Triveni Dutt, Gynendra Singh, Basavaraj K. Sajjanar
Summary: Environmental temperature is a major factor affecting the health and productivity of dairy cattle. This study compared the stress gene expression and DNA methylation patterns of Indian native zebu cattle with a crossbred zebu and taurus cattle. The results showed that zebu cattle had higher expression of stress genes and DNA methylation might play a role in regulating the expression of certain genes involved in stress response pathways.
INTERNATIONAL JOURNAL OF BIOMETEOROLOGY
(2022)
Article
Genetics & Heredity
Rajan Kumar Jha, Chhavi Dawar, Qurratulain Hasan, Akhilesh Pujar, Gaurav Gupta, Venugopalan Y. Vishnu, Ramesh Kekunnaya, Kumarasamy Thangaraj
Summary: The study revealed that LHON cases are mainly caused by three primary variants, but there are still patients without these primary variants who carry other LHON-associated variants. Additionally, no individual haplogroups were explicitly associated with LHON, while two specific variants showed a significant association with the LHON phenotype.
Article
Agriculture, Dairy & Animal Science
Chao Yan, Jinlong Xiao, Di Chen, Simon P. Turner, Zhiwei Li, Hao Liu, Wen Liu, Jian Liu, Siyu Chen, Xingbo Zhao
Summary: Different genotypes of slow- and fast-growing chickens show phenotypic changes in response to artificial selection. Feed restriction affects behavior, stress response, and gut microbiota composition in both types of chickens, but some changes are breed-specific.
Article
Biology
Hai Xiang, Siyu Chen, Hui Zhang, Xu Zhu, Dan Wang, Huagui Liu, Jikun Wang, Tao Yin, Langqing Liu, Minghua Kong, Jian Zhang, Hua Li, Simon Turner, Xingbo Zhao
Summary: The study compared the effects of housing hens with or without roosters on various aspects such as productivity, behavior, microbiome, and genetics, finding that hens housed without roosters showed better survival rates, egg production, and feed efficiency. Hens housed with roosters exhibited closer proximity to the roosters and lower activity levels in novel environment and object tests.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Zheng Ma, Na Luo, Lu Liu, Huanxian Cui, Jing Li, Hai Xiang, Huimin Kang, Hua Li, Guiping Zhao
Summary: The study observed a significant decrease in lipid content in DIMFPs compared to DAFPs, with 72 differentially expressed genes involved in lipid metabolism. Among them, 19 genes enriched in the PPAR signaling pathway were identified, providing insights into the molecular mechanisms underlying the differences in lipid deposition between DAFPs and DIMFPs.
Article
Microbiology
Hai Xiang, Jiankang Gan, Daoshu Zeng, Jing Li, Hui Yu, Haiquan Zhao, Ying Yang, Shuwen Tan, Gen Li, Chaowei Luo, Zhuojun Xie, Guiping Zhao, Hua Li
Summary: Genetically selected chickens with better growth and early maturation that show increased abdominal fat deposition (AFD) have been found to have a decrease in gut microbiota richness and diversity, with a decrease in Bacteroidetes and an increase in Firmicutes associated with AFD accumulation. The specific microbial taxa such as Bacteroidetes genera and Firmicutes genera were identified to play a role in alleviating obesity or contributing to fat accumulation in chickens. These findings provide insights into the complex relationship between gut microbiota and chicken fat accumulation, which could contribute to the development of effective therapies for reducing chicken fat deposition.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Applied
Yuxi Jin, Huanxian Cui, Xiaoya Yuan, Lu Liu, Xiaojing Liu, Yongli Wang, Jiqiang Ding, Hai Xiang, Xinxiao Zhang, Jianfeng Liu, Hua Li, Guiping Zhao, Jie Wen
Summary: The study analyzed the volatile organic compounds in chicken meat from 972 Chinese local chickens and identified various VOCs belonging to aldehyde, alcohol, and alkane classes. The breeds with the highest total aldehyde content were negatively correlated with the content of the other two classes, and their flavor could be distinguished by E-nose. Additionally, 9 common VOCs were shared by different breeds, and principal component analysis identified hexanal and 1-octen-3-ol as the major VOCs in each breed based on different criteria.
Article
Genetics & Heredity
Xing Zhang, Liu Yang, Lingyun Hou, Hua Li, Hai Xiang, Xingbo Zhao
Summary: This study confirms that approximately 4,000-year-old bovines from North China were taurine cattle, originating from the Near East. Ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. There was a rapid decrease in the female effective population size of Chinese taurine cattle around 4.65 thousand years ago.
FRONTIERS IN GENETICS
(2021)
Review
Ecology
Liu Yang, Xing Zhang, Xingbo Zhao, Hai Xiang
Summary: In this paper, we reviewed the history of coprolite research, explained the data recovered from coprolites, and emphasized their research value to palaeocoprology and evolutionary biology. Additionally, we summarized the current directions of coprolite research and discussed its future prospects.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Editorial Material
Genetics & Heredity
Hai Xiang, Martijn F. L. Derks, Guoqiang Yi, Xingbo Zhao
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Chao Yan, Wen Liu, Jinlong Xiao, Hai Xiang, Jikun Wang, Hui Zhang, Jian Liu, Siyu Chen, Xingbo Zhao
Summary: This study examines the impact of early-life enrichment and later-life environments on learning ability and hippocampal responses in chicks. The findings suggest that early-life environmental complexity has limited effects on learning ability in response to future life challenges, but it can improve neural- and immune-related gene expression and functional pathways.
Article
Genetics & Heredity
Xing Zhang, Liu Yang, Xingbo Zhao, Hai Xiang
Summary: The complete mitochondrial genome of a 4000-year-old cattle from Taosi site was determined using high throughput sequencing, revealing close genomic relationship between early taurine cattle in Northern China and modern domestic cattle.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Agriculture, Dairy & Animal Science
Wenpeng Li, Chao Yan, Kris Descovich, Clive J. C. Phillips, Yongyou Chen, Huijing Huang, Xuan Wu, Jian Liu, Siyu Chen, Xingbo Zhao
Summary: The study demonstrates that preslaughter stunning can enhance meat quality, improve flavor, and reduce stress in chickens, promoting animal welfare. This provides a theoretical basis for the promotion of animal welfare concepts in China.
Article
Genetics & Heredity
Hai Xiang, Zhi Wang, Liu Yang, Xing Zhang, Xingbo Zhao
Summary: This article introduces a loop-primer-mediated amplification method (L-PCR) for efficiently and accurately obtaining target sequences from ancient DNA samples. Through testing with 66 ancient samples and serially diluted modern animal DNA templates, it is proven that L-PCR is more efficient and accurate than nested PCR, and can obtain more amplicons from ancient samples.
FRONTIERS IN GENETICS
(2022)
Article
Agronomy
Ye Zhou, Chao Yan, Di Chen, Chengde Zhang, Xingbo Zhao
Summary: The combination of planting and breeding in agriculture maximizes land utilization and increases productivity. This study analyzed the behavior, meat quality, and microbiota of ducks and soil to investigate the grape-duck farming system. The results showed significant differences in positive behaviors between the breeding group and the combination group. Meat quality was also affected, with the combination group having higher yellow value b* and drip loss rate. The combination mode increased soil microbiota diversity but showed no effect on duck fecal microbiota.
Article
Agriculture, Dairy & Animal Science
Huimin Kang, Di Zhao, Hai Xiang, Jing Li, Guiping Zhao, Hua Li
Summary: We conducted association analyses based on breast muscle transcriptomic data to identify candidate genes for breast muscle weight and IMF contents in Tiannong partridge chickens. The study evaluated different statistical models and detected several candidate genes associated with these economic traits, which are involved in muscle development, contraction, and lipid metabolism. This research provides valuable insights for genetic improvement programs in broiler chickens.
GENETICS SELECTION EVOLUTION
(2021)
Article
Anthropology
Julia Becher, Alex Schoeman, Gavin Whitelaw, Stephen Buckley, Jean-Pierre Celliers, Sara Cafisso, Matthias Belser, Maxime Rageot, Cynthianne Spiteri
Summary: This study represents the first application of Organic Residue Analysis (ORA) to southern African early farming pottery to gain a deeper understanding of past human behavior and subsistence patterns. The study found evidence of dairy processing and multi-purpose functionality of the ceramics. It also discovered potential medicinal use and the involvement of dung in pottery sealing and mending.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
Article
Anthropology
Jon Clindaniel, Matthew Magnani
Summary: Large sources of digital trace data have become important in the study of material culture. The authors introduce a computational method to observe digital formation processes and highlight the importance of accounting for these processes in studies utilizing digital trace data.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
Article
Anthropology
Rebecca A. G. Reid, Miranda M. E. Jans, Lesley A. Chesson, Rebecca J. Taylor, Gregory E. Berg
Summary: Chemical treatment of skeletal remains can reduce overall DNA quality and quantity but has no significant impact on stable isotope ratio analysis. Examination of treated and untreated human remains through histological and stable isotope analysis reveals that treated remains exhibit better preservation compared to untreated remains. Stable isotope ratio analysis is viable for both treated and untreated remains, regardless of their origin.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
Article
Anthropology
Laura Tome, Eneko Iriartec, Antonio Blanco-Gonzalez, Margarita Jambrina-Enriquez, Natalia Eguez, Antonio V. Herrera-Herrera, Carolina Mallola
Summary: This paper presents the outcomes of a microcontextual geoarchaeological study conducted on earthen dwellings from the Early Iron Age village of Cerro de San Vicente. The study employed soil micromorphology, lipid biomarker analysis, XRD, and XRF analyses to investigate various aspects of the dwellings, including construction materials, site formation processes, and daily life practices. The results have shed light on the construction layers, floor use, maintenance, repaving, periods of abandonment and decay, and the presence of lipid biomarkers associated with dwelling functionality. The study significantly contributes to our understanding of ancient construction practices and the utilization of domestic spaces during the Early Iron Age.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)