Article
Plant Sciences
Rui Wang, Zhenzhen Zhou, Mengyuan Xiong, Mingyu Du, Xingxing Lin, Cuiping Liu, Mingwei Lu, Zhengbo Liu, Yinping Chang, Erbao Liu
Summary: Eight QTLs related to salt tolerance traits were detected, and three candidate genes were predicted, providing a reference for breeding salt-tolerant rice varieties.
Article
Plant Sciences
Song Mei, Guogen Zhang, Jing Jiang, Jingbing Lu, Fan Zhang
Summary: “Salinity-alkalinity stress is a major factor limiting rice production, and improving alkali tolerance in rice is essential. This study identified 90 loci associated with alkali tolerance in rice germplasms and identified eight candidate genes. The findings suggest that combining alkali-tolerant haplotypes of multiple genes may be an effective strategy for improving alkali tolerance in rice.”
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Xing Huo, Jian Wang, Luo Chen, Hua Fu, Tifeng Yang, Jingfang Dong, Yamei Ma, Lian Zhou, Jiansong Chen, Dilin Liu, Bin Liu, Junliang Zhao, Shaohong Zhang, Wu Yang
Summary: Grain chalkiness is a crucial factor influencing the market value of rice. This study identified 34 QTLs associated with grain chalkiness in 450 rice accessions through a genome-wide association analysis. Four candidate genes were identified as potential targets for molecular breeding to improve rice quality. These findings contribute to a better understanding of the genetic basis of grain chalkiness and provide gene resources for quality improvement in rice through molecular breeding.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lovepreet Singh, Rajat Pruthi, Sandeep Chapagain, Prasanta K. Subudhi
Summary: Alkalinity stress is a major obstacle to rice production, and understanding the mechanisms of alkalinity tolerance is limited. A genome-wide association study was conducted to identify tolerant genotypes and candidate genes for alkalinity tolerance in rice seedlings. Principal component analysis revealed the traits with the highest contributions to tolerance, and clustering analysis grouped the genotypes into different subgroups. Several significant SNPs associated with alkalinity tolerance were identified, as well as novel QTLs and candidate genes. These genomic and genetic resources are valuable for investigating alkalinity tolerance mechanisms and improving tolerance in rice.
Article
Agronomy
Leila Nayyeripasand, Ghasem Ali Garoosi, Asadollah Ahmadikhah
Summary: This study identified rice genomic regions associated with early stage salinity tolerance and candidate genes using genome-wide association study. The identified genes can be used for improving salinity tolerance in rice breeding programs and further study can help uncover the mechanisms of salinity tolerance at molecular level.
Article
Agronomy
San Mar Lar, Jeonghwan Seo, Seong-Gyu Jang, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Ja-Hong Lee, Na-Eun Kim, Yoonjung Lee, Yong-Jin Park, Joohyun Lee, Soon-Wook Kwon
Summary: This study identified three significant loci associated with salt tolerance at the seedling stage in Korean rice through genome-wide association study (GWAS), and selected five candidate genes for further investigation based on their known functions and gene expression profiles.
Article
Agronomy
Jia Li, Wei Xin, Weiping Wang, Shijiao Zhao, Lu Xu, Xingdong Jiang, Yuxuan Duan, Hongliang Zheng, Luomiao Yang, Hualong Liu, Yan Jia, Detang Zou, Jingguo Wang
Summary: This study identified genes related to low-nitrogen tolerance in rice through genome-wide association study and transcriptome sequencing, providing insights into improving rice varieties and enhancing nitrogen use efficiency.
Article
Agronomy
Jin Shi, Jianxin Shi, Wanqi Liang, Dabing Zhang
Summary: Several key QTLs and genes related to seed dormancy were identified, with SNP candidates influencing seed germination. The study provides valuable insights for understanding seed dormancy mechanisms and crop improvement in the future.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Agronomy
Shilei Liu, Wenli Zou, Xiang Lu, Jianmin Bian, Haohua He, Jingguang Chen, Guoyou Ye
Summary: The study identified QTLs associated with Zn2+ concentrations in both shoots and grains of rice, with some QTLs affecting Zn2+ concentration in both tissues. Candidate gene analysis suggested that LOC_Os02g06010 may play a crucial role in zinc accumulation in indica rice.
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)
Article
Genetics & Heredity
Changmin Hu, Jianhua Jiang, Yulong Li, Shaojie Song, Yu Zou, Chunyu Jing, Ying Zhang, Dezheng Wang, Qiang He, Xiaojing Dang
Summary: Heat tolerance is crucial for high and stable rice yields. In this study, we identified several QTLs associated with relative spikelet fertility (RSF) through a genome-wide association study. One novel QTL, qRSF9.2, was discovered, and its associated genes were narrowed down. We found that gene expression levels corresponded with RSF values, and the CC allele showed significantly higher RSF compared to the TT allele. Hap 2 and Hap 3 were found to increase heat tolerance by 7.9% and 11.3%, respectively.
FRONTIERS IN GENETICS
(2022)
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
Plant Sciences
Mouboni Dutta, Anusree Saha, Mazahar Moin, Pulugurtha Bharadwaja Kirti
Summary: This study analyzed the expression patterns of rice GRAS TF genes under abiotic and biotic stress conditions, identifying genes that were induced immediately after stress onset, especially in the roots of ABA-treated plants. OsGRAS39 was found to be highly expressed under sheath blight infection and abiotic stress treatments, with OsGRAS8, OsSHR1 and OsSLR1 also showing responsiveness. The research suggests that GRAS genes are potential candidate genes for enhancing stress tolerance in rice and other crop plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Yamei Ma, Jian Wang, Tifeng Yang, Jingfang Dong, Wu Yang, Luo Chen, Lian Zhou, Jiansong Chen, Bin Liu, Shaohong Zhang, David Edwards, Junliang Zhao
Summary: This study identified six quantitative trait loci associated with shoot length in rice and characterized OsCPS1 as a candidate gene for shoot length. The 36 bp deletion in the 5' UTR of OsCPS1 was found in accessions with long shoot length and associated with higher levels of bioactive GA(1) and GA(4). The expression of photosynthesis genes was higher in accessions with long shoot length, while genes involved in ABA-activated signal pathway showed lower expression. The findings provide valuable candidate genetic variation for seedling vigor in rice breeding.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Elham Kazemi, Javaad Zargooshi, Marzieh Kaboudi, Parviz Heidari, Danial Kahrizi, Behzad Mahaki, Youkhabeh Mohammadian, Habibolah Khazaei, Kawsar Ahmed
Summary: In this study, the gene expression profiles of normal and ED samples were investigated to identify 17 genes associated with ED. These genes were found to be involved in pathways related to human diseases and had diverse physicochemical properties and functions. Furthermore, interactions with the insulin pathway and identification of common cis-regulatory elements in the promoter sites of selected genes were also discussed. Additionally, conserved motifs and binding sites of miR-29-3p were identified in the upstream and untranslated regions of genes related to ED.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Agronomy
Frederike Zeibig, Benjamin Kilian, Michael Frei
Summary: The domestication of wheat has led to changes in its genetic diversity and grain quality. Through studying wild relatives such as the timopheevii lineage, we can potentially improve the quality of wheat by exploring the full diversity of the wheat gene pool.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Po-Ya Wu, Benjamin Stich, Marius Weisweiler, Asis Shrestha, Alexander Erban, Philipp Westhoff, Delphine Van Inghelandt
Summary: This study assessed the prediction ability of different omic datasets as predictors compared to a SNP array in genomic prediction (GP) for yield-related traits in plant breeding. The results showed that predictors from the transcriptome and metabolome provided higher prediction abilities compared to the SNP array. Combining multiple omic datasets improved the prediction ability, and a cost-effective approach for mRNA sequencing was proposed.
Article
Environmental Sciences
Muhammad Shahedul Alam, Angeline Wanjiku Maina, Yanru Feng, Lin-Bo Wu, Michael Frei
Summary: This study investigates the interactive effects of ozone and rice blast disease on different rice varieties, and finds that the tolerance to these stresses does not appear to be genetically linked in rice.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Biochemical Research Methods
Michael Schneider, Asis Shrestha, Agim Ballvora, Jens Leon
Summary: The proposed strategy accurately identifies the allele frequency of populations at low cost. This is particularly important for evolutionary plant breeding of crops with large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03x coverage per genotype accurately estimates allele frequency when a loci-based haplotyping approach is applied. The implementation of annotated haplotypes capitalizes on the biological background and statistical robustness.
Article
Plant Sciences
Boby Mathew, Andreas Hauptmann, Jens Leon, Mikko J. Sillanpaeae
Summary: Prediction of complex traits based on genome-wide marker information is crucial for animal and plant breeding. Many models have been proposed and efforts are being made to improve their accuracy, considering factors such as additive, dominance, and epistasis effects. In this study, a new algorithm that combines neural networks with LASSO is proposed, which accounts for local epistasis in the prediction. The new method was compared with commonly used prediction methods and showed superior accuracy.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Yoshiaki Ueda, Matthias Wissuwa
Summary: This study reveals that adding nitrate can improve phosphorus use efficiency (PUE) in rice under phosphorus deficiency, while P-inefficient plants have shorter roots compared to P-efficient plants under low phosphorus supply. Furthermore, P-efficient genotypes show lower accumulation of nitrate and expression of nitrate transporters in roots under low phosphorus supply, suggesting a positive correlation between PUE and nitrate utilization, which may modulate phosphorus utilization and uptake. These findings are of significance for improving crop production in phosphorus-impoverished soils.
Article
Multidisciplinary Sciences
Michael Schneider, Lucia Vedder, Benedict Chijioke Oyiga, Boby Mathew, Heiko Schoof, Jens Leon, Ali Ahmad Naz
Summary: The average sowing date for crops in temperate climates has shifted earlier by a few days, resulting in changes to the photoperiod during the emergence stage. A study comparing barley (a photoperiod-sensitive species) and tomato (a photoperiod-insensitive species) found differences in physiological development under short-day conditions. Barley showed reduced differentiation and photosynthetic activity compared to tomato, indicating slower physiological development. This may be due to underexpression of the photomorphogenesis controlling gene cry1 in barley.
Article
Agronomy
Mohammad Kamruzzaman, Asis Shrestha, Md Nurealam Siddiqui, Benedict Chijioke Oyiga, Agim Ballvora, Jens Leon, Ali Ahmad Naz
Summary: In this study, proline accumulation was found to increase significantly under water-deficit conditions in 150 bread wheat cultivars. Genome-wide association studies identified significant marker-trait associations on the 1A and 1B chromosomes. Cultivars originating from Europe were associated with higher proline content. Transcript analysis revealed higher expression of candidate genes in shoot/leaves under water-deficit stress conditions.
Article
Plant Sciences
Yanru Feng, Lin-Bo Wu, Sawitree Autarmat, Muhammad Shahedul Alam, Michael Frei
Summary: This study investigated the physiological responses and candidate genes for ozone tolerance in wheat. It found that sensitive genotypes showed a decrease in net photosynthetic rate and an increase in lipid peroxidation, while tolerant genotypes showed consistent antioxidant responses. Analysis of candidate genes located on chromosome 5A revealed differential expression and sequence polymorphisms between tolerant and sensitive genotypes. This study provides a step forward in understanding the molecular mechanism underlying ozone tolerance in wheat.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Agronomy
Flora Mueckschel, Elijah Ollo, Stefanie P. Glaeser, Rolf Duering, Feng Yan, Hermann Velten, Ulf Theilen, Michael Frei
Summary: Microalgae from wastewater treatments can serve as a source of nutrients for crops, particularly nitrogen. Wheat plants treated with microalgae biomass showed improved physiological performance, growth, and nutrient uptake compared to the control. However, their yields and nitrogen use efficiency were lower than with mineral fertilizer, and the abundance of rhizosphere microbes and ammonia-oxidizing microorganisms were not significantly affected.
JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE
(2023)
Article
Agronomy
Lam Thi Dinh, Yoshiaki Ueda, Daniel Gonzalez, Juan Pariasca Tanaka, Hideki Takanashi, Matthias Wissuwa
Summary: The rice root system consists of two types of lateral roots, L-type and S-type, which both contribute to nutrient and water uptake. The genotypic variation for lateral root density and length in rice could be used to improve its adaptations to nutrient and water-limited environments. Through screening in different growing media, it was found that nutrient solution screening exposed genotypic variation for S-type and L-type density, while only lateral roots of soil-grown plants varied in length. QTL mapping was used to identify markers linked to genotypic variation for lateral root traits. The QTL for L-type density on chromosome 5 had a major effect, accounting for 46% of the phenotypic variation. The identified markers provide opportunities for incorporating lateral root traits into a breeding program. Rating: 8/10
Article
Agronomy
Frederike Zeibig, Benjamin Kilian, Hakan Oezkan, Sumitra Pantha, Michael Frei
Summary: De novo domestication, which involves modifying the domestication genes in crop wild relatives using genome editing, is a method that utilizes the beneficial genetic diversity of these wild relatives. Phenotyping is a necessary step in identifying suitable genetic materials for cultivation in a specific environment. Certain wild wheats from the wheat genepool have shown to be adaptable to central European conditions and have desirable traits for domestication.
FOOD AND ENERGY SECURITY
(2023)
Article
Environmental Sciences
Ambika Pandey, Lin-Bo Wu, Varunseelan Murugaiyan, Gabriel Schaaf, Jauhar Ali, Michael Frei
Summary: Contamination of paddy soils with arsenic can have toxic effects on rice plants and increase arsenic accumulation in grains. The uptake and detoxification of different arsenic species in rice is not fully understood. This study investigated the toxic effects of arsenite and arsenate on rice plants and the role of glutathione S-transferase in detoxifying arsenic. The results showed that arsenite was more detrimental to plant growth and lipid peroxidation than arsenate. Overexpression of glutathione S-transferase led to improved plant growth and lower lipid peroxidation under acute arsenite stress. Overall, arsenite was found to be more toxic to plants than arsenate and glutathione S-transferase has differential effects on plant reactions and tolerance to different arsenic species.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yanru Feng, Muhammad Shahedul Alam, Feng Yan, Michael Frei
Summary: Tropospheric ozone has significant effects on the remobilization and allocation efficiency of aboveground biomass and nutrients in cereal crops. Long-term ozone exposure increases straw C:N ratio and affects grain C:N ratio. Grain N concentrations increase significantly under ozone stress, but N yield declines due to grain yield losses. Various indicators of N use efficiency are reduced, indicating reduced N absorption from soil and allocation from vegetative to reproductive organs. Straw C:N ratio is not suitable for predicting wheat productivity. Nitrogen harvest index (NHI) is not affected by ozone stress, but the relationship between harvest index (HI) and NHI is changed by elevated ozone concentration.
