Article
Agriculture, Dairy & Animal Science
Georgi Kalaydzhiev, Nadezhda Palova, Heliana Dundarova, Lyudmila Lozanova, Ivan Mehandjyiski, Georgi Radoslavov, Peter Hristov
Summary: Bulgaria's geographical, geomorphological, and climatic characteristics are highly suitable for animal breeding, especially pastoral farming and sheep breeding. The country has about 30 unique local breeds of sheep. This study investigated the genetic diversity of eight popular Bulgarian breeds using sequence analysis of the mitochondrial D-loop region. The results showed multiple maternal origins and high gene flow between the native breeds.
Article
Endocrinology & Metabolism
Yang Chen, Wei-jia Wu, Li-wei Xing, Xiao-juan Zhang, Jing Wang, Xiao-yan Xia, Rui Zhao, Rong Zhao
Summary: This study examined the correlations between mtDNA D-loop, its haplotypes, and PCOS in the Chinese population, and found that certain mtDNA D-loop mutations and haplotypes may confer protection against PCOS in Chinese women. In addition, elevated mtDNA copy number may serve as an indicator during early stages of PCOS.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Veterinary Sciences
Toloe Allahghadry, Duncan Y. K. Ng, Alireza Dibaei, Anders Miki Bojesen
Summary: The study found a high prevalence of multi-resistant Gallibacterium anatis in poultry flocks from major chicken production provinces in Iran. Identical clones of the bacteria were found to be shared among chickens within and between farms for the first time. Additionally, potential effective vaccine targets, such as the gtxA gene, were identified.
VETERINARY RESEARCH
(2021)
Article
Agriculture, Dairy & Animal Science
Grzegorz Mycka, Weronika Klecel, Monika Stefaniuk-Szmukier, Joanna Jaworska, Adrianna Dominika Musial, Katarzyna Ropka-Molik
Summary: In this study, we investigated the genetic composition of the Polish draft horse (PDH) breed by analyzing whole mitochondrial d-loop variabilities and comparing them to sequences of other cold-blooded breeds. Our results showed high nucleotide diversity among the PDH population and the existence of two main haplogroups with strong kinship to the Belgian breed.
Article
Genetics & Heredity
V. R. Kharzinova, N. A. Akopyan, A. Dotsev, T. E. Deniskova, A. A. Sermyagin, T. Karpushkina, A. D. Solovieva, G. Brem, N. A. Zinovieva
Summary: A decrease in genetic diversity is a major genetic concern in pig breeding worldwide. This study aimed to assess the genetic diversity and phylogenetic relationships among nine pig breeds in Russia using mtDNA D-loop sequences. The results showed that local breeds had lower nucleotide differences compared to transboundary breeds. The Kemerovo breed was the most differentiated among local breeds, while the Mangalitsa breed clustered with transboundary breeds due to its European origin. These findings are important for monitoring genetic diversity in transboundary breeds and developing conservation programs for local pig breeds.
RUSSIAN JOURNAL OF GENETICS
(2022)
Article
Biology
Thamer R. S. Aljubouri, Mohammed Baqur S. Al-Shuhaib
Summary: This study assessed mitochondrial D-loop genetic diversity in three breeds of Iraqi/Iranian prolific sheep, revealing different genetic patterns and diversity features, as well as shared haplotypes. Arabi exhibited the highest haplotype diversity, while Awassi showed the highest nucleotide polymorphism diversity. The fixation index indicated a high level of genetic material sharing among populations, with similar haplotypes mostly observed in Arabi and Karakul.
Article
Agronomy
Tatyana A. Larkina, Olga Y. Barkova, Grigoriy K. Peglivanyan, Olga Mitrofanova, Natalia Dementieva, Olga Stanishevskaya, Anatoly B. Vakhrameev, Alexandra Makarova, Yuri S. Shcherbakov, Marina Pozovnikova, Evgeni A. Brazhnik, Darren K. Griffin, Michael N. Romanov
Summary: Understanding phenotypic and genotypic variation is crucial for breeding progress in animal production, and our study identified six evolutionary lineages of breed formation through research on the domestic chickens. There are overlaps between the phenotypic and genotypic clustering models, indicating potential for marker-assisted breeding programs in the future.
Article
Agriculture, Dairy & Animal Science
Guangzhen Li, Jing Luo, Shengmei Chen, Quratulain Hanif, Decang He, Zhijie Ma
Summary: Our study comprehensively analyzed mitochondrial D-loop sequences of white yaks from the Qinghai-Tibet Plateau, revealing abundant maternal genetic diversity in the species. Genetic differentiation was high between Tianzhu and Menyuan populations, moderate between Menyuan and Huzhu populations, and low between Tianzhu and Huzhu populations. Maternal phylogenetic analysis indicated two maternal lineages in white yaks, with evidence of taurine genetic introgression in some populations. This study provides valuable information for the conservation and utilization of white yaks.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Cell Biology
Xiaohong Deng, Dongmei Ji, Xinyuan Li, Yuping Xu, Yu Cao, Weiwei Zou, Chunmei Liang, Jordan Lee Marley, Zhiguo Zhang, Zhaolian Wei, Ping Zhou, Yajing Liu, Yunxia Cao
Summary: Certain mtDNA D-loop variants were found to be associated with decreased risk of PCOS in a Chinese population, but no significant correlation was found between D-loop polymorphisms and clinical characteristics within the PCOS group. Haplotype analysis suggested that a specific haplotype was significantly associated with decreased risk of PCOS.
Review
Biology
George Wanjala, Zoltan Bagi, Szilvia Kusza
Summary: The study conducted a meta-analysis on 399 African sheep breeds to elucidate their genetic diversity, phylogenetic relationship, and demographic history. The findings revealed high levels of genetic diversity, the presence of three major haplogroups, and different evolutionary pressures among sheep populations in various regions.
Article
Agriculture, Multidisciplinary
T. T. B. Nguyen, N. H. Duc, D. V. A. Khoa, N. H. Tuong, H. Reyer, K. Wimmers, D. T. N. Thuy, N. T. D. Thuy
Summary: The genetic diversity of four Vietnamese indigenous chicken breeds was assessed using mitochondrial DNA analysis. The study found that these breeds exhibit a relatively high level of genetic diversity, which is important for their conservation and breeding strategies.
JOURNAL OF ANIMAL AND PLANT SCIENCES-JAPS
(2022)
Article
Genetics & Heredity
Bo Ran, Wei Zhu, Xiaoling Zhao, Linxiang Li, Zhixin Yi, Miao Li, Tao Wang, Diyan Li
Summary: This study analyzed the genetic structure and evolutionary relationships of the Mountainous Meihua chicken. It found that the chicken has high genetic diversity and good breeding potential. It also showed a moderate degree of differentiation from other chicken breeds and no evidence of past population expansions. The study identified four unique maternal lineages in the Mountainous Meihua chicken.
Article
Biochemistry & Molecular Biology
Ramin Abdoli, Tarikul Huda Mazumder, Shahla Nematollahian, Reza Sourati Zanjani, Rahim Abdollahi Mesbah, Arif Uddin
Summary: This study compared the mitochondrial genomes of different types of silkworms and found relationships between codon usage bias, genetic similarity, and phylogenetics. Results showed that the genomes had higher AT content than GC content and codons with A or T endings were over-represented. The codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure, with natural selection playing a larger role. In addition, the mitochondrial genomes of Bombyx mori and Bombyx mandarina were most similar, while the COX1, COX2, and COX3 genes showed the most differences.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Lei Peng, Wenyuan Hua, Yan Chen, Wei Wang, Zhuang Xue
Summary: This study examined the genetic diversity and natural population structure of the black rockfish in northern Chinese cities using mtDNA analysis. The results showed low genetic diversity and no genetic differentiation among the populations. The study suggests the need for in situ conservation of the black rockfish.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Genetics & Heredity
Olga Koshkina, Tatiana Deniskova, Arsen Dotsev, Elisabeth Kunz, Marina Selionova, Ivica Medugorac, Natalia Zinovieva
Summary: Russia has a rich variety of local sheep breeds, but their genetic diversity and maternal origin have not been thoroughly investigated. This study analyzes the mitochondrial genomes of Russian sheep breeds from different regions, revealing their diversity and phylogeny.
Article
Ecology
Joost F. F. de Jong, Laura Iacolina, Herbert H. T. Prins, Pim van Hooft, Richard P. M. A. Crooijmans, Sip E. E. van Wieren, Joaquin Vicente Banos, Eric Baubet, Sean Cahill, Eduardo Ferreira, Carlos Fonseca, Peter M. M. Glazov, Ida Jelenko Turinek, Victor M. Lizana M. Martin, Andras Nahlik, Bostjan Pokorny, Tomasz Podgorski, Nikica Sprem, Rauno Veeroja, Ronald C. C. Ydenberg, Hendrik-Jan Megens
Summary: European wildlife has been impacted by human activities, but genetic partitioning of many species still reflects the glacial refugia. By analyzing the genetic structure of wild boar across Europe, we found population fragmentation, inbreeding, and hybridization with domestic pigs at the local scale. However, a deep genetic structure indicating a natural continental division was still present. Our findings suggest weaker evidence for glacial refugia, but support the importance of Southern France and the Balkans as recolonization routes.
Article
Genetics & Heredity
Yebo Peng, Martijn F. L. Derks, Martien A. M. Groenen, Yiqiang Zhao, Mirte Bosse
Summary: Studying gene flow between different livestock breeds can lead to the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played a crucial role in the breeding of Western commercial pigs, but the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet clear.
FRONTIERS IN GENETICS
(2023)
Article
Food Science & Technology
Desalew Tadesse, Negussie Retta, Mekonnen Girma, Nicholas Ndiwa, Tadelle Dessie, Olivier Hanotte, Paulos Getachew, Dirk Dannenberger, Steffen Maak
Summary: Adding flaxseed can decrease feed oxidative stability and increase the antioxidant needs of chickens. This study evaluated the effects of feeding plant polyphenol extracts as an antioxidant alongside flaxseed on fatty acid content, oxidative stability, and lipid health indices in breast muscle of slow-growing Sasso T451A dual-purpose chicken.
Article
Biotechnology & Applied Microbiology
Young-Lim Lee, Mirte Bosse, Haruko Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Tom Druet, Claire Oget-Ebrad, Wouter Coppieters, Roel F. Veerkamp, Martien A. M. Groenen, Michel Georges, Aniek C. Bouwman, Carole Charlier
Summary: This study aimed to generate and explore a high-quality bovine structural variant (SV) catalogue and discovered two high impact duplications affecting gene expression. These duplications are associated with postpartum feed intake and hoof health traits. However, most copy number variants (CNVs) were not captured by the 50K genotyping array.
Article
Biotechnology & Applied Microbiology
Marije J. Steensma, Y. L. Lee, A. C. Bouwman, C. Pita Barros, M. F. L. Derks, M. C. A. M. Bink, B. Harlizius, A. E. Huisman, R. P. M. A. Crooijmans, M. A. M. Groenen, H. A. Mulder, C. M. Rochus
Summary: This study identified four de novo structural variants (dnSVs) in pig germline, all located in intronic regions of protein-coding genes. The study provides an estimation of the dnSV rate in the pig germline and highlights the complexity of dnSVs.
Article
Biotechnology & Applied Microbiology
Rayner Gonzalez-Prendes, Martijn F. L. Derks, Martien A. M. Groenen, Raquel Quintanilla, Marcel Amills
Summary: The relationship between predicted functional consequences of missense mutations in genes related to lipid metabolism and lipid phenotypes is weak. Only nine out of 72 associated SNPs showed consistent predicted functional mutations and were not associated with expected lipid traits affected by gene inactivation. The study suggests that current bioinformatic tools have limited ability to predict the impact of missense mutations on complex phenotypes.
Article
Genetics & Heredity
Liyan Deng, Wangchang Li, Weiwei Liu, Yanwen Liu, Bingkun Xie, Martien A. M. Groenen, Ole Madsen, Xiaogan Yang, Zhonglin Tang
Summary: This study compared the metabolic and transcriptomic profiles of Duroc and Luchuan pigs' longissimus dorsi muscle. The results showed that Luchuan pigs had lower levels of certain amino acids, organic acids and nucleic acids, bile acids and hormones, while higher levels of glycerophospholipids, fatty acids, oxidized lipids, alcohols, and amines. Transcriptome analysis also revealed upregulation of genes related to key energy metabolic pathways in Luchuan muscle, while downregulation of genes related to fatty acid oxidation and cholesterol synthesis.
FRONTIERS IN GENETICS
(2023)
Article
Food Science & Technology
Desalew Tadesse, Negussie Retta, Mekonnen Girma, Nicholas Ndiwa, Tadelle Dessie, Olivier Hanotte, Paulos Getachew, Dirk Dannenberger, Steffen Maak
Summary: This study investigated the effects of feeding flaxseed and plant polyphenol extracts on fatty acid content, oxidative stability, and lipid health indices in eggs. The results showed that the inclusion of flaxseed and moderate doses of plant polyphenol extracts significantly increased the content of n-3 polyunsaturated fatty acids in eggs and improved lipid health indices.
Article
Biodiversity Conservation
Endashaw Terefe, Gurja Belay, Abdulfatai Tijjani, Jianlin Han, Olivier Hanotte
Summary: This study analyzed the whole genome sequences of 151 samples from 14 Ethiopian indigenous cattle populations to assess genomic diversity, differentiation, and selection signatures. The results revealed high genomic differentiation between Ethiopian and non-Ethiopian cattle populations, as well as low differentiation and inbreeding within Ethiopian cattle populations. Furthermore, candidate genes associated with various biological functions and molecular pathways were identified in Ethiopian cattle.
Article
Multidisciplinary Sciences
Jani de Vos, Richard P. M. A. Crooijmans, Martijn F. L. Derks, Susan L. Kloet, Bert Dibbits, Martien A. M. Groenen, Ole Madsen
Summary: This paper aims to provide a molecular and epigenetic characterization of the IPEC-J2 and SL-29 cell lines, which are of interest for the FAANG community and future biomedical research. Whole genome sequencing, gene expression, DNA methylation, chromatin accessibility, and ChIP-seq were used to investigate these cell lines. Heteroploidy of various chromosomes was observed, and higher gene expression was found in genes located on aneuploid chromosomes compared to diploid chromosomes. Regulatory complexity of gene expression, DNA methylation, and chromatin accessibility was also explored.
Article
Biochemistry & Molecular Biology
Neal R. Benjamin, Richard P. M. A. Crooijmans, Luke R. Jordan, Courtni R. Bolt, Lawrence B. Schook, Kyle M. Schachtschneider, Martien A. M. Groenen, Alfred L. Roca
Summary: Suids, both domesticated and wild, provide valuable resources for humans and serve as models for biomedical research. Genome sequencing allows researchers to compare suids' genomes, aiding in understanding their evolution and distribution. Analyzing these samples may improve disease resistance and productivity in domestic suids and help conserve genetic diversity in wild and captive suids. Collecting samples is resource-intensive and can impact endangered populations. This study catalogs tissue and DNA samples from suids in Europe and North America, providing a centralized resource for researchers accessing published databases.
Biographical-Item
Biochemistry & Molecular Biology
Pablo Orozco-terWengel, Eric Coissac, Olivier Hanotte, Francois Pompanon, Paul Sunnucks, Pierre Taberlet
Article
Evolutionary Biology
Joanne C. Stonehouse, Lewis G. Spurgin, Veronika N. Laine, Mirte Bosse, Martien A. M. Great Tit HapMap Consortium, Martien A. M. Groenen, Kees van Oers, Ben C. Sheldon, Marcel E. Visser, Jon Slate
Summary: The unprecedented rate of climate change emphasizes the urgency of understanding how organisms can adapt. Great tits are an attractive model system for studying the genomics of climate adaptation. Through genome-environment analysis, 36 genes linked to climate adaptation were identified. Enrichment analysis revealed that climate adaptation is polygenic and genetically complex. The study also suggests that great tits have been adapting geographically to climate changes since the last ice age. Furthermore, substantial climate-associated genetic variation remains in contemporary great tit populations.
Article
Agriculture, Dairy & Animal Science
Zhou Wu, Mirte Bosse, Christina. M. M. Rochus, Martien A. M. Groenen, Richard P. M. A. Crooijmans
Summary: This study investigated the complex population structure and genomic impact of 37 traditional Dutch chicken breeds. The results showed that selective breeding and geographic distance were the main factors contributing to the complexity of the population structure, and identified genomic regions associated with phenotypic selection differences between breeds. Furthermore, a case study on a hybrid chicken breed provided insights into the genomic effects of crossbreeding.
GENETICS SELECTION EVOLUTION
(2023)
Article
Biology
Carolina P. Barros, Martijn F. L. Derks, Jeff Mohr, Benjamin J. Wood, Richard P. M. A. Crooijmans, Hendrik-Jan Megens, Marco C. A. M. Bink, Martien A. M. Groenen
Summary: In this study, a high-quality turkey genome was assembled using long-read technologies and chromatin interaction data. The new assembly showed improved completeness and continuity compared to the previous draft quality assembly, and structural variations and potential breeding target genes were identified.