Article
Biochemistry & Molecular Biology
Jiangxu Wang, Tao Wang, Qi Wang, Xiaodong Tang, Yang Ren, Haiyan Zheng, Kai Liu, Luomiao Yang, Hui Jiang, Yidan Li, Qi Liu, Detang Zou, Hongliang Zheng
Summary: This study mapped QTLs for flag leaf length, width, and area in japonica rice using linkage analysis and GWAS, detecting a total of 64 QTLs, including pleiotropic QTLs mapped across both methods. Candidate genes were identified and LOC_Os10g20160 was shown to potentially regulate flag leaf width in japonica rice. The results provide valuable insights for mining main genes/QTLs related to leaf development and molecular breeding in japonica rice.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Plant Sciences
Annamalai Anandan, Siddharth Panda, S. Sabarinathan, Anthony J. Travis, Gareth J. Norton, Adam H. Price
Summary: The study highlights the advantages of the direct seeded rice (DSR) system in terms of saving freshwater resources, reducing labor requirements, and increasing productivity and resource use efficiency, while reducing greenhouse gas emissions. Early root vigor is crucial for ensuring good crop growth, water and nutrient uptake, and weed competition in the DSR system. Genome-wide association studies identified genetic regions and candidate genes related to root architecture and nutrient acquisition. Additionally, a new QTL controlling root length at 14 days was discovered.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Supatthra Narawatthana, Yotwarit Phansenee, Bang-On Thammasamisorn, Phanchita Vejchasarn
Summary: This study explored the quantitative trait loci and alleles related to rice flag leaf anatomical and vein traits using three different genetic models through genome-wide association analysis. The results showed that all three models were able to identify significant loci associated with these traits. The findings suggest that flag leaf traits can be improved via molecular breeding and can be a target for high-yield rice development.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Narayana Bhat Devate, Hari Krishna, Sunil Kumar V. Parmeshwarappa, Karthik Kumar Manjunath, Divya Chauhan, Shweta Singh, Jang Bahadur Singh, Monu Kumar, Ravindra Patil, Hanif Khan, Neelu Jain, Gyanendra Pratap Singh, Pradeep Kumar Singh
Summary: This study conducted a genome-wide association study to identify markers associated with traits under heat and drought stress in bread wheat. The results provide valuable markers that can be used for marker-assisted breeding to develop climate-resilient cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Matheus M. Suela, Camila F. Azevedo, Moyses Nascimento, Ana Carolina C. Nascimento, Marcos Deon de Resende
Summary: Although genome-wide association studies (GWAS) based on single-marker analysis have limitations in terms of high false-positive rates and limited power to detect associations, the use of Bayesian methods and regional heritability mapping (RHM) have shown to be more effective in identifying important gene markers and reducing false-positive rates.
Article
Plant Sciences
Nan Jiang, Jun Fu, Qin Zeng, Yi Liang, Yanlong Shi, Zhouwei Li, Youlun Xiao, Zhizhou He, Yuntian Wu, Yu Long, Kai Wang, Yuanzhu Yang, Xionglun Liu, Junhua Peng
Summary: By using genome-wide SNP association mapping, 77 and 7 loci associated with rice bacterial blight and bacterial leaf streak resistance were identified, potentially improving rice resistance. Screening 895 rice germplasm collections revealed potential sources of resistance, with certain subgroups showing higher resistance levels to bacterial blight and bacterial leaf streak. The GWAS analysis validated known resistance genes and identified novel loci, contributing to the enrichment of the current resistance gene pool and potential application in breeding for bacterial blight and bacterial leaf streak resistance.
Article
Plant Sciences
Yueming Yi, Muhammad A. Hassan, Xinxin Cheng, Yiru Li, Huan Liu, Wuyun Fang, Qian Zhu, Shimei Wang
Summary: This study investigated the phenotypic data of multiple agronomic and physiological traits in 120 recombinant inbred lines (RILs) under drought stress. Genome-wide association study (GWAS) identified 9 quantitative trait loci (QTLs) associated with drought-related traits and predicted 10 candidate genes related to drought response. This study provides important information for understanding the drought tolerance mechanisms in rice and facilitates marker-assisted breeding of drought-tolerant rice varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Yun Ma, Lan Yao, Liwei Zhang, Aiguo Su, Ronghuan Wang, Wei Song, Zhaowei Li, Jiuran Zhao
Summary: In this study, a new association mapping panel was constructed to investigate germination under chilling stress in maize. Through genome sequencing and analysis, 26 significant SNPs associated with chilling-tolerant germination were identified, which corresponded to 37 candidate genes. The study also found additional significant SNPs associated with two traits related to germination. These findings provide valuable genetic resources for future improvement of chilling-tolerant maize varieties.
FOOD AND ENERGY SECURITY
(2023)
Article
Plant Sciences
Xuli Zhu, Fengshuo Sun, Mengmeng Sang, Meixia Ye, Wenhao Bo, Ang Dong, Rongling Wu
Summary: Heterophylly is an adaptive strategy employed by certain plants to respond to environmental changes. In this study, the genetic characteristics underlying changes in leaf shape in the model species Populus euphratica were investigated. Single- and multi-leaf genome-wide association studies (GWAS) were utilized to associate single-nucleotide polymorphisms (SNPs) with leaf traits. The multi-leaf GWAS approach revealed more SNP-trait associations and identified markers on 19 chromosomes and 21 unique genes that could serve as potential targets for selection. These findings offer valuable insights into the genetic architecture of heterophylly and provide candidate genes for breeding or engineering P. euphratica.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Zhengbo Liu, Hao Sun, Yanan Zhang, Mingyu Du, Jun Xiang, Xinru Li, Yinping Chang, Jinghan Sun, Xianping Cheng, Mengyuan Xiong, Zhe Zhao, Erbao Liu
Summary: This study performed a genome-wide association study to determine the genetic determinants of panicle traits in rice. Several quantitative trait loci and candidate genes associated with panicle length, total grain number per panicle, filled grain number per panicle, seed setting rate, and grain weight per panicle were identified. These findings provide important genetic information for improving panicle traits and rice yield through marker-assisted selection.
FRONTIERS IN GENETICS
(2023)
Review
Agronomy
Dinesh K. Saini, Yuvraj Chopra, Jagmohan Singh, Karansher S. Sandhu, Anand Kumar, Sumandeep Bazzer, Puja Srivastava
Summary: This review provides a comprehensive overview of the importance of GWAS in wheat, including population design, high-throughput genotyping and phenotyping platforms, statistical models, and the utilization of MTAs in breeding programs. Future breakthroughs in genomic selection, multi-omics-based approaches, and machine and deep learning models in wheat breeding are also discussed.
MOLECULAR BREEDING
(2022)
Article
Genetics & Heredity
Endale G. Tafesse, Krishna K. Gali, V. B. Reddy Lachagari, Rosalind Bueckert, Thomas D. Warkentin
Summary: Heat and drought stress can limit pea productivity, but genetic diversity in pea germplasm offers potential for developing stress-adaptive cultivars. A genome-wide association study identified 15 marker trait associations (MTAs) for six stress-adaptive traits in pea, highlighting potential candidate genes for selecting stress-hardy pea cultivars through marker-assisted selection.
Article
Plant Sciences
Thao Duc Le, Floran Gathignol, Huong Thi Vu, Khanh Le Nguyen, Linh Hien Tran, Hien Thi Thu Vu, Tu Xuan Dinh, Francoise Lazennec, Xuan Hoi Pham, Anne-Alienor Very, Pascal Gantet, Giang Thi Hoang
Summary: This study explores the mechanisms of rice tolerance to salinity stress, identifying 26 QTLs related to salinity tolerance through a genome-wide association study on 179 Vietnamese rice landraces. Ten of these QTLs were associated with multiple traits, suggesting pleiotropic effects in controlling plant responses to salinity stress.Twenty-one of the identified QTLs colocalized with known QTLs, and the associated genes mainly function in gene regulation, signal transduction, or hormone signaling related to salinity stress tolerance.
Article
Biochemistry & Molecular Biology
Fengqi Li, Alaa S. Marzouk, Youssef Dewer, Houxiang Kang, Guirong Wang
Summary: This study conducted a genome-wide association analysis to investigate the biosynthetic pathways and regulatory networks of metabolites and volatiles in rice. The results revealed close relationships between metabolites and volatiles in rice and its development, biotic and abiotic stresses. Some important compounds were found to be strongly associated with certain phenotypes of rice, providing valuable insights into the understanding of biosynthetic pathways and regulatory networks.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
Radha Beena, Silvas Kirubakaran, Narayanan Nithya, Alagu Manickavelu, Rameshwar Prasad Sah, Puthenpeedikal Salim Abida, Janardanan Sreekumar, Poolakkal Muhammed Jaslam, Rajendrakumar Rejeth, Vijayalayam Gengamma Jayalekshmy, Stephen Roy, Ramakrishnan Vimala Manju, Mariasoosai Mary Viji, Kadambot H. M. Siddique
Summary: The study found that Asian cultivars were mainly used to discover new alleles for drought tolerance, while genetic resources adapted to the Indian subcontinent, despite being diverse, were not adequately represented. Through analyzing the genotype and traits of rice under different water conditions, key genes related to yield can be identified.
Article
Plant Sciences
Dong Van Nguyen, Huong Mai Nguyen, Nga Thanh Le, Kien Huu Nguyen, Hoa Thi Nguyen, Huong Mai Le, Anh Trung Nguyen, Ngan Thi Thu Dinh, Son Anh Hoang, Chien Van Ha
Summary: Copper nanoparticle priming enhances drought tolerance in maize by increasing leaf water content and plant biomass, as well as anthocyanin, chlorophyll, and carotenoid contents, while decreasing reactive oxygen species accumulation and increasing reactive oxygen species scavenging enzyme activities. Additionally, applying copper nanoparticles increases total seed number and grain yield under drought stress conditions, suggesting a promising approach for the production of drought-tolerant crop plants.
JOURNAL OF PLANT GROWTH REGULATION
(2022)
Article
Multidisciplinary Sciences
Phuong Nguyen Duy, Dai Tran Lan, Hang Pham Thu, Huong Phung Thi Thu, Ha Nguyen Thanh, Ngoc Phuong Pham, Florence Auguy, Huong Bui Thi Thu, Tran Bao Manh, Sebastien Cunnac, Xuan Hoi Pham
Summary: This study aimed to introduce BLB resistance in the TBR225 elite rice variety by using CRISPR/Cas9 editing system to obtain mutant lines with mutations in the OsSWEET14 promoter. One of the T-2 lines with a homozygous 6-bp deletion displayed decreased OsSWEET14 expression, significantly reduced susceptibility to one Vietnamese Xoo strains, and complete resistance to another.
Article
Genetics & Heredity
Giang Ngan Khong, Nhu Thi Le, Mai Thi Pham, Helene Adam, Carole Gauron, Hoa Quang Le, Dung Tien Pham, Kelly Colonges, Xuan Hoi Pham, Vinh Nang Do, Michel Lebrun, Stefan Jouannic
Summary: The study identified a cluster of differentially expressed genes encoding ANK and ANK-TPR proteins that play a role in regulating the diversity of secondary branching in rice panicles. These genes may act as positive or negative regulators of the transition of panicle meristem's identity from indeterminate to determinate state. This finding provides valuable insights for improving grain yield in rice breeding.
Article
Plant Sciences
Thao Duc Le, Floran Gathignol, Huong Thi Vu, Khanh Le Nguyen, Linh Hien Tran, Hien Thi Thu Vu, Tu Xuan Dinh, Francoise Lazennec, Xuan Hoi Pham, Anne-Alienor Very, Pascal Gantet, Giang Thi Hoang
Summary: This study explores the mechanisms of rice tolerance to salinity stress, identifying 26 QTLs related to salinity tolerance through a genome-wide association study on 179 Vietnamese rice landraces. Ten of these QTLs were associated with multiple traits, suggesting pleiotropic effects in controlling plant responses to salinity stress.Twenty-one of the identified QTLs colocalized with known QTLs, and the associated genes mainly function in gene regulation, signal transduction, or hormone signaling related to salinity stress tolerance.
Article
Agronomy
Cu Thi Le Thuy, Luis Augusto Becerra Lopez-Lavalle, Nguyen Anh Vu, Nguyen Huu Hy, Pham Thi Nhan, Hernan Ceballos, Jonathan Newby, Nguyen Ba Tung, Nguyen Trong Hien, Le Ngoc Tuan, Nguyen Hung, Nguyen Thi Hanh, Do Thi Trang, Pham Thi Thu Ha, Le Huy Ham, Xuan Hoi Pham, Do Thi Nhu Quynh, Ismail Y. Rabbi, Peter A. Kulakow, Xiaofei Zhang
Summary: Cassava is a crucial staple crop providing carbohydrate energy to over half a billion people in the tropics. The study identified clones with high CMD resistance in a population with high heritability, and validated CMD markers for predicting resistance in segregating populations.
Article
Plant Sciences
Severine Lacombe, Martine Bangratz, Hoang Anh Ta, Thanh Duc Nguyen, Pascal Gantet, Christophe Brugidou
Summary: Rice ragged stunt virus (RRSV) is a destructive virus in the rice culture areas of South and Far-Eastern Asia, for which no genetic resistance has been identified. Chemical treatments are currently used, but RNA-silencing approaches have been developed as resistance strategies. While miRNA-based strategies targeting viral genomes did not achieve efficient resistance against RRSV, siRNA-based strategies targeting viral fragments showed efficient and environmentally friendly resistance in transgenic rice plants.
Article
Genetics & Heredity
Hong Viet La, Ha Duc Chu, Cuong Duy Tran, Kien Huu Nguyen, Quynh Thi Ngoc Le, Chinh Minh Hoang, Bang Phi Cao, Anh Tuyen Cong Pham, Bach Duc Nguyen, Trung Quoc Nguyen, Loc Van Nguyen, Chien Van Ha, Hien Thi Le, Ham Huy Le, Thao Duc Le, Lam-Son Phan Tran
Summary: This study provides initial insights into the characteristics and transcriptional regulation of the CaSWEET family in chickpea, specifically under water-stress conditions. These findings serve as a foundation for further genetic engineering research using selected candidate genes.
Article
Plant Sciences
Kevin Bellande, Duy-Chi Trinh, Anne-Alicia Gonzalez, Emeric Dubois, Anne-Sophie Petitot, Mikael Lucas, Antony Champion, Pascal Gantet, Laurent Laplaze, Soazig Guyomarc'h
Summary: Lateral root organogenesis is crucial for the development of a plant's root system. The early phase of cell proliferation in lateral root formation leads to the establishment of a root meristem-like structure. PUCHI gene plays a role in repressing the ectopic establishment of meristematic cells during early stages of lateral root development. These findings provide insights into the gene network that regulates timing and patterning in lateral root formation.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Zhonghui Feng, Xiaohan Liang, Hongtao Tian, Yasuko Watanabe, Kien Huu Nguyen, Cuong Duy Tran, Mostafa Abdelrahman, Kun Xu, Mohammad Golam Mostofa, Chien Van Ha, Keiichi Mochida, Chunjie Tian, Maho Tanaka, Motoaki Seki, Zhengwei Liang, Yuchen Miao, Lam-Son Phan Tran, Weiqiang Li
Summary: Recent investigations have shown that SMAX1 and SMXL2 act as negative regulators of karrikin and strigolactone signaling during plant growth and development in Arabidopsis thaliana. However, their functions in drought resistance and related mechanisms are not well understood. This study found that the smax1 smxl2 double-mutant plants exhibited enhanced drought resistance and reduced leaf water loss compared to wild-type plants. Transcriptome analysis revealed that the cuticle formation mechanism was involved in the drought resistance of the mutant plants. Additionally, the mutant plants showed increased sensitivity to abscisic acid and higher reactive oxygen species detoxification capacity, as well as longer root hairs and a higher root-to-shoot ratio, indicating an improved water absorption capacity. These findings suggest that SMAX1 and SMXL2 negatively regulate drought resistance and disrupting these signaling-related genes may offer a potential strategy to enhance crop drought resistance.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Maryam Nasr Esfahani, Miyako Kusano, Mostafa Abdelrahman, Kien Huu Nguyen, Yasuko Watanabe, Keiichi Mochida, David J. Burritt, Lam-Son Phan Tran
Summary: This study aimed to identify key NO3- and/or Pi starvation-responsive metabolic pathways in chickpea and found significant differences in metabolic adaptation under single and double nutrient deficiencies. The simultaneous deficiency of NO3- and Pi generated unique metabolic changes that couldn't simply be explained by the combined deficiencies of the two nutrients.
Article
Plant Sciences
Chien Van Ha, Mohammad Golam Mostofa, Kien Huu Nguyen, Cuong Duy Tran, Yasuko Watanabe, Weiqiang Li, Yuriko Osakabe, Mayuko Sato, Kiminori Toyooka, Maho Tanaka, Motoaki Seki, David J. Burritt, Cheyenne Marie Anderson, Ru Zhang, Huong Mai Nguyen, Vy Phuong Le, Hien Thuy Bui, Keiichi Mochida, Lam-Son Phan Tran
Summary: Cytokinin signaling pathway, involving histidine phosphotransfer proteins (HPs), plays a crucial role in plant stress responses. In this study, the role of AHP4 in Arabidopsis drought adaptation was investigated. AHP4 was found to downregulate during dehydration, and ahp4 plants exhibited higher survival rates, thicker cuticles, narrower stomatal apertures, higher leaf temperatures, longer root length, and increased antioxidant capacity compared to wild-type plants. These findings suggest that AHP4 plays an important role in plant drought adaptation.
Article
Environmental Sciences
Md. Shahadat Hossain, Mostafa Abdelrahman, Cuong Duy Tran, Kien Huu Nguyen, Ha Duc Chu, Yasuko Watanabe, Masayuki Fujita, Lam-Son Phan Tran
Summary: It was found that acetate treatment can enhance cadmium stress tolerance in lentil by inhibiting root-to-shoot transport of cadmium, minimizing reduction in photosynthetic pigment contents. Acetate treatment also increases osmoprotection through proline accumulation and enhances antioxidant defense through increased ascorbic acid content and catalase activity, reducing oxidative stress-induced damage caused by cadmium stress.
ENVIRONMENTAL POLLUTION
(2022)
Article
Plant Sciences
Mohammad Golam Mostofa, Mostafa Abdelrahman, Md Mezanur Rahman, Cuong Duy Tran, Kien Huu Nguyen, Yasuko Watanabe, Misao Itouga, Weiqiang Li, Zhe Wang, Keiichi Mochida, Lam-Son Phan Tran
Summary: The KAI2 receptor plays an important role in plant tolerance to salt stress. Defects in KAI2 functions result in impaired seed germination and plant growth under salt stress, leading to ion imbalance, oxidative damage, and abnormal hormone signaling.
PLANT AND CELL PHYSIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Marie Rose Ndella Thiaw, Pascal Gantet
Summary: Mini zinc fingers play important roles in plant development, including control of cell division and expansion, meristem state transition, and growth and organ development. They have diverse modes of action, such as direct gene activation, interaction with specific transcription factors, and aggregation of protein complexes for chromatin remodeling. Further research is needed to explore their wider range of biological functions and their involvement in biotic and abiotic stress responses.
Article
Plant Sciences
Hongtao Tian, Yasuko Watanabe, Kien Huu Nguyen, Cuong Duy Tran, Mostafa Abdelrahman, Xiaohan Liang, Kun Xu, Claudia Sepulveda, Mohammad Golam Mostofa, Chien Van Ha, David C. Nelson, Keiichi Mochida, Chunjie Tian, Maho Tanaka, Motoaki Seki, Yuchen Miao, Lam-Son Phan Tran, Weiqiang Li
Summary: Using reverse genetics, researchers identified that KUF1 plays a negative regulatory role in drought tolerance by modulating physiological traits and ABA responses to enhance plant resistance to drought stress.