Article
Genetics & Heredity
Caihui Wang, Bo Liu, Min Chen, Junhao Ning, Xia Lu, Chunde Wang
Summary: Treating fertilized eggs with 20 mM EMS for 3 hours induced 9 times more mutations in scallop genomes, with mutations in MFS and Tubulin potentially related to fast growth in large-sized scallops, and mutations in Homeobox and SOCs potentially associated with slow growth in small-sized scallops. EMS shows promise in accelerating the selection of economically important traits in molluscs.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Huancheng Fu, Ce Shan, Fanchen Kang, Ling Yu, Zhonghan Li, Yike Yin
Summary: CRISPR-GRANT is a user-friendly tool for CRISPR indel analysis, allowing laboratory scientists to easily analyze genome editing events from large sequencing datasets, making it accessible for novices.
BMC BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Marie A. Brunet, Sebastien Leblanc, Xavier Roucou
Summary: OpenVar is a genomic variant annotator that integrates non-canonical open reading frames (ORFs) in the analysis of genomic variants, allowing researchers to better understand the genotype-phenotype relationships.
CELL AND BIOSCIENCE
(2022)
Article
Multidisciplinary Sciences
Xinyu Xu, Bihua Chen, Juan Zhang, Siren Lan, Shasha Wu
Summary: This study evaluated the genomic characteristics of Gardenia jasminoides by re-sequencing wild and cultivated materials. The results showed that Gardenia jasminoides has rich genetic diversity and identified numerous SNPs and other gene variations. Additionally, the study further explored gene variations in the biosynthetic pathway of the main medicinal substances in Gardenia jasminoides.
Article
Agronomy
Xiaochun Wei, Md Abdur Rahim, Yanyan Zhao, Shuangjuan Yang, Henan Su, Zhiyong Wang, Saleh Ahmed Shahriar, Jundang Li, Zhiyuan Yang, Yuxiang Yuan, Xiaowei Zhang
Summary: This study investigated the genetic characteristics of late-bolting Chinese cabbage through genetic analysis and whole genome re-sequencing. It identified a gene that controls the late-bolting trait and discovered multiple genetic variations within the candidate interval. Additionally, three potential candidate genes were found. These findings are of great importance for marker-assisted breeding of Chinese cabbage.
Article
Genetics & Heredity
Bartosz Ulaszewski, Joanna Meger, Bagdevi Mishra, Marco Thines, Jaroslaw Burczyk
Summary: Advances in genomics technology have allowed for in-depth exploration of organelle genomics, with this study specifically focusing on the genetic diversity of European beech based on complete chloroplast genomes. The research confirmed low cpDNA diversity in European beech and identified polymorphic markers mainly in single copy regions, suggesting efficient suppression of mutation. Additionally, phylogeographic analysis indicated clustering of individuals based on geographic distance, indicating potential sources of diversity from nuclear-encoded plastome remnants.
Article
Biotechnology & Applied Microbiology
Juanjuan Feng, Xuexian Zhang, Meng Zhang, Liping Guo, Tingxiang Qi, Huini Tang, Haiyong Zhu, Hailin Wang, Xiuqin Qiao, Chaozhu Xing, Jianyong Wu
Summary: This study successfully located the restore gene Rf(2) within a candidate interval of 1.48Mb on chromosome D05 by investigating fertility ratios, using BSA resequencing technology, high-throughput SNP genotyping, and InDel markers. The study also found that InDel markers co-segregated with Rf(2), enhancing the selection of the restorer line.
Article
Biochemical Research Methods
Wei Quan, Bo Liu, Yadong Wang
Summary: This study introduces SALT, an SNP-aware alignment tool that efficiently maps reads to a reference genome incorporating an SNP database, resulting in improved accuracy. Experimental results demonstrate the superior performance of SALT in read alignment accuracy.
BMC BIOINFORMATICS
(2021)
Article
Biodiversity Conservation
Meile Sun, Xiangrong Ren, Ya Liu, Jing Yang, Jingtao Hui, Yukun Zhang, Yanhua Cui, Jun Zhang, Guocang Lin, Yan Li
Summary: In this study, the genetic structure of 57 rose cultivars and one wild species with different scents was evaluated through whole genome re-sequencing. The study revealed that the genetic background of roses is complex and can be divided into three main clusters. Genes related to fatty acid derivatives, terpenoids, and benzenoids/phenylpropanoids showed positive selection in rose cultivars with strong fragrance.
Article
Genetics & Heredity
Wen Zhang, Xiao Yan Zhao, Jie Wu, Ling Jin, Jianjian Lv, Baoquan Gao, Ping Liu
Summary: This study used Bulked Segregant Analysis (BSA) to screen molecular markers associated with salt-alkali tolerance trait in Portunus trituberculatus. Through this analysis, 20 markers were successfully validated and eight candidate genes related to salt-alkali tolerance were identified. qPCR results confirmed the important role of these genes in salt-alkali adaptation.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Zhen Wang, Ruolan Wang, Chuanying Pan, Hong Chen, Lei Qu, Lian Wu, Zhengang Guo, Haijing Zhu, Xianyong Lan
Summary: Dynein Axonemal Heavy Chain 1 (DNAH1) encodes proteins that are crucial for the structural support and function of sperm and ova. This study identified several genetic variations within DNAH1 that were significantly associated with litter size in Shaanbei white cashmere goats. These genetic variations can be used as molecular markers for selecting reproductive traits in goats.
Article
Plant Sciences
Wenchao Zhang, Yun Kang, Xiaofei Cheng, Jiangqi Wen, Hongying Zhang, Ivone Torres-Jerez, Nick Krom, Michael K. Udvardi, Wolf-Rudiger Scheible, Patrick Xuechun Zhao
Summary: HapMap projects provide valuable genetic resources for life science research, but the validation of individuals is necessary before conducting GWAS analyses, and there are currently no existing methods to distinguish multiple individuals in a HapMap population effectively.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Apurba Anirban, Ardashir Kharabian Masouleh, Robert J. Henry, Tim J. O'Hare
Summary: A novel purple-pericarp super-sweetcorn line, 'Tim1' (A1A1.sh2sh2), was derived from the purple-pericarp maize 'Costa Rica' and white shrunken2 (sh2) super-sweetcorn 'Tims-white'. The differences in the CDS and promoter regions of anthocyanin biosynthesis and sweetcorn genes were investigated, revealing that the purple-sweet line is different to the yellow-nonsweet reference line in both anthocyanin biosynthesis and sweetcorn genes.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Medical Laboratory Technology
Matthijs Vynck, Friedel Nollet, Lode Sibbens, Helena Devos
Summary: The study suggests that screening at least 40 biallelic markers is necessary to achieve enough informative markers. There is room for optimization in current chimerism assays, and more effective assays can be designed through support of the introduced simulation framework.
CLINICA CHIMICA ACTA
(2022)
Article
Multidisciplinary Sciences
Marco Antonio Perpetuo de Sousa, Flavia Regina Florencio de Athayde, Mariangela Bueno Cordeiro Maldonado, Andressa Oliveira de Lima, Marina Rufino S. Fortes, Flavia Lombardi Lopes
Summary: The study found that approximately 71.6% of the predicted miRNA targets were altered as a result of SNPs located within the seed region of the mature miRNAs, potentially affecting miRNA maturation. Analysis revealed that 48.6% of the sequences had values sufficient enough to alter miRNA maturation.
Article
Genetics & Heredity
Aniek C. Bouwman, Hans D. Daetwyler, Amanda J. Chamberlain, Carla Hurtado Ponce, Mehdi Sargolzaei, Flavio S. Schenkel, Goutam Sahana, Armelle Govignon-Gion, Simon Boitard, Marlies Dolezal, Hubert Pausch, Rasmus F. Brondum, Phil J. Bowman, Bo Thomsen, Bernt Guldbrandtsen, Mogens S. Lund, Bertrand Servin, Dorian J. Garrick, James Reecy, Johanna Vilkki, Alessandro Bagnato, Min Wang, Jesse L. Hoff, Robert D. Schnabel, Jeremy F. Taylor, Anna A. E. Vinkhuyzen, Frank Panitz, Christian Bendixen, Lars-Erik Holm, Birgit Gredler, Chris Hoze, Mekki Boussaha, Marie-Pierre Sanchez, Dominique Rocha, Aurelien Capitan, Thierry Tribout, Anne Barbat, Pascal Croiseau, Cord Drogemuller, Vidhya Jagannathan, Christy Vander Jagt, John J. Crowley, Anna Bieber, Deirdre C. Purfield, Donagh P. Berry, Reiner Emmerling, Kay-Uwe Goetz, Mirjam Frischknecht, Ingolf Russ, Johann Soelkner, Curtis P. Van Tassell, Ruedi Fries, Paul Stothard, Roel F. Veerkamp, Didier Boichard, Mike E. Goddard, Ben J. Hayes
Article
Multidisciplinary Sciences
Lingzhao Fang, Peter Sorensen, Goutam Sahana, Frank Panitz, Guosheng Su, Shengli Zhang, Ying Yu, Bingjie Li, Li Ma, George Liu, Mogens Sando Lund, Bo Thomsen
SCIENTIFIC REPORTS
(2018)
Article
Evolutionary Biology
Andres Chana-Munoz, Agnieszka Jendroszek, Malene Sonnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Bendixen, Frank Panitz
BMC EVOLUTIONARY BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Agnieszka Jendroszek, Jeppe B. Madsen, Andres Chana-Munoz, Daniel M. Dupont, Anni Christensen, Frank Panitz, Ernst-Martin Fuchtbauer, Simon C. Lovell, Jan K. Jensen
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Correction
Multidisciplinary Sciences
Einar E. Nielsen, Alessia Cariani, Eoin Mac Aoidh, Gregory E. Maes, Ilaria Milano, Rob Ogden, Martin Taylor, Jakob Hemmer-Hansen, Massimiliano Babbucci, Luca Bargelloni, Dorte Bekkevold, Eveline Diopere, Leonie Grenfell, Sarah Helyar, Morten T. Limborg, Jann T. Martinsohn, Ross McEwing, Frank Panitz, Tomaso Patarnello, Fausto Tinti, Jeroen K. J. Van Houdt, Filip A. M. Volckaert, Robin S. Waples, Jan E. J. Albin, Juan M. Vieites Baptista, Vladimir Barmintsev, Jose M. Bautista, Christian Bendixen, Jean-Pascal Berge, Dietmar Blohm, Barbara Cardazzo, Amalia Diez, Montserrat Espineira, Audrey J. Geffen, Elena Gonzalez, Nerea Gonzalez-Lavin, Ilaria Guarniero, Marc Jerome, Marc Kochzius, Grigorius Krey, Olivier Mouchel, Enrico Negrisolo, Corrado Piccinetti, Antonio Puyet, Sergey Rastorguev, Jane P. Smith, Massimo Trentini, Veronique Verrez-Bagnis, Alexander Volkov, Antonella Zanzi, Mark de Bruyn, Gary R. Carvalho
NATURE COMMUNICATIONS
(2019)
Article
Biology
Weiwen Wang, Ashutosh Das, David Kainer, Miriam Schalamun, Alejandro Morales-Suarez, Benjamin Schwessinger, Robert Lanfear
Article
Agriculture, Dairy & Animal Science
Ashutosh Das, Mishuk Shaha, Mukta Das Gupta, Avijit Dutta, Omar Faruk Miazi
Summary: This study explored genetic markers associated with prolificacy in the indigenous Black Bengal goat breed in Bangladesh, focusing on the genes BMP15 and GDF9. Significant associations were found between certain SNP loci in these genes and litter size, as well as a highly significant impact of parity on litter size. Further research with genetically unrelated animals is recommended to assess the potential association of these loci with fecundity genes and litter size.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2021)
Article
Agriculture, Dairy & Animal Science
Mishuk Shaha, Gous Miah, Arjuman Lima, Omar Faruk Miazi, Mukta Das, Ashutosh Das
Summary: The associations between polymorphisms in the GDF9 and BMP15 genes and litter size were investigated in Jamunapari and crossbred goats in Bangladesh. Four SNPs in GDF9 and three SNPs in BMP15 were identified. The G1330T locus was found to have a significant difference in litter size in Jamunapari goats. This finding suggests that the G1330T locus could be used as a marker for litter size traits in goats in Bangladesh.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2022)
Article
Veterinary Sciences
Mukta Das Gupta, Arup Sen, Mishuk Shaha, Avijit Dutta, Ashutosh Das
Summary: This study is the first to reveal a substantial percentage of antimicrobial-resistant STEC isolated from sheep in rural Bangladesh.
VETERINARY MEDICINE AND SCIENCE
(2022)
Article
Microbiology
Vienna Kowallik, Ashutosh Das, Alexander S. Mikheyev
Summary: Microbiomes can enhance the health and evolutionary potential of hosts, but can be disrupted by stressors like antibiotics, leading to harm to host's progeny.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Dan Hao, Xiao Wang, Yu Yang, Hong Chen, Bo Thomsen, Lars-Erik Holm
Summary: In this study, SNPs in bovine miRNAs were detected using whole-genome re-sequencing data from 1632 cattle. A total of 1109 SNPs in the precursor region, 334 SNPs in the mature region, and 130 SNPs in the seed region were identified. Most SNPs were in Hardy-Weinberg equilibrium and SNPs in the seed region altered the repertoire of target genes, which were enriched in different pathways or functional annotations.
Article
Agriculture, Dairy & Animal Science
J. Noor, M. K. Khan, M. M. Momin, A. Das, D. Wright, M. Alvarez-Rodriguez, H. Rodriguez-Martinez
Summary: This study investigated the effect of PMEL17 plumage color gene diversity on the production performance of indigenous chicken varieties, finding that the spotted-single-round chicken had the highest live weight and egg production. The study also observed differences in external and internal egg characteristics between varieties, with the spotted- single-round variety being superior. Additionally, mutations in the PMEL17 gene were found in brownish and black-white chicken varieties at specific nucleotide positions.
INDIAN JOURNAL OF ANIMAL RESEARCH
(2021)
Article
Agriculture, Dairy & Animal Science
Md. Iqbal Hossain, Md. Kabirul Islam Khan, Md. Moksedul Momin, Asuthosh Das
JOURNAL OF APPLIED ANIMAL RESEARCH
(2020)
Article
Agriculture, Dairy & Animal Science
Mukta Das Gupta, Arup Sen, Ashutosh Das