Article
Plant Sciences
Harsh Raman, Rosy Raman, Yu Qiu, Yuanyuan Zhang, Jacqueline Batley, Shengyi Liu
Summary: This study identified a major resistance locus, Rlm13, for blackleg disease in canola through genetic analysis of an Australian canola population. Twenty-four candidate R genes were predicted to be located within the QTL region. The results provide insights into the Avr-Rlm13 gene interaction and offer a valuable tool for enhancing resistance to blackleg in canola germplasm.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Homa Askarian, Alireza Akhavan, Leonardo Galindo Gonzalez, Sheau-Fang Hwang, Stephen E. Strelkov
Summary: The study found a clear relationship between the genetic structure and virulence phenotypes of the clubroot pathogen, with low genetic variability within each pathotype group but significant genetic differentiation among the pathotypes. Matrices produced with genetic data and the hosts of the CCD set showed the highest correlation between genetic structure and virulence.
Article
Horticulture
Xingbo Wu, Amanda M. Hulse-Kemp, Phillip A. Wadl, Zach Smith, Keithanne Mockaitis, Margaret E. Staton, Timothy A. Rinehart, Lisa W. Alexander
Summary: Hydrangea, an important ornamental crop cultivated for over 300 years, has been limited in genetic studies due to lack of genetic resources. However, a recent transcriptomic study and large-scale marker development have greatly expanded the genetic resources available for hydrangea, including high-density genetic linkage maps.
Article
Agriculture, Multidisciplinary
Yin Yue, An Wei, Zhao Jian-hua, Li Yan-long, Fan Yun-fang, Chen Jin-huan, Cao You-long, Zhan Xiang-qiang
Summary: In this study, a genetic linkage map of the wolfberry was constructed using SSR and AFLP markers, providing a basis for improving genes and selective breeding of the species.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Agronomy
Pippa J. Michael, Ashmita Rijal Lamichhane, Sarita Jane Bennett
Summary: Management of Sclerotinia stem rot disease in Brassica napus heavily relies on fungicides applied at flowering, but the effectiveness is inconsistent. This study found that different B. napus varieties have varying responses to the disease, and the impact of environment is the most influential factor. The research recommends combining long-term and short-term disease outcomes with lesion length measurement for future host screening studies.
Article
Plant Sciences
Harjot Singh Sohi, Manav Indra Singh Gill, Parveen Chhuneja, Naresh Kumar Arora, Sukhjinder Singh Maan, Jagmohan Singh
Summary: In this study, high leaf-anthocyanin reflective-index (ARI1) content cultivars of guava were developed through hybridization and a genetic linkage map was established. A marker closely associated with leaf anthocyanin content was identified.
Article
Plant Sciences
Guofang Zhang, Jinzhi Zhou, Yan Peng, Zengdong Tan, Yuting Zhang, Hu Zhao, Dongxu Liu, Xiao Liu, Long Li, Liangqian Yu, Cheng Jin, Shuai Fang, Jiawei Shi, Zedong Geng, Shanjing Yang, Guoxing Chen, Kede Liu, Qingyong Yang, Hui Feng, Liang Guo, Wanneng Yang
Summary: Salt stress affects the survival and growth of crops, and understanding the genetic resources related to salt stress tolerance in Brassica napus is important. This study quantified the salt stress tolerance of B. napus using a high-throughput phenotyping platform and identified candidate genes associated with salt stress response through genome-wide association study and linkage analysis.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Qian Yang, Xiaoyi Nong, Jize Xu, Fan Huang, Fang Wang, Jiangsheng Wu, Chunyu Zhang, Chao Liu
Summary: The CMS/Rf system is important for rapeseed production, and this study reveals the mechanisms underlying fertility restoration through morphological observation, gene mapping, and transcriptomic analysis, identifying potential key genes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Soo-In Sohn, Senthil Kumar Thamilarasan, Subramani Pandian, Young-Ju Oh, Hyeon-Jung Kang, Eun-Kyoung Shin
Summary: Interspecific hybridization between GM Brassica napus and Brassica rapa can result in viable hybrids that can actively hybridize up to F-3 generations or more. This suggests that transgene flow from GM B. napus to B. rapa is highly possible, and can occur through hand pollination in a greenhouse environment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Fangying Liu, Hao Chen, Liu Yang, Liang You, Jianye Ju, Shujie Yang, Xiaolin Wang, Zhongsong Liu
Summary: In this study, a mapping population was constructed to identify QTL loci for seed color in rapeseed. Two QTL loci were identified, one major QTL on chromosome A09 and one minor QTL on chromosome C03. Differential expression analysis and coexpression network analysis identified candidate genes involved in flavonoid biosynthesis. This study provides a foundation for further understanding the genetic basis and regulatory mechanism of yellow seed formation in Brassica napus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Li Zhang, Xiangsheng Li, Lichun Chang, Tianpeng Wang, Jianli Liang, Runmao Lin, Jian Wu, Xiaowu Wang
Summary: This study successfully increased the genetic diversity of Brassica juncea by introgressing the A genome of Brassica rapa. New B. juncea germplasm with expanded phenotypic variations was developed, and the introgression of B. rapa segments was tracked using SNP markers. The results showed that the introgression of the B. rapa genome significantly increased the genetic diversity of B. juncea.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Lieqiong Kuang, Nazir Ahmad, Bin Su, Lintao Huang, Keqi Li, Hanzhong Wang, Xinfa Wang, Xiaoling Dun
Summary: Marker-assisted selection was used to study root-related and shoot biomass traits in a new recombinant inbred line population. A high-density linkage map was constructed and 86 quantitative trait loci were detected. Using fine mapping and comparative sequencing, important candidate genes for root development were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Ali Ahmad, Wenhui Li, Hui Zhang, Hao Wang, Pengfei Wang, Yushun Jiao, Chenqi Zhao, Guangsheng Yang, Dengfeng Hong
Summary: In this study, the genetic basis of ovule number (ON) in oilseed rape was investigated using linkage mapping and genome-wide association analysis. The results revealed the presence of 5 QTLs and a number of significant SNPs associated with ON. Integration of the results identified four consensus genomic regions associated with ON. This study provides important insights into the genetic basis of ON in oilseed rape and offers useful molecular markers for yield improvement.
MOLECULAR BREEDING
(2023)
Article
Agronomy
Yusha Meng, Chenxing Zheng, Hui Li, Aixian Li, Hong Zhai, Qingmei Wang, Shaozhen He, Ning Zhao, Huan Zhang, Shaopei Gao, Qingchang Liu
Summary: The study developed high-density SSR genetic linkage maps for sweet potato, consisting of 90 linkage groups and 15 homologous groups, which are consistent with the autohexaploid nature of sweetpotato. These maps provide a foundation for QTL mapping, marker-assisted breeding, and comparative genomics research of sweet potato.
Article
Agronomy
Aibibula Paizila, Harun Karci, Elmira Ziya Motalebipour, Murat Guney, Salih Kafkas
Summary: The study constructed genetic linkage maps using SSR markers in two almond populations and identified QTLs related to flower color, stigma-anther position, and full blooming date. The results show that the linkage maps in both populations have high reliability and stability, providing valuable information for QTL analysis and marker assisted selection in almond breeding programs.
Article
Plant Sciences
Xun Chen, Xianhong Ge, Jing Wang, Chen Tan, Graham J. King, Kede Liu
FRONTIERS IN PLANT SCIENCE
(2015)
Article
Multidisciplinary Sciences
Zhikun Wu, Bo Wang, Xun Chen, Jiangsheng Wu, Graham J. King, Yingjie Xiao, Kede Liu
Article
Biochemical Research Methods
Xun Chen, Jason Kost, Dawei Li
BRIEFINGS IN BIOINFORMATICS
(2019)
Article
Agronomy
Shanjing Yang, Bao Zhang, Gang Liu, Baohua Hong, Jinsong Xu, Xun Chen, Bo Wang, Zhikun Wu, Fan Hou, Xiaopeng Yue, Jing Wang, Qinghua Zhang, Graham J. King, Kede Liu
THEORETICAL AND APPLIED GENETICS
(2018)
Article
Biotechnology & Applied Microbiology
Xun Chen, Xuemin Li, Bing Zhang, Jinsong Xu, Zhikun Wu, Bo Wang, Haitao Li, Muhammad Younas, Lei Huang, Yingfeng Luo, Jiangsheng Wu, Songnian Hu, Kede Liu
Article
Biochemistry & Molecular Biology
Cong Tan, Zhongmin Han, Huihui Yu, Wei Zhan, Weibo Xie, Xun Chen, Hu Zhao, Fasong Zhou, Yongzhong Xing
JOURNAL OF GENETICS AND GENOMICS
(2013)
Article
Agronomy
Haitao Li, Muhammad Younas, Xiaofeng Wang, Xuemin Li, Lin Chen, Bo Zhao, Xun Chen, Jinsong Xu, Fan Hou, Baohua Hong, Gang Liu, Hongyang Zhao, Xueli Wu, Hongzhi Du, Jiangsheng Wu, Kede Liu
THEORETICAL AND APPLIED GENETICS
(2013)
Article
Plant Sciences
Liuliu Shi, Jurong Song, Chaocheng Guo, Bo Wang, Zhilin Guan, Pu Yang, Xun Chen, Qinghua Zhang, Graham J. King, Jing Wang, Kede Liu
Article
Biochemical Research Methods
Xun Chen, Dawei Li
Article
Biochemistry & Molecular Biology
Xun Chen, Jason Kost, Arvis Sulovari, Nathalie Wong, Winnie S. Liang, Jian Cao, Dawei Li
Article
Biotechnology & Applied Microbiology
Xun Chen, Dawei Li
Summary: By analyzing whole-genome sequencing data, researchers found that viral sequences in human blood were closely associated with sequencing facilities or DNA sources; patterns of virus-mappable reads indicated possible origins from artificial sequences, recombinant vectors, or phages; the study provides new insights for improved bioinformatics filtering in deep sequencing data.
Article
Virology
Pranav P. Mathkar, Xun Chen, Arvis Sulovari, Dawei Li
Summary: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality, with about half of cases associated with hepatitis B virus (HBV) infections. Accurate identification of HBV integration sites is crucial for understanding the landscape of HCC genome. Through pathway enrichment analysis, it was found that HBV integrations were linked to various metabolism pathways. The VIcaller method showed potential in identifying novel clonal integrations in cancer-related genes.
Article
Virology
Haozhen Ren, Xun Chen, Jinglin Wang, Ying Chen, Alex Hafiz, Qian Xiao, Shiwei Fu, Advaitha Madireddy, Wei Vivian Li, Xiaolei Shi, Jian Cao
Summary: This study used whole-genome sequencing to investigate viral integration events during tumor development in hepatitis B virus (HBV)-positive hepatocellular carcinoma (HCC) cases. The study revealed diverse evolutionary trajectories and identified oncogenic integrations occurring before and during tumor development. Additionally, long-read sequencing uncovered chromosome rearrangements and tandem repeats of the HBV sequence within integrations. The study highlights the important role of HBV integrations in HCC development and genome instability.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Cell Biology
Cristian Groza, Xun Chen, Alain Pacis, Marie-Michelle Simon, Albena Pramatarova, Katherine A. Aracena, Tomi Pastinen, Luis B. Barreiro, Guillaume Bourque
Summary: This study demonstrates that genome graphs can reveal regulatory regions that would have been overlooked by other approaches, providing important insights into the impact of genetic variants on processes such as immunity.
Article
Cell Biology
Xun Chen, Alain Pacis, Katherine A. Aracena, Saideep Gona, Tony Kwan, Cristian Groza, Yen Lung Lin, Renata Sindeaux, Vania Yotova, Albena Pramatarova, Tomi Pastinen, Marie -Michelle Simon, Tomi Pastinen, Luis B. Barreiro, Guillaume Bourque
Summary: This study explored the contribution of transposable elements (TEs) to the human immune response and found significant inter-individual variation in viral load after influenza A virus (IAV) infection. The accessibility of certain TE families was enhanced or reduced upon infection and they were associated with immune regulators. TEs and host factors regulating TEs were predictive of viral load post-infection.