Article
Agronomy
Ding Shilin, Liu Chaolei, Shang Lianguang, Yang Shenglong, Zhang Anpeng, Jiang Hongzhen, Ruan Banpu, Fang Guonan, Tian Biao, Ye Guoyou, Guo Longbiao, Qian Qian, Gao Zhenyu
Summary: Through QTL analysis, 36 loci related to Cd tolerance in rice seedlings were identified, with 6 of them associated with Cd tolerance coefficient. Key QTLs were qCDSL1.1 and qCDSL1.2. Further research indicated that the newly introduced CSSLqCDSL1 variety exhibited increased shoot length under Cd stress conditions.
Article
Plant Sciences
Hui Gao, Xiaoman Suo, Ling Zhao, Xinlei Ma, Ruhong Cheng, Genping Wang, Haoshan Zhang
Summary: This study investigated the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 may play a role in the ABA-dependent drought response pathway. The MADS gene family, which regulates plant growth, reproduction, and responses to abiotic stress, was analyzed in foxtail millet, green millet, and switchgrass using bioinformatics. Phylogenetic analysis categorized the genes into M and MIKC types, with similar motif distribution and gene structure. The expansion of this gene family was mainly due to segmental duplication, while a shrinking trend was observed in the three species. Purifying selection and positive selection sites were identified in the MADS genes, and many promoters contained stress and hormonal response-related cis-elements. RNA-seq and qRT-PCR analysis supported changes in SiMADS gene expression under various treatments. This study provides new insights into the evolution and expansion of the MADS family and lays the foundation for further research on their functions.
PLANT CELL REPORTS
(2023)
Article
Multidisciplinary Sciences
Taslima Haque, Sabrina M. Elias, Samsad Razzaque, Sudip Biswas, Sumaiya Farah Khan, G. M. Nurnabi Azad Jewel, Md Sazzadur Rahman, Thomas E. Juenger, Zeba Seraj
Summary: In this study, we utilized rice landraces from coastal Bangladesh to identify genetic loci contributing to salt adaptation in rice. We found unique QTLs for specific developmental stages and observed the significant effect of the cytoplasmic genome on certain traits. Additionally, we identified the constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Huimin Shi, Yang Wu, Liuxi Yi, Haibo Hu, Feiyan Su, Yanxia Wang, Dandan Li, Jianhua Hou
Summary: Improving drought tolerance in sunflower is crucial for breeding, and this study identified several effective traits and genes related to drought tolerance. The study provides insights into the molecular mechanisms of sunflower's response to drought stress and lays a foundation for sunflower drought tolerance breeding and genetic improvement.
Article
Agronomy
So-Myeong Lee, Nkulu Rolly Kabange, Ju-Won Kang, Youngho Kwon, Jin-Kyung Cha, Hyeonjin Park, Ki-Won Oh, Jeonghwan Seo, Hee-Jong Koh, Jong-Hee Lee
Summary: In this study, QTLs controlling grain filling in rice were investigated using KASP markers in a DH population derived from a cross between indica and japonica varieties. Three significant QTLs associated with grain filling were identified, and genes associated with diverse biological processes and molecular functions were found. Genes such as MYB, WRKY60, and OsSh1 played a key role in controlling grain filling under early cultivation conditions.
Article
Plant Sciences
Lei Chen, Weixia Lei, Wangfei He, Yifan Wang, Jie Tian, Jihui Gong, Bing Hao, Xinxin Cheng, Yingjie Shu, Zhixiong Fan
Summary: Research on the flowering habit of rapeseed is important for breeding early maturing varieties. This study identified multiple quantitative trait loci (QTL) related to the days-to-flowering trait in rapeseed. Two major QTLs were identified, and several genes potentially related to flowering time were found. A marker closely linked to the flowering time trait was also developed.
Article
Environmental Sciences
Juanli Chen, Xueyong Zhao, Yuqiang Zhang, Yongqing Luo, Zhaoquan He, Rui Zhang, Hailun Liu, Runxia Zhang
Summary: The study investigates the adaptation of Agriophyllum squarrosum and Setaria viridis seeds to drought stress in China's Horqin Sandy Land. Results indicate that A. squarrosum has stronger drought resistance compared to S. viridis. Different levels of drought impact seedling growth and physiological properties differently in the two species.
FRESENIUS ENVIRONMENTAL BULLETIN
(2021)
Article
Genetics & Heredity
Xiao-Yu Zhang, Huiying Gong, Qing Fang, Xuli Zhu, Libo Jiang, Rongling Wu
Summary: The study introduces a novel approach using a Holling type II functional response model to map genes affecting interspecific interactions. By applying this model to competition experiment data of two microbial species, previously uncharacterized QTLs responsible for microbial cooperation and competition were identified. This model offers a quantitative means for predicting the genetic architecture shaping the dynamic behavior of ecological communities.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Walid Raafat Nakhla, Wenqiang Sun, Kai Fan, Kang Yang, Chaopu Zhang, Sibin Yu
Summary: The study identified QTLs related to salt tolerance in rice using a BIL population. ACC9 showed higher germination rate but more repressed seedling growth under salt stress. These major loci will help improve salt-tolerance in rice through genome-breeding programs.
Article
Plant Sciences
Yuan Huang, Yang Jiao, Sha Yang, Dandan Mao, Feng Wang, Liangbi Chen, Manzhong Liang
Summary: This study revealed the molecular mechanism of the 9-cis-epoxycarotenoid dioxygenase gene, SiNCED1, in the drought stress response of foxtail millet. Ectopic overexpression of SiNCED1 enhanced drought stress resistance by increasing endogenous ABA levels and promoting stomatal closure. SiNCED1 also delayed seed germination. SiNCED1 is an important candidate gene for improving drought stress tolerance in foxtail millet.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Abinaya Manivannan, Koeun Han, Sun Yi Lee, Hye-Eun Lee, Jong Pil Hong, Jinhee Kim, Ye-Rin Lee, Eun Su Lee, Do-Sun Kim
Summary: The study revealed that the fruit color of strawberries is regulated by multiple genes, with the MYB10 transcription factor playing a crucial role in the anthocyanin pathway. Through genome-wide investigation and QTL identification, candidate genes influencing fruit color were predicted, providing important insights into the formation of fruit color in strawberries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agronomy
Xinmin Hu, Guihua Wang, Xuemei Du, Hongwei Zhang, Zhenxiang Xu, Jie Wang, Guo Chen, Bo Wang, Xuhui Li, Xunji Chen, Junjie Fu, Jun Zheng, Jianhua Wang, Riliang Gu, Guoying Wang
Summary: This study created a doubled haploid (DH) maize population to investigate the genetic basis of traits related to drought tolerance, identifying QTL associated with drought tolerance as well as environment-dependent QTL. The findings confirm the significant impact of four chromosome regions on maize drought tolerance and provide valuable insights for fine mapping and marker-assisted breeding of drought-tolerant maize.
Article
Agronomy
Lei Chu, Yiping Gao, Lingling Chen, Patrick E. McCullough, David Jespersen, Suraj Sapkota, Muthukumar Bagavathiannan, Jialin Yu
Summary: The key factors for successful germination and emergence of white clover are light, temperature, planting depth, drought, and salt stress. White clover seeds are negatively photoblastic and show differential responses to temperature. Deeper planting depth leads to lower germination rate, and the optimal depth is <= 1 cm. White clover seeds are highly sensitive to drought and salt stress. These findings provide a foundation for achieving successful establishment of white clover stands.
Article
Plant Sciences
Parthiban Thathapalli Prakash, Darshi Banan, Rachel E. Paul, Maximilian J. Feldman, Dan Xie, Luke Freyfogle, Ivan Baxter, Andrew D. B. Leakey
Summary: Mechanistic modeling suggests that reducing stomatal conductance can enhance water use efficiency in C-4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in Setaria, a C-4 genus. Multiple QTL were identified for stomatal density and canopy temperature, indicating a common genetic architecture between stomatal patterning and WUE.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Karoline Estefani Duarte, Marcos Fernando Basso, Nelson Geraldo de Oliveira, Jose Cleydson Ferreira da Silva, Bruno de Oliveira Garcia, Barbara Andrade Dias Brito Cunha, Thiago Bergamo Cardoso, Alexandre Lima Nepomuceno, Adilson Kenji Kobayashi, Thais Ribeiro Santiago, Wagner Rodrigo de Souza, Hugo Bruno Correa Molinari
Summary: Water deficit is a major constraint for economic crops, but plants have an active defense system involving miRNAs for adaptation. This study investigated the miRNA expression profile in response to different levels of water deficit in Setaria viridis. The results showed differential modulation of miRNAs and their target genes related to cell wall remodeling, antioxidant system, and drought-related transcription factors. These findings have implications for improving drought tolerance in economically important crops.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2022)
Article
Biochemical Research Methods
Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable
Summary: RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. The comparative gene expression tool qTeller has been revamped to take advantage of the growing number of public RNA-Seq datasets, enabling users to evaluate gene expression data in a defined genomic interval and perform two-gene comparisons across multiple user-chosen tissues. The updated qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets, along with support for additional data formats and a modernized interface.
Article
Plant Sciences
Guangchao Sun, Ravi V. Mural, Jonathan D. Turkus, James C. Schnable
Summary: Southern rust is a severe foliar disease of maize caused by infection of the fungus Puccinia polysora. Environmental conditions like increased temperatures and humidity, as well as warmer winters, may lead to more severe outbreaks in the U.S. Corn Belt. Genome-wide and transcriptomewide studies have identified various genetic loci associated with resistance to southern rust in temperate-adapted maize germplasm.
Article
Multidisciplinary Sciences
Huihui Yu, Mu Li, Jaspreet Sandhu, Guangchao Sun, James C. Schnable, Harkamal Walia, Weibo Xie, Bin Yu, Jeffrey P. Mower, Chi Zhang
Summary: The study developed computational pipelines to identify microexons in plants and showed their importance and diversity in plant evolution.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Ravi V. Mural, James C. Schnable
Article
Plant Sciences
J. Lucas Boatwright, Sirjan Sapkota, Hongyu Jin, James C. Schnable, Zachary Brenton, Richard Boyles, Stephen Kresovich
Summary: Association mapping panels are important resources for understanding the genetic basis of phenotypic diversity and advancing plant breeding. In this study, the whole-genome sequencing of 400 sorghum accessions enabled the development of a high-density genomic marker set and the identification of novel genomic associations for plant height and tannin content. The use of whole-genome sequencing markers improved the predictive ability of genomic models, and the population served as a significant public resource for sorghum research.
Article
Biology
Michael A. Meier, Gen Xu, Martha G. Lopez-Guerrero, Guangyong Li, Christine Smith, Brandi Sigmon, Joshua R. Herr, James R. Alfano, Yufeng Ge, James C. Schnable, Jinliang Yang
Summary: The composition of the rhizobiome is influenced by host plant genetics, with a greater impact under low nitrogen conditions. This study also identifies genetic markers associated with the abundance of specific microbial groups in the maize rhizobiome and their correlation with plant vigor.
Article
Microbiology
Nate Korth, Leandra Parsons, Mallory J. Van Haute, Qinnan Yang, Preston Hurst, James C. Schnable, David R. Holding, Andrew K. Benson
Summary: The study found that high-quality protein popcorn can promote the production of more butyrate by human gut microbiomes. The opaque-2 mutation leads to the synthesis of beneficial new seed proteins, which in turn have a positive impact on the gut microbiota.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Delin Li, Dong Bai, Yu Tian, Ying-Hui Li, Chaosen Zhao, Qi Wang, Shiyu Guo, Yongzhe Gu, Xiaoyan Luan, Ruizhen Wang, Jinliang Yang, Malcolm J. J. Hawkesford, James C. C. Schnable, Xiuliang Jin, Li-Juan Qiu
Summary: Advances in plant phenotyping technologies have reduced the costs of collecting phenotypic measurements across multiple time points. The use of time-series phenotypic data in this study enabled the identification of previously uncharacterized loci and improved the accuracy of genome-wide association studies. Additionally, this data set revealed the presence of adaptive selection in certain loci during domestication.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Plant Sciences
Marcin W. Grzybowski, Ravi V. Mural, Gen Xu, Jonathan Turkus, Jinliang Yang, James C. Schnable
Summary: Maize populations show vast diversity in both genetic and phenotypic traits. Resequencing strategies have been used to identify millions of genetic variants within and between maize populations, but inconsistencies in analytical pipelines, reference genome assemblies, and minor allele frequency filtering often limit the reuse and remixing of genetic diversity data for new research questions. This study utilized resequencing data from published and newly sequenced maize samples to create a unified marker set of over 366 million segregating variants, providing increased power to identify known flowering-time genes and track changes in allele frequency across the global distribution of maize.
Article
Agriculture, Multidisciplinary
Mathieu Gaillard, Bedrich Benes, Michael C. Tross, James C. Schnable
Summary: We propose a new method for solving the joint problem of correspondence and triangulation of points from multiple calibrated perspective views. This method has been successfully applied to counting the number of leaves on plants photographed from multiple angles. Our algorithm is robust to noise and occlusion, and can infer occluded points by reasoning on the 3D geometry of the scene. It can handle a large number of points reconstructed from a reduced set of views.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2023)
Article
Plant Sciences
Nuwan K. Wijewardane, Huichun Zhang, Jinliang Yang, James C. Schnable, Daniel P. Schachtman, Yufeng Ge
Summary: A spectral library of maize and sorghum is developed to estimate leaf properties and is effective in predictions for soybean and camelina using extra-weighted spiking. Leaf-level hyperspectral reflectance is an effective tool in plant leaf phenotyping. However, model transferability among different datasets is poor. This study aims to assemble a large leaf hyperspectral library, evaluate machine-learning approaches to estimate leaf properties, and investigate the usefulness of the library for predicting external datasets.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Kang Zhang, Yinqing Yang, Xin Zhang, Lingkui Zhang, Yu Fu, Zhongwei Guo, Shumin Chen, Jian Wu, James C. Schnable, Keke Yi, Xiaowu Wang, Feng Cheng
Summary: Orychophragmus violaceus, known as eryuelan in China, is an early-flowering ornamental plant with potential as a high-quality oilseed crop. By sequencing technologies, a 1.3 Gb genome was assembled for O. violaceus, which went through tetraploidization from a diploid progenitor. Comparative analysis suggests subgenome dominance and independent tetraploidization in O. violaceus, which is closely related to the Brassica genus. The findings shed light on polyploidization evolution and functional innovation in O. violaceus.
PLANT COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Guangchao Sun, Huihui Yu, Peng Wang, Martha Lopez-Guerrero, Ravi V. Mural, Olivier N. Mizero, Marcin Grzybowski, Baoxing Song, Karin van Dijk, Daniel P. Schachtman, Chi Zhang, James C. Schnable
Summary: This study examined how changes in transcriptional regulation allow maize to adapt to temperate environments. Through RNA-seq analysis of maize genotypes, they identified genes with different heritability of expression and alternative splicing. They also discovered loci regulating co-expression modules involved in various biological processes. Additionally, a GWAS identified candidate genes related to adaptation to temperate environments.
Article
Biology
Ravi Mural, Guangchao Sun, Marcin Grzybowski, Michael C. Tross, Hongyu Jin, Christine Smith, Linsey Newton, Carson M. Andorf, Margaret R. Woodhouse, Addie M. Thompson, Brandi Sigmon, James C. Schnable
Summary: Classical genetic studies have found that mutations in individual genes can affect multiple phenotypes. However, current quantitative genetic studies of natural genetic variants often only examine a few traits, limiting the potential to identify pleiotropic effects. This study used high-density genetic marker data and a genome-wide association strategy to identify marker-trait associations in the maize genome. Many associations were found between genetic loci and diverse traits, as well as the same or similar traits across different environments. Additionally, significant signals were located near genes with previously unknown functions.
Proceedings Paper
Engineering, Electrical & Electronic
Shakir-ul Haque Khan, Mohit Karkhanis, Bryan Hatasaka, Sayali Tope, Seungbeom Noh, Rana Dalapati, Ashrafuzzaman Bulbul, Ravi Mural, Aishwaryadev Banerjee, KyeongHeon Kim, James C. Schnable, Mingyue Ji, Carlos H. Mastrangelo, Ling Zang, Hanseup Kim
Summary: This study reports the successful detection of actual hexanal released from damaged sorghums using a field-deployed nano-gap gas sensor, demonstrating the feasibility of monitoring the mechanical stress status of sorghums through gas monitoring.
2022 IEEE 35TH INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS CONFERENCE (MEMS)
(2022)
