Article
Plant Sciences
Dylan J. Ziegler, Deirdre Khan, Nadege Pulgar-Vidal, Isobel A. P. Parkin, Stephen J. Robinson, Mark F. Belmonte
Summary: This study investigated the DNA methylation and small RNA expression patterns during seed development in Brassica napus, and found the biased expression and methylation in the C-n subgenome. The results also showed conserved transcription patterns of small RNAs in the ancestral triplicated subgenomes of B. napus, but not in the A(n) and C-n subgenomes. The study discussed the relationship between methylation patterns and genes, promoter regions, small RNA loci, and transposable elements, as well as the impact of genome fractionation and polyploidization on the epigenetic components of the B. napus seed.
Article
Plant Sciences
Lijuan Wei, Hai Du, Xiaodong Li, Yonghai Fan, Mingchao Qian, Yali Li, Huiyi Wang, Cunmin Qu, Wei Qian, Xinfu Xu, Zhanglin Tang, Kai Zhang, Jiana Li, Kun Lu
Summary: This study provides a comprehensive analysis of gene function and homoeologous gene expression in different tissues at various developmental stages in Brassica napus. The findings suggest that certain gene functions are similar across different tissues, while transcription factor genes are more specific. Tissue-preferred genes have been identified and shown to play important roles in gene regulatory networks and hormone pathways. The study also reveals that biased expression of homoeologous genes is associated with structural divergence, the presence of transposable elements, and regulatory elements.
Article
Multidisciplinary Sciences
Kang Zhang, Lingkui Zhang, Yinan Cui, Yinqing Yang, Jian Wu, Jianli Liang, Xing Li, Xin Zhang, Yiyue Zhang, Zhongwei Guo, Lei Zhang, Shumin Chen, Jue Ruan, Michael Freeling, Xiaowu Wang, Feng Cheng
Summary: Polyploidization plays a crucial role in plant evolution. Subgenome dominance, characterized by higher expression levels of genes on the dominant subgenome, is a common phenomenon in allopolyploids. The underlying mechanism of subgenome dominance remains unclear, but it is suggested that differences in transposon and DNA methylation density near genes may be involved. In this study, eight generations of allotetraploid progenies were generated from the fusion of parental genomes Brassica rapa and Brassica oleracea. Despite the differences in transposon/methylation density between the parental genomes being maintained in the neotetraploids (synthetic Brassica napus), no subgenome dominance was observed. These findings challenge the idea that differences in methylated transposon near genes alone are sufficient to initiate subgenome dominance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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.
Review
Plant Sciences
Elizabeth Ihien Katche, Annaliese S. Mason
Summary: Resynthesized rapeseed lines have recreated the historical hybridization between Brassica rapa and B. oleracea, providing valuable genetic resources for rapeseed breeding and insights into polyploid plant meiosis evolution. This review discusses the production of these lines through interspecific crosses, their resulting fertility and agronomically important traits, meiotic instability issues, and the potential role of meiosis genes and gene regulatory networks in stabilizing meiosis. The direct use of resynthesized and semi-resynthesized Brassica napus for hybrid breeding and the study of other agronomic traits is also explored.
CRITICAL REVIEWS IN PLANT SCIENCES
(2023)
Article
Biology
Zeyu Li, Mengdi Li, Jianbo Wang
Summary: This study analyzed the changes in chromatin accessibility and its relationship with epigenetic modifications and gene expression during the process of allopolyploidization in Brassica napus. The results showed that there was a shock in chromatin accessibility in both allopolyploidization and natural evolutionary processes, and gene accessible chromatin regions (ACRs) increased after allopolyploidization. ACRs associated with H3K27ac or H3K4me3 modifications were more accessible than those associated with H3K27me3. Furthermore, the subgenome C-n exhibited higher chromatin accessibility compared to A(n), which was mainly due to the higher chromatin accessibility of C-n-unique genes.
COMMUNICATIONS BIOLOGY
(2022)
Article
Plant Sciences
Tao Yan, Yao Yao, Dezhi Wu, Lixi Jiang
Summary: The study introduces a web-based rapeseed genomic variation database that allows querying SNPs and InDels across rapeseed accessions worldwide. The database contains a large number of high-quality SNPs and InDels and provides search tools for genomic variations and gene annotations across 1,007 rapeseed accessions.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Plant Sciences
Grant W. de Jong, Keith L. Adams
Summary: Polyploidy has had a significant impact on the evolution of flowering plants. Allopolyploids, particularly Brassica napus, show extensive changes in gene expression and alternative splicing patterns when infected with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses reveal these differences and their role in enhancing the defense response against the pathogen.
Article
Biochemistry & Molecular Biology
Weixian Zhou, Libin Zhang, Jianjie He, Wang Chen, Feifan Zhao, Chunhua Fu, Maoteng Li
Summary: Interspecific crosses between Brassica rapa and B. napus result in transcriptome shock in the developing seeds, leading to overall changes in gene expression patterns. The hybrids show expression bias towards B. rapa and significant changes in key transcription factors, which may be responsible for phenotype change.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Guoqiang Zheng, Xiaoyun Dong, Jiaping Wei, Zigang Liu, Ali Aslam, JunMei Cui, Hui Li, Ying Wang, Haiyan Tian, Xiaodong Cao
Summary: In this study, the DNA methylation pattern and its regulated pathway of winter rapeseed under freezing stress were explored using methylome and transcriptome analysis. The results showed that the average methylation level decreased under freezing stress, with CG methylation level being the highest. Functional enrichment analysis identified several differentially expressed genes associated with differentially methylated genes, including core transcription factors involved in plant response to stress.
Review
Agronomy
Nadia Raboanatahiry, Huaixin Li, Longjiang Yu, Maoteng Li
Summary: Brassica napus L. is a versatile vegetable oil crop that can be used for oil extraction, protein production, medicinal purposes, energy source, and industrial applications. Every part of rapeseed is useful, contributing to reducing waste and promoting sustainability.
Article
Genetics & Heredity
Qian Wang, Tao Yan, Zhengbiao Long, Luna Yue Huang, Yang Zhu, Ying Xu, Xiaoyang Chen, Haksong Pak, Jiqiang Li, Dezhi Wu, Yang Xu, Shuijin Hua, Lixi Jiang
Summary: Utilizing the genomic-selection (GS) strategy and models that significantly increase predictability of heterosis, this research found that the parental genetic-similarity index (PGSI) affects grain yield and traits, with the C subgenome having a greater impact on heterosis. Maps of quantitative-trait loci responsible for heterosis were provided, and high impacting gene annotations were given. This study provides a successful case for predicting heterosis in polyploid genomes with relatively large genome sizes.
Article
Plant Sciences
Mengdi Li, Meimei Hu, Yafang Xiao, Xiaoming Wu, Jianbo Wang
Summary: This study utilized long-read RNA sequencing technology to investigate the evolutionary changes in transcripts of Brassica napus during its early establishment and subsequent evolution. The results showed an increase in upregulated genes and isoform numbers, as well as genes potentially involved in alternative splicing events, in B. napus after evolution. These changes may contribute to the adaptation of plants to the natural environment.
HORTICULTURE RESEARCH
(2022)
Review
Plant Sciences
Chunji Liu, You-Gan Wang
Summary: Polyploids, common in flowering plants, often have wider distribution ranges than their diploid progenitors. Previous studies have shown that polyploidy leads to novel changes and differences in gene number, gene expression levels, and epigenetic alteration between subgenomes of allopolyploid species. Contrary to popular belief, subgenome biases mainly reflect legacy from the progenitors and can be detected before polyploidization is complete.
Article
Biotechnology & Applied Microbiology
Xuequn Chen, Chaobo Tong, Xingtan Zhang, Aixia Song, Ming Hu, Wei Dong, Fei Chen, Youping Wang, Jinxing Tu, Shengyi Liu, Haibao Tang, Liangsheng Zhang
Summary: The study presents a high-quality genome assembly of a rapeseed cultivar 'Zhongshuang11', revealing characteristics and genomic features. It serves as an important resource for rapeseed genomics research and understanding genetic variations associated with important agronomic traits.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Plant Sciences
Xinshuai Qi, Hong An, Tara E. Hall, Chenlu Di, Paul D. Blischak, Michael T. W. McKibben, Yue Hao, Gavin C. Conant, J. Chris Pires, Michael S. Barker
Summary: The study found a close relationship between domestication and polyploidy in Brassica rapa crops, with genetic diversity derived from ancient polyploidy playing a key role in the domestication of B. rapa and supporting its importance in the success of modern agriculture.
Article
Plant Sciences
Jose C. Tovar, Jeffrey C. Berry, Carlos Quillatupa, S. Elizabeth Castillo, Lucia Acosta-Gamboa, Noah Fahlgren, Malia A. Gehan
Summary: This study investigated the effects of heat stress in the roots or shoots of quinoa plants on the elemental concentrations in quinoa seed. The results showed that heat treatment significantly changed the elemental concentrations in quinoa seed, and the type of panicle and heat treatment method also had an impact. Additionally, the position of the plant section and the timing of heat exposure had significant effects on the seed elemental concentrations.
Article
Health Care Sciences & Services
Enric Aragones, German Lopez-Cortacans, Narcis Cardoner, Catarina Tome-Pires, Daniel Porta-Casteras, Diego Palao
Summary: The study aims to evaluate the trial implementation of the INDI collaborative care program in primary health care centers in Catalonia, in order to identify barriers, facilitators, and proposals for improvement. The main barriers identified include heavy workloads, lack of time, high staff turnover and shortages, and competing demands. Proposed improvements include institutional buy-in and organizational changes to ensure successful implementation.
BMC HEALTH SERVICES RESEARCH
(2022)
Review
Plant Sciences
Michael T. Pisias, Harmeet Singh Bakala, Alex C. McAlvay, Makenzie E. Mabry, James A. Birchler, Bing Yang, J. Chris Pires
Summary: Modern agriculture is highly vulnerable to climate change and population expansion due to its reliance on a narrow range of crop species. Crop improvement using plant genetic diversity is one solution, but new approaches like neodomestication and redomestication are being explored. Redomestication focuses on feral crops, which have escaped cultivation and adapted to local environments, but still retain some domestication traits. This review explores the potential of using genome editing techniques to develop novel crops through de novo redomestication, which could be important for global food security.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemical Research Methods
S. Elizabeth Castillo, Jose C. Tovar, Anastasia Shamin, Jorge Gutirerrez, Paige Pearson, Malia A. Gehan
Summary: This study provides a method for in vitro pollen germination in quinoa and tested the germination efficiency under different conditions. This method can be used to estimate pollen viability in quinoa and test how stress affects quinoa fertility.
Article
Genetics & Heredity
Yue Hao, Jonathon Fleming, Joanna Petterson, Eric Lyons, Patrick P. Edger, J. Chris Pires, Jeffrey L. Thorne, Gavin C. Conant
Summary: The study finds that the evolutionary forces acting on polyploids are remarkably similar regardless of the species they occur in. The rate of duplicate gene loss is relatively high in the early stages of polyploid evolution, suggesting that most selectively neutral duplicate gene losses occur during this period. There is strong evidence of biases in the duplicate losses, indicating that allopolyploidies with distinct progenitors are common. Additionally, reciprocal gene losses are ongoing and extensive between these polyploid genomes, making the formation of viable diploid hybrid species highly unlikely. The ability of new polyploidies to bypass reciprocal gene loss barriers may explain the relatively high frequency of recurrent polyploidy in certain lineages.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Won Cheol Yim, Mia L. Swain, Dongna Ma, Hong An, Kevin A. Bird, David D. Curdie, Samuel Wang, Hyun Don Ham, Agusto Luzuriaga-Neira, Jay S. Kirkwood, Manhoi Hur, Juan K. Q. Solomon, Jeffrey F. Harper, Dylan K. Kosma, David Alvarez-Ponce, John C. Cushman, Patrick P. Edger, Annaliese S. Mason, J. Chris Pires, Haibao Tang, Xingtan Zhang
Summary: This study reports the chromosome-scale genome assembly of Ethiopian mustard and provides insights into the evolutionary history and agronomic traits of this crop. The research also identifies the expansion of transcription factor networks and important gene families.
Review
Plant Sciences
Sontosh K. Deb, Patrick P. Edger, J. Chris Pires, Michael R. McKain
Summary: Allopolyploids are formed by hybridization between different evolutionary lineages with genome doubling. Homoeologous chromosomes can undergo recombination immediately after allopolyploid formation and continue over successive generations. Homoeologous exchanges have both negative and positive effects, leading to unbalanced gametes, reduced fertility, novel phenotypic diversity, and the formation of neo-allopolyploids. The causes and consequences of homoeologous exchanges vary across lineages, generations, and genomes. Recent technological advances provide insights into the mechanistic basis of homoeologous exchanges in allopolyploid angiosperms, which have implications for understanding allopolyploid evolution and developing important traits in polyploid crops.
Article
Biochemical Research Methods
Sam De Meyer, Daniel Felipe Cruz, Tom De Swaef, Peter Lootens, Jolien De Block, Kevin Bird, Heike Sprenger, Michael Van de Voorde, Stijn Hawinkel, Tom Van Hautegem, Dirk Inze, Hilde Nelissen, Isabel Roldan-Ruiz, Steven Maere
Summary: In this study, the authors developed a strategy for studying plant traits directly in the field, bypassing the translation step from lab experiments. They found that gene expression in autumn can predict yield traits in spring for rapeseed plants. The top predictor genes are involved in developmental processes that occur in autumn, indicating the influence of autumnal development on crop yield.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Kevin A. Bird, J. Chris Pires, Robert VanBuren, Zhiyong Xiong, Patrick P. Edger
Summary: The gene balance hypothesis suggests that selection acts on gene dosage within dosage-sensitive parts of networks, pathways, and protein complexes to maintain balanced stoichiometry, due to the fitness cost of imbalanced stoichiometry. This selection is known as dosage balance selection. It is also hypothesized that dosage balance selection constrains expression responses to changes in dosage, resulting in similar expression changes among genes encoding interacting proteins. In this study, researchers tested the gene balance hypothesis by analyzing genomic and transcriptomic data from resynthesized Brassica napus lines. They found that dosage-sensitive genes had less variable expression responses to homoeologous exchanges, indicating that their relative dosage is constrained. Additionally, the expression response to homoeologous exchanges was more variable than the response to whole-genome duplication, suggesting that homoeologous exchanges create genomic imbalance.
Article
Biodiversity Conservation
Kevin A. Bird, MacKenzie Jacobs, Audrey Sebolt, Kathleen Rhoades, Elizabeth I. Alger, Marivi Colle, Mitchell L. Alekman, Paulina K. Bies, Adare J. Cario, Ramya S. Chigurupati, Delaney R. Collazo, Savannah Finley, Brooke Garland, Kaitlyn M. Hein, Jailyn Hicks, Annie R. Hillenberg, Lawrence I. Kado, Vanessa R. Kilian, Philip F. Longueuil, Vibha Mahesha, Charlie Mervak, Kat Munsell, Roshan M. Patel, Nicole M. L. Peters, Megan O. Steffes, Sathvik Suryadevara, Akshita Thummalapally, Grace Urban, Aditya K. Walia, Taylor B. Wirsing, Michael R. McKain, Amy F. Iezzoni, Patrick P. Edger
Summary: This study conducted phylogenetic analysis of plastid genomes and nuclear genes to determine the progenitor species of tetraploid sour cherry. The results identified P. fruticosa as the likely maternal contributor and provide valuable resources for future breeding efforts in sour cherry.
PLANTS PEOPLE PLANET
(2022)
Article
Genetics & Heredity
Zhiyong Xiong, Robert T. Gaeta, Patrick P. Edger, Yao Cao, Kanglu Zhao, Siqi Zhang, J. Chris Pires
Summary: Resynthesized allopolyploid Brassica napus exhibit high chromosomal instability during meiosis, including nonhomologous centromere association, homoeologous recombination leading to translocation, and homoeologous chromosome replacement. In contrast, natural B. napus resolves meiotic errors mainly by suppressing homoeologous pairing and reducing homoeologous cross-overs.
G3-GENES GENOMES GENETICS
(2021)
