Article
Plant Sciences
Jiri Cerven, Viktor Vrbovsky, Jiri Horacek, Martin Bartas, Lenka Endlova, Petr Pecinka, Vladislav Curn
Summary: This paper presents the breeding technology of new low morphine poppy genotypes using a combination of TILLING approach and single-molecule real-time NGS sequencing. Mutants in the TILLING population were verified using RT-PCR and HPLC methods. Only three out of eleven genes in the morphine pathway were used for identifying mutant genotypes. Point mutations were found in one gene (CNMT) and an insertion in another gene (SalAT). Expected transition SNPs from G:C to A:T were obtained. The production of morphine in the low morphine mutant genotype decreased to 0.1% from 1.4% in the original variety. The paper also provides a comprehensive description of the breeding process, basic characterization of main alkaloid content, and gene expression profile for the main alkaloid-producing genes. Difficulties with the TILLING approach are discussed.
Review
Biotechnology & Applied Microbiology
Dharmendra Singh, Priya Chaudhary, Jyoti Taunk, Chandan Kumar Singh, Viswanathan Chinnusamy, Amitha Mithra Sevanthi, Vikram Jeet Singh, Madan Pal
Summary: Conventional crop breeding alone cannot solve global hunger, but the development of high throughput reverse genetics approaches, such as TILLING, has greatly benefited plant breeding programs. TILLING employs mutagenesis to create new genetic sources and identify superior alleles. Modifications to the original TILLING protocol, such as EcoTILLING and De-TILLING, have widened its applicability to different crops. Combining next generation sequencing with TILLING allows for efficient screening of germplasm collections and mutant populations.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Review
Plant Sciences
Raman Selvakumar, Gograj Singh Jat, Dalasanuru Chandregowda Manjunathagowda
Summary: The article provides a comprehensive overview of allele mining and allele exploration methods for genetic improvement in vegetable crops. By exploiting wild resources and employing genomic tools, novel alleles can be discovered from genetic stocks and introgressed into cultivated types to enhance economic traits. Allele mining, as a sophisticated technique, is useful for identifying naturally occurring allelic variants in candidate genes that influence important traits. TILLINGs and EcoTILLING, which are mutation detection avenues, are particularly valuable when genomic sequence information is limited or not available.
Article
Genetics & Heredity
Juanita Gil, Juan Sebastian Andrade-Martinez, Jorge Duitama
Summary: TILLING is a powerful reverse genetics method used in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. However, the main issue lies in the fact that current bioinformatics tools are not designed to detect low frequency mutations in pooled samples or assign variants detected in overlapping pools to individual samples.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Arianna Frittelli, Ermelinda Botticella, Samuela Palombieri, Stefania Masci, Silvia Celletti, Maria Chiara Fontanella, Stefania Astolfi, Pasquale De Vita, Mirko Volpato, Francesco Sestili
Summary: Micronutrient malnutrition affects more than half of the world population. The reduced bioavailability of microelements in raw materials is a major cause of mineral deficiency in populations who mainly consume staple crops. The production of low phytic acid (lpa) cereals is a goal of breeding programs to improve nutritional value. Targeting Induced Local Lesions IN Genomes (TILLING) has been used to silence genes involved in the accumulation of phytic acid in durum wheat, leading to increased micronutrient content. These mutant lines show promising potential for obtaining durum wheats with higher nutritional value.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Environmental Sciences
Kexin Song, Wengang Du, Xiaona Ma, Yangjun Chen, Yixin Sun, Tao Zhang, Wei Huang, Zhihua Feng
Summary: Microplastics in fish pose risks to ecology and food safety. This study investigated the characteristics of microplastics in fugu and found that over 98.85% of fugu were contaminated by microplastics. Wild fugu had a lower abundance of microplastics compared to cultured fugu, and the abundance of microplastics varied among different tissues and life patterns.
MARINE POLLUTION BULLETIN
(2022)
Article
Multidisciplinary Sciences
Pin Xu, Kazuhiro Shimomura, Changhoon Lee, Xiaofei Gao, Eleanor H. Simpson, Guocun Huang, Chryshanthi M. Joseph, Vivek Kumar, Woo-Ping Ge, Karen S. Pawlowski, Mitchell D. Frye, Said Kourrich, Eric R. Kandel, Joseph S. Takahashi
Summary: Through in vivo mutagenesis screening, researchers identified a mutation in the Kcnc3 gene that leads to spatial learning deficits. Further investigation revealed that this mutation results in the loss of function in voltage-gated potassium channels, affecting conductance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Plant Sciences
Miriam Szurman-Zubrzycka, Marzena Kurowska, Bradley J. Till, Iwona Szarejko
Summary: Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Congcong Jiang, Miaomiao Lei, Yu Guo, Guangqi Gao, Lijie Shi, Yanlong Jin, Yu Cai, Axel Himmelbach, Shenghui Zhou, Qiang He, Xuefeng Yao, Jinhong Kan, Georg Haberer, Fengying Duan, Lihui Li, Jun Liu, Jing Zhang, Manuel Spannagl, Chunming Liu, Nils Stein, Zongyun Feng, Martin Mascher, Ping Yang
Summary: In this study, we created an EMS-mutagenized population of barley and established a highly efficient and cost-effective TILLING platform using a three-dimensional DNA pooling strategy and multiplexed amplicon sequencing. We successfully identified abundant allelic mutants for various genes, including the BRI1 gene. Additionally, we demonstrated the value of this resource by rapidly determining the causal gene responsible for a chlorotic mutant.
PLANT COMMUNICATIONS
(2022)
Article
Fisheries
Qian Li, Hong Yu, Qi Li
Summary: Genome editing using CRISPR/Cas9 methodology holds great potential for improving aquaculture, but the screening and identification of successfully edited individuals remains challenging. In this study, we developed and optimized a high-resolution melting analysis (HRM) assay to rapidly screen and identify CRISPR/Cas9-edited oysters. The HRM assay showed sensitivity in detecting temperature shifts and successfully identified oysters with indel mutations. This reproducible, sensitive, and efficient method has the potential to accelerate genetic improvement in aquaculture.
Article
Chemistry, Multidisciplinary
Anthoula Gleridou, Ioannis Tokatlidis, Alexios Polidoros
Summary: Genetic differentiation among 40 lentil genotypes was tested using molecular markers. Results showed low variation among consecutive generations produced via honeycomb breeding methodology. Molecular analysis revealed that the variation was higher within each generation's population than between them. Population structure analysis indicated that ongoing selection could effectively alter the allelic composition in each generation.
APPLIED SCIENCES-BASEL
(2022)
Article
Multidisciplinary Sciences
Darui Xu, Stephen Lyon, Chun Hui Bu, Sara Hildebrand, Jin Huk Choi, Xue Zhong, Aijie Liu, Emre E. Turer, Zhao Zhang, Jamie Russell, Sara Ludwig, Elena Mahrt, Evan Nair-Gill, Hexin Shi, Ying Wang, Duanwu Zhang, Tao Yue, Kuan-wen Wang, Jeffrey A. SoRelle, Lijing Su, Takuma Misawa, William McAlpine, Lei Sun, Jianhui Wang, Xiaoming Zhan, Mihwa Choi, Roxana Farokhnia, Andrew Sakla, Sara Schneider, Hannah Coco, Gabrielle Coolbaugh, Braden Hayse, Sara Mazal, Dawson Medler, Brandon Nguyen, Edward Rodriguez, Andrew Wadley, Miao Tang, Xiaohong Li, Priscilla Anderton, Katie Keller, Amanda Press, Lindsay Scott, Jiexia Quan, Sydney Cooper, Tiffany Collie, Baifang Qin, Jennifer Cardin, Rochelle Simpson, Meron Tadesse, Qihua Sun, Carol A. Wise, Jonathan J. Rios, Eva Marie Y. Moresco, Bruce Beutler
Summary: The study uses machine-learning software called Candidate Explorer (CE) to identify mutations causing immune phenotypes in mice and has found that over half of the genes may be responsible for this variation. Many of these genes were not previously known to be related to immune function or homeostasis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Jia-Ping Wan, Zheng Wang, Cao-Xu Zhang, Ya Fang, Liu Yang, Chen-Yan Yan, Feng-Yao Wu, Shuang-Xia Zhao, Huai-Dong Song, Mei Dong
Summary: The origin and regulation of thyroid follicular cells are essential for understanding developmental disorders and diseases. A zebrafish model was used to screen for genes involved in thyroid follicular cell development and function. Through an ENU-based mutagenesis screen, 112 mutant families with thyroid dysfunction were identified. Further studies on these mutants will provide insights into thyroid development and function in zebrafish and vertebrates.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Plant Sciences
Natsume Koshika, Naohiro Shioya, Takashi Fujimura, Rina Oguchi, Chie Ota, Emi Kato, Reiko Takahashi, Shuichi Kimura, Shinsuke Furuno, Koichi Saito, Kazuhiro Okabe, Masanori Watanabe, Tomoki Hoshino
Summary: Induced mutation is an effective breeding strategy widely used in the development of elite plant varieties. In this study, a novel mutant population of soybeans was constructed using ethyl methanesulfonate to improve the variety of edamame. The TILLING method was employed to identify DNA mutations in the mutant populations, leading to the discovery of mutants with early flowering and harvest dates. These mutants can serve as DNA markers and are detectable using high-resolution melting analysis.
Article
Genetics & Heredity
Sophie Jamet, Seungshin Ha, Tzu-Hua Ho, Scott Houghtaling, Andrew Timms, Kai Yu, Alison Paquette, Ali Murat Maga, Nicholas D. E. Greene, David R. Beier
Summary: By performing ENU mutagenesis in mice and screening for mutations affecting embryonic development, we discovered a mutation in the Carm1 gene that is implicated in heart development defects. Our study found that Carm1 mutant mice exhibit various cardiac defects, including cardiac rupture, hemorrhaging, and different types of heart defects. Transcriptome analysis revealed the dysregulation of several genes involved in cardiac morphogenesis and muscle development and function.
G3-GENES GENOMES GENETICS
(2022)
Article
Fisheries
Hiroyuki Yoshikawa, Yasuko Ino, Kouhei Shigenaga, Takashi Katayama, Miwa Kuroyanagi, Yasutoshi Yoshiura
Article
Fisheries
Takayoshi Matsunaga, Risa Ieda, Sho Hosoya, Miwa Kuroyanagi, Shigenori Suzuki, Hiroaki Suetake, Satoshi Tasumi, Yuzuru Suzuki, Toshiaki Miyadai, Kiyoshi Kikuchi
Article
Fisheries
Kenta Kishimoto, Youhei Washio, Yu Murakami, Takashi Katayama, Miwa Kuroyanagi, Keitaro Kato, Yasutoshi Yoshiura, Masato Kinoshita
Article
Genetics & Heredity
Dong In Kim, Wataru Kai, Sho Hosoya, Mana Sato, Aoi Nozawa, Miwa Kuroyanagi, Yuka Jo, Satoshi Tasumi, Hiroaki Suetake, Yuzuru Suzuki, Kiyoshi Kikuchi
Article
Biochemistry & Molecular Biology
M Kuroyanagi, K Yamada, N Hatsugai, M Kondo, M Nishimura, I Hara-Nishimura
JOURNAL OF BIOLOGICAL CHEMISTRY
(2005)
Review
Plant Sciences
I Hara-Nishimura, N Hatsugai, S Nakaune, M Kuroyanagi, M Nishimura
CURRENT OPINION IN PLANT BIOLOGY
(2005)
Article
Multidisciplinary Sciences
N Hatsugai, M Kuroyanagi, K Yamada, T Meshi, S Tsuda, M Kondo, M Nishimura, I Hara-Nishimura
Article
Biochemistry & Molecular Biology
T Shimada, K Yamada, M Kataoka, S Nakaune, Y Koumoto, M Kuroyanagi, S Tabata, T Kato, K Shinozaki, M Seki, M Kobayashi, M Kondo, M Nishimura, I Hara-Nishimura
JOURNAL OF BIOLOGICAL CHEMISTRY
(2003)
Article
Biochemistry & Molecular Biology
M Kuroyanagi, E Shimamura, M Kim, N Arakawa, Y Fujiwara, M Otsuka
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2002)
Article
Biochemistry & Molecular Biology
E Watanabe, T Shimada, M Kuroyanagi, M Nishimura, I Hara-Nishimura
JOURNAL OF BIOLOGICAL CHEMISTRY
(2002)
Article
Plant Sciences
M Kuroyanagi, M Nishimura, I Hara-Nishimura
PLANT AND CELL PHYSIOLOGY
(2002)
Review
Biochemistry & Molecular Biology
N. Hatsugai, M. Kuroyanagi, M. Nishimura, I. Hara-Nishimura