Article
Biochemistry & Molecular Biology
Claudia Maria Hattinger, Chiara Casotti, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: This study investigated the relationship between SNPs and CDDP resistance in high-grade osteosarcoma cells, providing a basis for further research on the topic.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Pharmacology & Pharmacy
Chiara Casotti, Claudia Maria Hattinger, Maria Pia Patrizio, Silvia Luppi, Leonardo Fantoni, Michela Pasello, Katia Scotlandi, Toni Ibrahim, Massimo Serra
Summary: In this study, an innovative mmNGS approach was used to investigate SNPs associated with MTX resistance in HGOS cell lines. The results showed that allele changes in TP53, SLC19A1, and MTHFR were functionally involved in the development of MTX resistance. In addition, a fusion transcript of DHFR and MSH3 was identified in the cells with the highest MTX resistance level.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Agronomy
Rodrigo Contreras-Soto, Ariel Salvatierra, Carlos Maldonado, Jacob Mashilo
Summary: This study utilized SNP markers and SSR loci to determine genetic relationships and population structure in different accessions of bottle gourd, revealing low genetic differentiation between populations and a random mating system dominating inbreeding. The research identified two genetically distinct groups and highlighted the usefulness of the SNP markers in breeding programs for assessing genetic diversity and effective parental selection.
Article
Biochemistry & Molecular Biology
Lin Wang, Jixuan Yang, Hong Zhang, Qin Tao, Yuxin Zhang, Zhenyu Dang, Fengjun Zhang, Zewei Luo
Summary: Polyploidy plays a crucial role in plant evolution, but genotyping by sequencing (GBS) presents different challenges in diploid and polyploid species. This paper introduces statistical methods for predicting the sequence reads required for accurate GBS in polyploids and validates the theoretical predictions using RAD-seq data from tetraploid potato cultivars.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Jonas Schmidt, Sandro Berghaus, Frithjof Blessing, Holger Herbeck, Josef Blessing, Peter Schierack, Stefan Rodiger, Dirk Roggenbuck, Folker Wenzel
Summary: Nanopore sequencing has great potential for clinical diagnostics, but further validation and certification are required.
Article
Plant Sciences
Mao Yang, Jianbo He, Shubei Wan, Weiyan Li, Wenjing Chen, Yangming Wang, Xiaomei Jiang, Pengfei Cheng, Pu Chu, Wenbiao Shen, Rongzhan Guan
Summary: Plant height is an important trait in crop yield determination. Dwarf or semi-dwarf varieties are desirable in breeding due to their benefits in increasing harvest index, planting density, and lodging resistance. A new dwarf mutant Bndwarf2 in oilseed rape was studied, and a dwarf locus BnDWARF2 was mapped to a specific chromosome interval. This study identified a dominant dwarfing gene, BnaC04.BIL1, that negatively regulates plant height and may improve lodging resistance in oilseed rape.
Article
Biotechnology & Applied Microbiology
Dongjia Chen, Yan Xu, Chenhui Ding, Yali Wang, Yu Fu, Bing Cai, Jing Wang, Rong Li, Jing Guo, Jiafu Pan, Yanhong Zeng, Yiping Zhong, Xiaoting Shen, Canquan Zhou
Summary: This study compared the ability of two commonly used PGT-A platforms, NGS and SNP array, in detecting mosaic embryos. The results showed that the consistency of the two platforms in diagnosing embryo mosaicism is extremely low.
Article
Cell Biology
Yao Zhou, Xiaohui Yang, Zheng Liu, Yu Zhang, Huaye Chen, Yongfang Zhang, Yuxin Hu, Yanlin Ma, Qi Li
Summary: The study identified two novel mutations in the FREM2 gene related to the risk of Fraser syndrome, and described a next-generation sequencing-based single nucleotide polymorphism haplotyping method for selecting embryos from patients with Fraser syndrome for in vitro fertilization and embryo transfer treatment. This approach resulted in the successful delivery of a healthy baby without complications.
Article
Biochemical Research Methods
Dongjia Chen, Xiaoting Shen, Yan Xu, Bing Cai, Chenhui Ding, Yiping Zhong, Yanwen Xu, Canquan Zhou
Summary: Neurofibroma type 1 (NFI) is a genetic disease associated with cancer and cognitive dysfunction, posing challenges to preimplantation genetic testing (PGT) due to its 50% de novo mutation rate and numerous mutation types of the NF1 gene. A couple underwent next-generation sequencing (NGS)-based PGT, with biopsied trophectoderm samples undergoing whole-genome amplification and NGS to detect NF1 mutations and SNP analysis. A successful outcome resulted in obtaining unaffected and euploid blastocysts for transfer in a frozen-thawed embryo transfer (FET) cycle.
Article
Agricultural Engineering
Hussein Abdel-Haleem, Zinan Luo, Aaron Szczepanek
Summary: This study investigated the genetic diversity and relatedness in the USDA collection of Brassica juncea. By genotyping 340 samples, a total of 99030 high-quality SNP markers were identified. Population structure and PCA analysis revealed five distinct subpopulations, with the largest subpopulation traced back to Pakistan and India. The results demonstrated a high genetic diversity and genetic differentiation among subpopulations in the USDA collection of B. juncea.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Review
Plant Sciences
Stylianos Tympakianakis, Emmanouil Trantas, Evangelia V. V. Avramidou, Filippos Ververidis
Summary: The contribution of vine cultivation to human welfare and civilization has been significant, with a wide array of genetic variants used for cultivation. Understanding the origin and relationships among cultivars is of interest for phylogenetics and biotechnology. Molecular markers and next generation sequencing technologies have advanced the study of Vitis germplasm.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Congyan Li, Yuying Li, Jie Zheng, Zhiqiang Guo, Xiuli Mei, Min Lei, Yongjun Ren, Xiangyu Zhang, Cuixia Zhang, Chao Yang, Li Tang, Yang Ji, Rui Yang, Jifeng Yu, Xiaohong Xie, Liangde Kuang
Summary: This study analyzed rabbit traits using single-nucleotide polymorphism markers in genotyping-by-sequencing data. It identified genes associated with fur color and weight and provided a database for research and improvement of rabbit breeding program.
Article
Genetics & Heredity
Dongjia Chen, Yan Xu, Yu Fu, Yali Wang, Yuliang Liu, Chenhui Ding, Bing Cai, Jiafu Pan, Jing Wang, Rong Li, Jing Guo, Han Zhang, Yanhong Zeng, Xiaoting Shen, Canquan Zhou
Summary: This study evaluated the effectiveness of next generation sequencing (NGS)-based preimplantation genetic testing (PGT) for germline mosaicism. The NGS-SNP method successfully achieved PGT for two families with germline mosaicism. Compared with PCR methods, NGS-SNP method showed higher diagnostic accuracy.
ORPHANET JOURNAL OF RARE DISEASES
(2023)
Review
Biochemistry & Molecular Biology
Gladys G. Olivera, Andrea Urtasun, Luis Sendra, Salvador F. Alino, Yania Yanez, Vanessa Segura, Pablo Gargallo, Pablo Berlanga, Victoria Castel, Adela Canete, Maria Jose Herrero
Summary: Pharmacogenetics is essential in tailoring therapies for patients, especially in pediatric cancer and complex malignancies, to maximize efficacy and minimize toxicity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Shuwei Zhang, Chen Li, Zhiying Zhang, Yuchao Li, Qian Li, Fengxue Geng, Junchao Liu, Yaping Pan
Summary: This study identified differential expression of 3307 mRNAs and 522 lncRNAs in HIOECs infected with F. nucleatum, and investigated the potential functions of these dysregulated genes through GO and KEGG pathway analyses. The study identified top 10 hub genes involved in malignant transformation through protein-protein interaction network, and generated a co-expression network of dysregulated lncRNAs associated with hub genes.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2021)
Article
Plant Sciences
Yuefeng Ruan, Bianyun Yu, Ron E. Knox, Wentao Zhang, Asheesh K. Singh, Richard Cuthbert, Pierre Fobert, Ron DePauw, Samia Berraies, Andrew Sharpe, Bin Xiao Fu, Jatinder Sangha
Summary: In the genetic study of durum wheat in Canada, QTL mapping was conducted to identify loci associated with grain protein concentration (GPC). Several major and minor QTL were discovered on different chromosomes, with some being consistently detected across multiple years and showing potential for improving both GPC and grain yield. The results of traditional and conditional mapping provide valuable insights for the development of high GPC and high yielding durum cultivars.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Matthew G. Links, Tim J. Dumonceaux, E. Luke McCarthy, Sean M. Hemmingsen, Edward Topp, Jennifer R. Town
Summary: The study introduced a novel hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Results showed that CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility compared to 16S amplification, and provided greater depth of coverage and sensitivity of detection in natural ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health.
Article
Plant Sciences
Ti Zhang, Sally Vail, Hema S. N. Duddu, Isobel A. P. Parkin, Xulin Guo, Eric N. Johnson, Steven J. Shirtliffe
Summary: Phenotyping crop performance is crucial for plant breeding. Utilizing vegetation indices and aerial imagery from UAVs can effectively estimate canola flower numbers and develop models for predicting canola seed yield. The normalized difference yellowness index (NDYI) and flowering pixel numbers extracted from imagery over time show promise in predicting canola yield.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Peng Gao, Teagen D. Quilichini, Hui Yang, Qiang Li, Kirby T. Nilsen, Li Qin, Vivijan Babic, Li Liu, Dustin Cram, Asher Pasha, Eddi Esteban, Janet Condie, Christine Sidebottom, Yan Zhang, Yi Huang, Wentao Zhang, Pankaj Bhowmik, Leon Kochian, David Konkin, Yangdou Wei, Nicholas J. Provart, Sateesh Kagale, Mark Smith, Nii Patterson, C. Stewart Gillmor, Raju Datla, Daoquan Xiang
Summary: This study presents a comprehensive 3D transcriptome atlas for the six species of U's Triangle Brassicas, capturing gene expression data for the major subcompartments of seed development. Comparisons of gene expression reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species during seed development. The study provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species.
Article
Plant Sciences
Deirdre Khan, Dylan J. Ziegler, Jenna L. Kalichuk, Vanessa Hoi, Nina Huynh, Abolfazl Hajihassani, Isobel A. P. Parkin, Stephen J. Robinson, Mark F. Belmonte
Summary: The study analyzed the global gene expression landscape of Brassica napus throughout its reproductive lifecycle, revealing the contributions of each subgenome to plant reproduction and identifying BZIP11 as a transcriptional regulator of early seed development. Subgenome-specific transcription factor networks enriched in distinct transcription factor families were found in the A(n) and C-n subgenomes early in seed development. Subgenome bias was observed in gene expression throughout seed development, with regulators encoded by the A(n) subgenome primarily expressed in the seed coat and those encoded by the C-n subgenome primarily in the embryo.
Article
Plant Sciences
Jordan Ubbens, Isobel Parkin, Christina Eynck, Ian Stavness, Andrew G. Sharpe
Summary: Genomic prediction is a promising technology for breeding, with deep neural networks potentially better at capturing complex genetic effects but still not outperforming classical linear methods. Research suggests that deep neural networks may rely more on overall genetic relatedness rather than the effects of specific markers for prediction.
Article
Plant Sciences
Jana Ebersbach, Nazifa Azam Khan, Ian McQuillan, Erin E. Higgins, Kyla Horner, Venkat Bandi, Carl Gutwin, Sally Lynne Vail, Steve J. Robinson, Isobel A. P. Parkin
Summary: Phenotyping is important for crop improvement. This study assesses the feasibility of using high-throughput phenotyping, image processing, and machine learning to capture the phenotypic diversity of agronomically important traits in Brassica napus. The results demonstrate the potential of machine learning for phenotyping studies, particularly for complex traits such as drought stress resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Lawrence E. Bramham, Tongtong Wang, Erin E. Higgins, Isobel A. P. Parkin, Guy C. Barker, John A. Walsh
Summary: Two Brassica juncea lines with resistance against important TuMV isolates were identified and characterized. QTL analyses were performed using genetic mapping populations segregating for TuMV resistance, and statistically significant resistance-associated loci were identified on chromosomes A03 and A06. The reductive screening strategy employed in this study offers an alternative method for QTL mapping.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Azam Nikzad, Berisso Kebede, Swati Megha, Miles Buchwaldt, Isobel Parkin, Habibur Rahman
Summary: A GWAS was conducted using a B. napus population developed from interspecific crosses and SNP markers to identify QTLs for agronomic and seed quality traits. The heritability of these traits ranged from 52.9% to 84.1%. The majority of the SNPs were located on the C genome chromosomes, indicating little genetic variation in the A genome. Several novel QTL regions and potential candidate genes were discovered, highlighting the utility of the B. oleracea gene pool for breeding and QTL identification in B. napus.
Article
Plant Sciences
Peng Gao, Shuqing Qiu, Xingliang Ma, Isobel A. P. Parkin, Daoquan Xiang, Raju Datla
Summary: In this study, the researchers used high-throughput RNA-sequencing methods to investigate the gene expression profiles during the key reproductive phase of flax, providing new insights into the molecular mechanisms of seed development. The co-expression networks and functional analysis revealed pathways involved in the development of different tissues, and essential genes for embryo development and synthesis of storage reserves were identified. These findings have potential implications for improving flax crops.
Article
Plant Sciences
Dwayne Hegedus, Cathy Coutu, Branimir Gjetvaj, Abdelali Hannoufa, Myrtle Harrington, Sara Martin, Isobel A. P. Parkin, Suneru Perera, Janitha Wanasundara
Summary: Genetic variation in seed protein composition, gene expression, and physiochemical properties were found in C. sativa and other Camelina species. Four different types of cruciferins were identified in C. sativa, each with unique functional properties. This study provides opportunities to create C. sativa cultivars with tailored seed protein profiles for specific technical applications.
Article
Multidisciplinary Sciences
Emily K. Murphy, Eduardo P. Cappa, Raju Y. Soolanayakanahally, Yousry A. El-Kassaby, Isobel A. P. Parkin, William R. Schroeder, Shawn D. Mansfield
Summary: In this study, the genetic diversity and population structure of two willow species in Canada were analyzed, leading to the identification of five main clusters and the determination of geoclimatic factors as major influences. The study also revealed that the highest genetic variation occurred within genotypes. These findings provide valuable insights for willow breeding programs in Canada.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Raju Chaudhary, Chu Shin Koh, Sampath Perumal, Lingling Jin, Erin E. Higgins, Sateesh Kagale, Mark A. Smith, Andrew G. Sharpe, Isobel A. P. Parkin
Summary: This study analyzed the genome sequence of Camelina neglecta and its relationship with Camelina sativa, providing insights into the evolution of the hexaploid genome of C. sativa.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Agronomy
Mikolaj Cieslak, Nazifa Khan, Pascal Ferraro, Raju Soolanayakanahally, Stephen J. Robinson, Isobel Parkin, Ian McQuillan, Przemyslaw Prusinkiewicz
Summary: This article discusses the potential of using artificial neural networks to recognize and quantify relevant aspects of crop plants in image-based phenomics. The authors propose that realistic plant models, which can be automatically annotated, serve as an attractive alternative to real plant images for training purposes. The construction and calibration of such models are demonstrated using maize and canola as case studies.
Article
Plant Sciences
Zhesi He, Ruiqin Ji, Lenka Havlickova, Lihong Wang, Yi Li, Huey Tyng Lee, Jiaming Song, Chushin Koh, Jinghua Yang, Mingfang Zhang, Isobel A. P. Parkin, Xiaowu Wang, David Edwards, Graham J. King, Jun Zou, Kede Liu, Rod J. Snowdon, Surinder S. Banga, Ivana Machackova, Ian Bancroft
Summary: Correcting organizational errors of the Brassica A, B and C genomes reveals the conserved structure of each genome across species and genome evolutionary pathways. Genus-wide pan-genomes were constructed, helping to elucidate the genomic impacts of alien introgressions.