Review
Biochemical Research Methods
Koki Hayashi, Saleh Alseekh, Alisdair R. Fernie
Summary: Plant metabolites are primarily produced through enzymatic reactions encoded by genes in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by affecting enzyme activity or abundance. Insertion of transposable elements into non-coding regions can also impact transcription and metabolite content. Epigenetic variations, both transgenerational and non-transgenerational, have been found to control metabolism by regulating gene transcription. However, the role of epigenetics in metabolic control has been relatively understudied.
Article
Plant Sciences
Erwin Tandayu, Priyakshee Borpatragohain, Ramil Mauleon, Tobias Kretzschmar
Summary: This study dissected the genetic architecture of glucosinolate (GSL) content in Indian mustard and identified several candidate genes associated with total GSL content and the content of two major GSLs. The results provide a comprehensive map of the genetic control of GSL biosynthesis in Indian mustard.
Review
Plant Sciences
Kaoru Tonosaki, Ryo Fujimoto, Elizabeth S. S. Dennis, Victor Raboy, Kenji Osabe
Summary: It has been shown that both DNA sequence diversity and epigenetic diversity can contribute to increased phenotypic diversity. Epigenetics bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding, leading to successful outcomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Christine Sambles, Marta Suarez-Fernandez, Federico Lopez-Moya, Luis Vicente Lopez-Llorca, David J. Studholme
Summary: In this study, the genome sequence assembly of P. chlamydosporia 123 was improved using long-read PacBio sequencing, and alternative splicing of the chitosanase 3 encoding gene was discovered. Chitosan significantly increased the expression of cns3, and the putatively encoded enzyme is likely important for chitosan degradation.
Article
Plant Sciences
Zifeng Ouyang, Yimeng Wang, Tiantian Ma, Gisele Kanzana, Fan Wu, Jiyu Zhang
Summary: This study utilized LTR retrotransposon-based markers to analyze the genetic diversity and population structure of Melilotus. A high amount of LTR retrotransposon sequences were identified, and 350 pairs of primers were designed for assessing polymorphisms. The transferable primers showed high informativeness, with 292 alleles detected at 47 LTR retrotransposon loci. The results provide important data for future breeding programs and implementing genetic improvements in the Melilotus genus.
Article
Multidisciplinary Sciences
Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A. Doudna
Summary: The fusion of PRDM9 and Cas9 in CRISPR-Cas genome editing can increase the efficiency of homology-directed repair (HDR) and avoid off-target editing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biophysics
Karola Gerecht, Niklas Freund, Wei Liu, Yang Liu, Maximilian J. L. J. Furst, Philipp Holliger
Summary: Synthetic biology aims to explore fundamental aspects of biological form and function by constructing and synthesizing rather than deconstructing and analyzing. It follows the lead of chemical sciences and provides novel approaches to answer biological questions and find solutions to global problems. This review focuses on the synthesis paradigm applied to nucleic acids in biological systems, including genome resynthesis, synthetic genetics, and the development of orthogonal biosystems and components.
ANNUAL REVIEW OF BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Eun Yu Kim, Kyung Do Kim, Jungnam Cho
Summary: This article discusses the important role of epigenetic mechanisms in plant biological processes and the concept of epigenetic breeding in crop improvement. Various methods, including chemical drug treatment, tissue culture, and CRISPR-Cas9 technology, have been used to induce methylome changes in plants, providing possibilities for epigenetic breeding.
Article
Multidisciplinary Sciences
Ismael A. Vergara, Christopher P. Mintoff, Shahneen Sandhu, Lachlan McIntosh, Richard J. Young, Stephen Q. Wong, Andrew Colebatch, Daniel L. Cameron, Julia Lai Kwon, Rory Wolfe, Angela Peng, Jason Ellul, Xuelin Dou, Clare Fedele, Samantha Boyle, Gisela Mir Arnau, Jeanette Raleigh, Athena Hatzimihalis, Pacman Szeto, Jennifer Mooi, Daniel S. Widmer, Phil F. Cheng, Valerie Amann, Reinhard Dummer, Nicholas Hayward, James Wilmott, Richard A. Scolyer, Raymond J. Cho, David Bowtell, Heather Thorne, Kathryn Alsop, Stephen Cordner, Noel Woodford, Jodie Leditschke, Patricia O'Brien, Sarah-Jane Dawson, Grant A. McArthur, Graham J. Mann, Mitchell P. Levesque, Anthony T. Papenfuss, Mark Shackleton
Summary: Research findings suggest that the evolution of melanoma is mainly influenced by whole genome doubling and large-scale aneuploidy. In some patients, widespread loss of heterozygosity sculpt the burden of point mutations, neoantigens and structural variants, even in treatment-naive and primary cutaneous melanomas.
NATURE COMMUNICATIONS
(2021)
Article
Agronomy
Deepa Dhatwalia, Raghavendra Aminedi, Vinay Kalia, Veena Pande, Ramcharan Bhattacharya
Summary: This study demonstrates the important role of sucrase 1 (SUC1) in mitigating osmotic pressure in the insect gut and successfully develops transgenic Indian mustard plants expressing SUC1 hairpin RNA for host-mediated delivery into infesting aphids. The research also shows a significant reduction in aphid fecundity and detection of SUC1-specific siRNA molecules in aphids fed on transgenic plants, indicating the potential for engineering RNAi-based resistance against aphids in Brassica crops.
PEST MANAGEMENT SCIENCE
(2022)
Article
Ecology
Brian Alfaro, Diane L. Marshall
Summary: Understanding the impact of environmental factors on trait variation is crucial for important plants both in ecology and economy. This study investigates whether differences in soil moisture contribute to trait variation in Sahara mustard by subjecting plants from different range sources to varying water addition treatments. Results show that plants from native and invasive populations reach a plateau in vegetative traits but exhibit a continuous linear increase in reproductive traits under excessive watering. On the other hand, landrace plants exhibit plateaus in composite trait values for various traits due to domestication. The study suggests that the ecological adaptability of Brassica tournefortii may be attributed to evolutionary drought tolerance in its source populations.
ECOLOGY AND EVOLUTION
(2023)
Review
Oncology
Kosuke Yamaguchi, Xiaoying Chen, Asami Oji, Ichiro Hiratani, Pierre-Antoine Defossez
Summary: Chromatin changes in cancer have significant implications for gene expression, genome stability, and cancer progression, making them important for diagnosis and treatment.
Article
Multidisciplinary Sciences
K. J. Pienta, E. U. Hammarlund, J. S. Brown, S. R. Amend, R. M. Axelrod
Summary: The theory introduces a new mechanism for cancer drug resistance, highlighting the importance of PACC formation and repopulation in treatment failure.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Chuan Zhou, Michelle M. Halstead, Amelie Bonnet-Garnier, Richard M. Schultz, Pablo J. Ross
Summary: Using CUT&Tag, researchers profiled histone modifications in bovine oocytes, embryos, and blastocysts to understand gene expression changes during preimplantation development. They found that broad bivalent domains mark developmental genes in oocytes, and repressive marks H3K9me3 and H3K27me3 are present before embryonic genome activation (EGA), suggesting a global transcription repression mechanism. Chromatin accessibility is established before activating marks H3K4me3 and H3K27ac during EGA. Transcription is required for the remodeling process, indicating the insufficiency of maternal products alone. H3K27me3 plays a major role in cellular potency restriction and blastocyst lineage determination.
Article
Agriculture, Multidisciplinary
Yang Ji-wei, Liu Zong-hua, Qu Yan-zhi, Zhang Ya-zhou, Li Hao-chuan
Summary: This study compared the cytological mechanism of SHGD through crossing inbred lines with differing abilities, revealing a foundation for further exploration of the underlying mechanism of SHGD.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Biochemistry & Molecular Biology
Neha Gupta, Mehak Gupta, Javed Akhatar, Anna Goyal, Rimaljeet Kaur, Sanjula Sharma, Prinka Goyal, Archana Mukta, Navneet Kaur, Meenakshi Mittal, Mohini Prabha Singh, Baudh Bharti, V. K. Sardana, Surinder S. Banga
Summary: Genome wide association studies identified 17 candidate genes associated with nitrogen use efficiency in Indian mustard, with CAT9, NRT1.8, and NRT3.1 predicted to be key genes influencing NUE and NUPEFF. The sequence information of these candidate genes can be utilized to develop molecular markers for breeding high NUE varieties.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Agronomy
Snehdeep Kaur, Chhaya Atri, Javed Akhatar, Meenakshi Mittal, Rimaljeet Kaur, Surinder S. Banga
Summary: Genome wide association studies have identified numerous candidate genes affecting flowering, maturity, and plant height under different day-length conditions. Functional annotation and genotype analysis helped predict 43 genes associated with these traits. This research provides valuable insights into the genetic features of Brassica rapa and enhances breeding efforts.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Agricultural Engineering
Snehdeep Kaur, Javed Akhatar, Harjeevan Kaur, Chhaya Atri, Meenakshi Mittal, Anna Goyal, Usha Pant, Gurpreet Kaur, Surinder S. Banga
Summary: A study was conducted on 195 germplasm lines of Brassica rapa to investigate oil, protein, and glucosinolate content, aiming to identify genetic markers associated with these traits. The research revealed phenotypic variations and extreme phenotypes among the germplasm lines.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Multidisciplinary Sciences
Javed Akhatar, Anna Goyal, Navneet Kaur, Chhaya Atri, Meenakshi Mittal, Mohini Prabha Singh, Rimaljeet Kaur, Indu Rialch, Surinder S. Banga
Summary: Genetic analysis of Indian mustard revealed significant effects of nitrogen levels on flowering, maturity, and plant height; genome-wide association studies identified 30 candidate genes related to these traits.
SCIENTIFIC REPORTS
(2021)
Article
Agronomy
Neha Agrawal, Mehak Gupta, Chhaya Atri, Javed Akhatar, Sarwan Kumar, Pat (J. S. ) Heslop-Harrison, Surinder S. Banga
Summary: Heavy doses of gamma irradiation can reduce linkage drag and improve resistance to Lipaphis erysimi in Brassica juncea. However, introgressed chromatin fragments causing linkage drag have hindered the deployment of this resistance source in commercial cultivars. Studies using GISH and chromosome-specific probes have investigated donor chromatin segment substitutions in ILs.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Gurleen Bhinder, Sanjula Sharma, Harjeevan Kaur, Javed Akhatar, Meenakshi Mittal, Surinder Sandhu
Summary: The defatted rapeseed meal can be a valuable protein feed for livestock. However, the presence of antinutritional factors limits its use and marketing. In this study, a genome-wide association study (GWAS) was conducted to investigate the genetic architecture of various traits in rapeseed meal samples. Several genotypes with high-quality protein and fewer antinutrients were identified. Functional validation of candidate genes could enhance the protein quality and reduce antinutritional components in B. napus.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Rahul Kumar, Dinesh Kumar Saini, Mukesh Kumar, Veerala Priyanka, Javed Akhatar, Deepak Kaushik, Amit Sharma, Parmdeep Singh Dhanda, Prashant Kaushik
Summary: A meta-QTL analysis was conducted to identify robust and stable meta-QTLs in Indian mustard, and several candidate genes related to yield and quality traits were also discovered. These findings have implications for improving plant architecture and enhancing quality traits through marker-assisted breeding, genetic engineering, and genome editing approaches.
Article
Plant Sciences
Priyanka Upadhyay, Mehak Gupta, Simarjeet Kaur Sra, Rakesh Sharda, Sanjula Sharma, Virender K. Sardana, Javed Akhatar, Gurpreet Kaur
Summary: This study evaluated Apase activity in 280 genotypes of Indian mustard and identified genomic regions and candidate genes associated with Apase activity. These findings contribute to improving phosphorus use efficiency and enhancing crop productivity under limited phosphorus reserves and degrading agro-environments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Pooja Kanwar Shekhawat, Anna Goyal, Javed Akhatar, Sanjula Sharma, Navneet Kaur, Baudh Bharti, Meenakshi Mittal, V. K. Sardana, Parveen Chhuneja, Surinder S. Banga, Chhaya Atri
Summary: This study used ICP-OES to determine the concentrations of eleven minerals in the leaves and seeds of 195 advanced generation inbred lines of Brassica rapa L. and identified SNP markers associated with leaf and seed mineral compositions. Genome wide association mapping and transcriptome analysis predicted genes involved in mineral acquisition, transport, and accumulation, as well as heavy metal detoxification.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
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.
Article
Plant Sciences
I Dhaliwal, S. Banga, N. Kumar, P. Salisbury, S. S. Banga
Summary: Yield losses in rapeseed breeding due to unsynchronized pod shattering remain a major challenge. Insufficient variation for shatter resistance in germplasm collections hinders breeding manipulations. Introducing resistance to pod shattering from Brassica carinata to Brassica napus has successfully enhanced rupture energy and identified promising germplasm resources for future breeding. Candidate gene marker trait associations offer potential for developing molecular markers for marker-assisted deployment of introgressed shatter resistance.
INDIAN JOURNAL OF TRADITIONAL KNOWLEDGE
(2021)
