Article
Agronomy
Takanori Kuronuma, Hitoshi Watanabe
Summary: Tipburn is a severe problem in lisianthus cultivar production, with previous studies showing excessive Ca accumulation in the roots of affected cultivars. RNA-seq analysis identified CAX5 and ACA12 as candidate genes possibly causing excessive Ca accumulation in the roots of tipburn-occurrence lisianthus cultivars.
Article
Plant Sciences
Qibin Wu, Yachun Su, Yong-Bao Pan, Fu Xu, Wenhui Zou, Beibei Que, Peixia Lin, Tingting Sun, Michael P. P. Grisham, Liping Xu, Youxiong Que
Summary: In this study, a large number of progenies were generated by crossing different sugarcane varieties, and the differential gene expression between resistant and susceptible progenies was analyzed by RNA sequencing. SNP markers and candidate genes associated with smut resistance were identified, and a potential molecular mechanism of sugarcane's resistance to smut was proposed.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Computer Science, Information Systems
Muhab Hariri, Ercan Avsar
Summary: In this study, a sequential convolutional neural network (CNN) model, PSO-CNN, was developed for tipburn detection in strawberry leaf images. Through optimization of the CNN architecture, dropout, and learning rates based on the particle swarm optimization (PSO) algorithm, the PSO-CNN achieved the best performance in accuracy, sensitivity, and specificity. The PSO-CNN model also requires less computation due to its smaller number of parameters compared to benchmark models.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Article
Horticulture
John Ertle, Chieri Kubota
Summary: Low evaporative conditions in indoor farms lead to tipburn of lettuce, which affects the appearance and economic value of the crop. Differences in tipburn sensitivity among cultivars are not significantly correlated with morphology or anthocyanin content.
Article
Plant Sciences
Shu Zhang, Hanzhong Gao, Lixia Wang, Yihui Zhang, Dandan Zhou, Ali Anwar, Jingjuan Li, Fengde Wang, Cheng Li, Ye Zhang, Jianwei Gao
Summary: This study comprehensively analyzed the transcriptomic differences between control and calcium treatments in Chinese cabbage and identified the molecular mechanisms involved in tipburn. The most enriched gene ontology categories were photosynthesis, thylakoid, and cofactor binding, while the KEGG pathway analysis showed enrichment in photosynthesis, carbon metabolism, and carbon fixation. Ten critical hub differentially expressed genes (DEGs) were identified in each gene regulatory network, indicating their potential roles in various biological processes. Under calcium deficiency, certain proteins and genes involved in calcium distribution, plant hormone biosynthesis, and transcription factors were downregulated. These results provide important evidence of the calcium signal transduction pathway and candidate genes governing tipburn in Chinese cabbage.
Article
Plant Sciences
Samar G. Thabet, Yasser S. Moursi, Ahmed Sallam, Mohamed A. Karam, Ahmad M. Alqudah
Summary: The study evaluated salt stress tolerance in 121 global spring barley accessions, identifying 80 significant SNPs associated with the traits studied, many of which encode potassium channels. Genes linked to salinity stress tolerance during seedling developmental phase were identified for the first time in this study.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Horticulture
John Ertle, Chieri Kubota
Summary: Indoor vertical farms commonly face tipburn in lettuce plants due to calcium deficiency. Lowering the daily light integral can reduce tipburn, but it also decreases final yield. This study examines the effect of lowering the daily light integral during the end of production and finds that it only yields profit for certain cultivars.
Article
Genetics & Heredity
Michael J. Gloudemans, Brunilda Balliu, Daniel Nachun, Theresia M. Schnurr, Matthew G. Durrant, Erik Ingelsson, Martin Wabitsch, Thomas Quertermous, Stephen B. Montgomery, Joshua W. Knowles, Ivan Carcamo-Orive
Summary: Identification of causal genes for cardiometabolic diseases, such as diabetes, obesity, and dyslipidemia, is challenging. The study combines linkage disequilibrium-adjusted colocalization analyses with expression and splicing quantitative trait loci to identify potential causal genes and their regulators associated with insulin resistance.
Review
Biochemistry & Molecular Biology
Alice Caldiroli, Enrico Capuzzi, Letizia M. M. Affaticati, Teresa Surace, Carla L. L. Di Forti, Antonios Dakanalis, Massimo Clerici, Massimiliano Buoli
Summary: Social anxiety disorder (SAD) is a common psychiatric condition that requires prompt treatment to prevent psychiatric comorbidity and impairment in social and occupational functioning. This study systematically reviewed the literature on potential biomarkers for SAD. While some preliminary evidence suggests the role of certain genes and neuroimaging findings in SAD, the results overall remain inconsistent and need further investigation on larger samples to identify more specific biomarkers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Binbin Wen, Xingyao Gong, Xiude Chen, Qiuping Tan, Ling Li, Hongyu Wu
Summary: This study identified differentially expressed genes in apple leaves under early and late nitrogen deficiency stress. Functional analysis revealed the involvement of these genes in pathways and metabolic networks related to apple adaptation to nitrogen deficiency stress. Furthermore, MdNAC4 was identified as a key transcription factor regulating nitrogen deficiency stress.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Plant Sciences
Hongchun Xiong, Yuting Li, Huijun Guo, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Yuping Ding, Luxiang Liu
Summary: This study constructed a high-density genetic linkage map for wheat using the Wheat55K SNP Array and identified QTLs affecting heading date, plant height, thousand grain weight, and spike length in RILs. KASP markers were developed for validation of detected QTLs, and candidate genes affecting PH and TGW were identified, providing new insight into genetic study for wheat traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Sunil S. Gangurde, Aamir W. Khan, Pasupuleti Janila, Murali T. Variath, Surendra S. Manohar, Prashant Singam, Annapurna Chitikineni, Rajeev K. Varshney, Manish K. Pandey
Summary: Seed weight has a direct impact on the yield and market price of groundnut. Marker-based early generation selection can accelerate breeding for large-seeded varieties. QTL-seq was used to identify candidate genes and develop markers for seed weight in groundnut.
Article
Plant Sciences
Chong Zhang, Wenping Xie, Huiwen Fu, Yuting Chen, Hua Chen, Tiecheng Cai, Qiang Yang, Yuhui Zhuang, Xin Zhong, Kun Chen, Meijia Gao, Fengzhen Liu, Yongshan Wan, Manish K. Pandey, Rajeev K. K. Varshney, Weijian Zhuang
Summary: QTL-seq was used to identify a candidate genomic region associated with resistance to Ralstonia solanacearum, which contained 180 nonsynonymous SNPs and 14 InDels affecting 75 and 11 putative candidate genes, respectively. Two diagnostic SNP markers were validated and showed high phenotypic variation in resistant and susceptible lines.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Horticulture
Servet Aras, Hakan Keles, Erhan Bozkurt
Summary: Calcium is crucial for the growth and development of peach plants, with deficiency leading to growth inhibition, damage to cell membranes, and impaired chlorophyll synthesis. Garnem rootstock showed more tolerance to calcium deficiency compared to GF 677, possibly due to larger cortical cells and hyperplasia and hypertrophy of xylem vessel elements increasing stomatal conductance.
SCIENTIA HORTICULTURAE
(2021)
Article
Plant Sciences
Yawei Li, Li Chu, Xiaofeng Liu, Nannan Zhang, Yufei Xu, Benjamin Karikari, Yu Wang, Fangguo Chang, Zexinan Liu, Lianmei Tan, Han Yue, Guangnan Xing, Tuanjie Zhao
Summary: In this study, the genetic mechanisms of soybean pubescence traits were investigated through QTL mapping, leading to the identification of candidate genes related to pubescence length and density. The study also revealed the relationship between these traits and resistance to common cutworm in soybean.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
M. Macias-Gonzalez, M. J. Truco, R. Smith, M. Cahn, I. Simko, R. Hayes, R. W. Michelmore
Summary: This study investigated the genetics of robustness in lettuce under changing nitrogen and water application conditions. It was found that efficiency, sensitivity, and plant nitrogen uptake and utilization were important traits affecting robustness. The research also revealed that the performance of efficiency and sensitivity in lettuce under nitrogen and water conditions was genetically independent and could be improved through breeding efforts.
Article
Plant Sciences
Rongkui Han, Andy J. Y. Wong, Zhehan Tang, Maria J. Truco, Dean O. Lavelle, Alexander Kozik, Yufang Jin, Richard W. Michelmore
Summary: The study utilized a combination of remote sensing, machine learning, Bayesian statistics, and genome-wide marker data to research the genetics of the difficult trait of floral opening and closure. Through imaging scoring and locus analysis, genetic determinants controlling floral opening time were revealed.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Letter
Biotechnology & Applied Microbiology
Guanghui An, Ivan Simko, Jiongjiong Chen, Changchun Yu, Dean Lavelle, Weiyi Zhang, Richard W. Michelmore, Hanhui Kuang
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Agronomy
Rongkui Han, Dean Lavelle, Maria Jose Truco, Richard Michelmore
Summary: Genetic mapping in lettuce revealed distinct sets of QTLs controlling flowering time independently of day length and in response to photoperiod, which have significant impact on agricultural production. Variations in flowering time and photoperiod sensitivity exist among wild and cultivated lettuce accessions, with orthology and sequence analysis indicating potential functional equivalents to key regulators in Arabidopsis.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Agronomy
Harry Pink, Adam Talbot, Abi Graceson, Juliane Graham, Gill Higgins, Andrew Taylor, Alison C. Jackson, Maria Truco, Richard Michelmore, Chenyi Yao, Frances Gawthrop, David Pink, Paul Hand, John P. Clarkson, Katherine Denby
Summary: This study demonstrated genetic variation in quantitative resistance to important fungal pathogens in lettuce and its wild relatives. Transcriptome profiling was used to identify genes associated with resistance, highlighting the importance of post-transcriptional gene regulation in lettuce defense response.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Tawni Bull, Juan Debernardi, Megan Reeves, Theresa Hill, Lien Bertier, Allen Van Deynze, Richard Michelmore
Summary: Chimeric proteins created from GRF-GIF genes from multiple species can enhance in vitro regeneration in both wild and cultivated lettuces, including butterheads, romaines, and crispheads. Manipulation of key transcription factors such as BABY BOOM, WUSCHEL, and GROWTH-REGULATING FACTORs (GRFs) has been shown to improve regeneration and transformation efficiencies in various plant species. The study also presents a co-transformation strategy for increased transformation efficiency and recovery of transgenic plants harboring a gene of interest.
PLANT CELL REPORTS
(2023)
Article
Genetics & Heredity
William Palmer, Ewelina Jacygrad, Sagayamary Sagayaradj, Keri Cavanaugh, Rongkui Han, Lien Bertier, Bob Beede, Salih Kafkas, Deborah Golino, John Preece, Richard Michelmore
Summary: Understanding the genetic basis of phenotypic variability in pistachio rootstocks is crucial for crop breeding and improvement. Through genome assemblies and genotyping, we identified loci associated with tree size, shape, sex, and phenotypic measures in UCB-1 rootstocks. Two loci were found to interact epistatically and generate the bimodal distribution of tree size observed in commercial orchards. These findings provide valuable insights for marker development and selection of vigorous pistachio UCB-1 rootstock.
G3-GENES GENOMES GENETICS
(2023)
Article
Genetics & Heredity
John T. Davis, Ruijuan Li, Seungmo Kim, Richard Michelmore, Shinje Kim, Julin N. Maloof
Summary: In this study, a new genome assembly of the synthetic B. napus cultivar Da-Ae was generated using third-generation sequencing and assembly technologies, providing a high-quality reference genome of a synthetic B. napus. Additionally, potential hotspots of homoeologous exchange between subgenomes within Da-Ae were identified based on their presence in other independently derived lines, shedding light on the genetic rearrangements necessary for B. napus viability following the hybridization of B. rapa and B. oleracea.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Wei Xiong, Lidija Berke, Richard Michelmore, Dirk-Jan M. van Workum, Frank F. M. Becker, Elio Schijlen, Linda V. Bakker, Sander Peters, Rob van Treuren, Marieke Jeuken, Klaas Bouwmeester, M. Eric Schranz
Summary: Lactuca saligna, a wild relative of cultivated lettuce, exhibits hybrid incompatibility and broad-spectrum resistance against lettuce downy mildew. The resistance is attributed to the presence of pathogen recognition receptors, including NLRs and RLKs, in certain genomic regions. A chromosome-level genome assembly of L. saligna revealed the presence of large inversions compared to L. sativa. RNA-seq analysis identified differentially expressed RLKs in the NHR regions, suggesting their role as determinants of the NHR phenotype.
Article
Genetics & Heredity
Wei Xiong, Dirk-Jan M. van Workum, Lidija Berke, Linda Bakker, Elio Schijlen, Frank F. M. Becker, Henri van de Geest, Sander Peters, Richard Michelmore, Rob van Treuren, Marieke Jeuken, Sandra Smit, M. Eric Schranz
Summary: This study presents a de novo reference assembly of L. virosa with high continuity and complete gene space. It compares the genome of L. virosa with that of L. sativa and L. saligna, providing insights into genetic variations and potential breeding challenges. The analysis reveals chromosomal inversions and the role of long-terminal repeat elements in genome expansion. It also investigates immune genes and receptor-like kinases, contributing to the understanding of evolutionary patterns. These findings are important for breeding improved lettuce varieties.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Csanad Gurdon, Alexander Kozik, Rong Tao, Alexander Poulev, Isabel Armas, Richard W. Michelmore, Ilya Raskin
Summary: Dietary flavonoids play a crucial role in human nutrition and health. Mutants of flavonoid biosynthesis genes in lettuce have been characterized, revealing the impact of transposon insertions on gene expression levels. Analysis of flavonoid content suggests a positive correlation between leaf cyanidin levels and gene expression levels.
