Article
Multidisciplinary Sciences
Junli Zhang, Hongchun Xiong, German F. Burguener, Hans Vasquez-Gross, Qiujie Liu, Juan M. Debernardi, Alina Akhunova, Kimberly Garland-Campbell, Shahryar F. Kianian, Gina Brown-Guedira, Curtis Pozniak, Justin D. Faris, Eduard Akhunov, Jorge Dubcovsky
Summary: In this study, the researchers conducted a sequencing analysis on mutagenized wheat plants and identified millions of induced mutations. They also predicted the effects of these mutations on annotated genes. By selecting and studying specific mutations, they demonstrated the biological value of the promoter data set. These mutant collections provide valuable tools for understanding and modulating gene expression and phenotypes in wheat.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Amanda J. Burridge, Mark O. Winfield, Paul A. Wilkinson, Alexandra M. Przewieslik-Allen, Keith J. Edwards, Gary L. A. Barker
Summary: In this study, the bread wheat genome was analyzed using exome capture and sequencing techniques, revealing variable regions and potential undocumented introgressions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Zhenyu Wang, Shu Tao, Shaoshuai Liu, Meiling Jia, Dada Cui, Guoliang Sun, Zhongyin Deng, Fang Wang, Xingchen Kong, Mingxue Fu, Yuqing Che, Ruyi Liao, Tao Li, Shuaifeng Geng, Long Mao, Aili Li
Summary: In this study, we identified the genomic locus underlying a wheat dense spike mutant using a multi-omics approach. We found that genes located in the deleted regions were associated with reduced spike length and grain development. Our findings suggest that hormone-related genes, particularly the candidate gene TraesCS6B01G334600, may play a role in regulating spike architecture in wheat. This study provides valuable resources and insights for future research on wheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Hao Tang, Huixue Dong, Xiaojiang Guo, Mengping Cheng, Maolian Li, Qian Chen, Zhongwei Yuan, Zhien Pu, Jirui Wang
Summary: The AK-3537 mutant of wheat, obtained through EMS treatment, exhibits a recessive inheritance pattern and is characterized by hollow endosperm and shrunken grain. Using BSR-seq, BSE-seq, and SNP-index algorithm, two candidate regions (DCR1 and DCR2) on chromosome 7A were identified for the grain Dek phenotype. The candidate gene TraesCS7A03G0625900 (HMGS-7A) encodes a 3-hydroxy-3-methylglutaryl-CoA synthase and its functional changes may affect the expression of key enzyme genes involved in wheat starch synthesis.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Biotechnology & Applied Microbiology
Dharmendra Singh, Priya Chaudhary, Jyoti Taunk, Chandan Kumar Singh, Viswanathan Chinnusamy, Amitha Mithra Sevanthi, Vikram Jeet Singh, Madan Pal
Summary: Conventional crop breeding alone cannot solve global hunger, but the development of high throughput reverse genetics approaches, such as TILLING, has greatly benefited plant breeding programs. TILLING employs mutagenesis to create new genetic sources and identify superior alleles. Modifications to the original TILLING protocol, such as EcoTILLING and De-TILLING, have widened its applicability to different crops. Combining next generation sequencing with TILLING allows for efficient screening of germplasm collections and mutant populations.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Dongzhi Wang, Yongpeng Li, Haojie Wang, Yongxin Xu, Yiman Yang, Yuxin Zhou, Zhongxu Chen, Yuqing Zhou, Lixuan Gui, Yi Guo, Chunjiang Zhou, Wenqiang Tang, Shuzhi Zheng, Lei Wang, Xiulin Guo, Yingjun Zhang, Fa Cui, Xuelei Lin, Yuling Jiao, Yuehui He, Junming Li, Fei He, Xigang Liu, Jun Xiao
Summary: In this study, a library for the popular wheat variety KN9204 was created using EMS mutagenesis, providing a comprehensive understanding of its genome, transcriptome, and epigenome. Exome capture sequencing revealed a high mutation rate in coding genes, with an average of 1383 EMS-type SNPs per line. New allelic variations for important agronomic trait-related genes were identified, and altered sensitivity to drought and salinity stress was observed in certain NAC transcription factors. This research provides valuable resources for functional genomics research and genetic manipulation of wheat.
PLANT COMMUNICATIONS
(2023)
Article
Agronomy
Zhangchen Zhao, Qinglin Wen, Li Zhe, Xianglan Kong, Valentina Spanic, Liang Chen, Yin-Gang Hu
Summary: The interaction between Rht15 and Rht1 could not overcome the inhibitory effect of Rht1 on coleoptile growth but alleviated the negative effect of Rht1 on root length. The combination of Rht15 and Rht1 showed strong effects on reducing plant height and improving lodging resistance, but the grain yield per plant was still lower than that of Rht1 lines.
EUROPEAN JOURNAL OF AGRONOMY
(2023)
Article
Plant Sciences
Elizabeth A. Chapman, Simon Orford, Jacob Lage, Simon Griffiths
Summary: Study confirms two wheat cultivars exhibit beneficial staygreen traits, delaying senescence and improving grain filling. Utilization of genetic mapping and mutation analysis provides insight into candidate genes regulating senescence.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Clinical Neurology
Olivia V. Poole, Chiara Pizzamiglio, David Murphy, Micol Falabella, William L. Macken, Enrico Bugiardini, Cathy E. Woodward, Robyn Labrum, Stephanie Efthymiou, Vincenzo Salpietro, Viorica Chelban, Rauan Kaiyrzhanov, Reza Maroofian, Anthony A. Amato, Allison Gregory, Susan J. Hayflick, Hallgeir Jonvik, Nicholas Wood, Henry Houlden, Jana Vandrovcova, Michael G. Hanna, Alan Pittman, Robert D. S. Pitceathly
Summary: The expanding catalog of neurogenetic disorders has led to a shift towards early clinical whole exome sequencing (WES). By reanalyzing exomes enriched with neurological diseases, pathogenic mtDNA variants were identified which resulted in diagnostic improvements in neurological diseases.
ANNALS OF NEUROLOGY
(2021)
Article
Medicine, Research & Experimental
Serena Brundu, Virginia Napolitano, Giulia Franzolin, Ettore Lo Cascio, Roberta Mastrantonio, Gabriele Sardo, Eliano Cascardi, Federica Verginelli, Sergio Sarnataro, Gennaro Gambardella, Alberto Pisacane, Alessandro Arcovito, Carla Boccaccio, Paolo M. Comoglio, Enrico Giraudo, Luca Tamagnone
Summary: The genetic changes responsible for the development of cancers of unknown primary (CUP) remain unknown. However, a study comparing the mutational landscape of CUPs with that of other tumors identified a consistent enrichment of changes in the axon guidance genes. Specifically, a G842C mutation of PlexinB2 (PlxnB2) was found to be activating. Knocking down the mutated PlxnB2 impaired self-renewal and proliferation in CUP stem cells, while genetic transfer of G842C-PlxnB2 promoted proliferation and tumorigenesis. The mutated PlxnB2 also induced invasiveness in CUP cells, which could be blocked by EGFR inhibition.
EMBO MOLECULAR MEDICINE
(2023)
Article
Plant Sciences
Yunfeng Jiang, Luyao Duan, Fangnian Guan, Fangjie Yao, Li Long, Yuqi Wang, Xuyang Zhao, Hao Li, Wei Li, Qiang Xu, Qiantao Jiang, Jirui Wang, Yuming Wei, Jian Ma, Houyang Kang, Pengfei Qi, Mei Deng, Youliang Zheng, Guoyue Chen
Summary: In this study, a candidate genomic region strongly associated with stripe rust resistance on chromosome 1AL was identified using bulked segregant analysis coupled with exome capture sequencing (BSE-seq). The gene, designated as YrXH-1AL, was validated by a conventional quantitative trait locus analysis and explained up to 48.50% of the phenotypic variance. Two cosegregating KASP markers showed high polymorphisms among Chinese wheat cultivars and could be used for marker-assisted selection.
Article
Multidisciplinary Sciences
Mathieu Quinodoz, Virginie G. Peter, Nicola Bedoni, Beryl Royer Bertrand, Katarina Cisarova, Arash Salmaninejad, Neda Sepahi, Raquel Rodrigues, Mehran Piran, Majid Mojarrad, Alireza Pasdar, Ali Ghanbari Asad, Ana Berta Sousa, Luisa Coutinho Santos, Andrea Superti-Furga, Carlo Rivolta
Summary: Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, and AutoMap efficiently identifies runs of homozygosity in WES and WGS data, showing clear benefits for molecular diagnosis and research activities in medical genetics.
NATURE COMMUNICATIONS
(2021)
Article
Biodiversity Conservation
Allison Q. Byrne, Corinne L. Richards-Zawacki, Jamie Voyles, Ke Bi, Roberto Ibanez, Erica Bree Rosenblum
Summary: This study focused on the genetics of two endangered harlequin frog species facing extinction in Panama, revealing a significant decrease in genetic diversity in contemporary A. varius populations compared to historical populations. While no strong evidence of selection for Bd resistance genes was found, preliminary evidence of genetic rescue potential in one of the largest persisting A. varius populations in Panama was uncovered. Additionally, the study proposed modifications to previous conservation units based on the lack of clear genetic breaks beyond local population levels.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yi Han, Prasenjit Das, Yiwen He, Dan C. Sorescu, Kenneth D. Jordan, Nathaniel L. Rosi
Summary: Crucial steps in designing water sorption materials include precise identification of adsorption sites and understanding water adsorption process. By mapping the adsorbed water molecules in ALP-MOF-1 and conducting density functional theory computations, it was found that the identity of open metal sites in MOFs can significantly affect water adsorption behavior, and multiple proximal water anchoring sites along the MOF skeleton facilitate water uptake.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Fereshte Damavandi, Weiwei Wang, Wei-Zheng Shen, Sibel Cetinel, Tracy Jordan, Juan Jovel, Carlo Montemagno, Gane Ka-Shu Wong
Summary: This study presents a probe-based capture method utilizing DNA-clicked iron oxide nanoparticles for enrichment of target sequences, compared to commercial capture assays. The method showed higher specificity and sensitivity, likely achieved through an inert silica coating and high density of DNA probes, potentially transforming the management of infectious diseases.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Estanislao Burgos, Maria Belen De Luca, Isidore Diouf, Luis A. de Haro, Elise Albert, Christopher Sauvage, Zhao J. Tao, Luisa Bermudez, Ramon Asis, Adriano N. Nesi, Michel Matringe, Claire Brehelin, Thomas Guiraud, Carine Ferrand, Isabelle Atienza, Joana Jorly, Jean P. Mauxion, Pierre Baldet, Alisdair R. Fernie, Leandro Quadrana, Christophe Rothan, Mathilde Causse, Fernando Carrari
Summary: By studying the genetic determinants of tocochromanol accumulation in tomato fruits and genetically engineering their biosynthetic pathway, a total of 25 quantitative trait loci were identified across the genome. By bypassing specific pathway points, the engineered tomatoes showed increased tocopherols and tocotrienols content, indicating a trade-off between VTE and natural variation in chorismate metabolism.
Article
Agronomy
Chon-Sik Kang, Young-Jun Mo, Kyeong-Min Kim, Kyeong-Hoon Kim, Jae-Buhm Chun, Chul-Soo Park, Seong-Woo Cho
Summary: This study identified several QTLs affecting yield potential in wheat by using a recombinant inbred line population derived from Korean wheat cultivars. Multiple stable QTLs were detected in at least two environments, including those influencing spike length, tiller number, and length of center rachis. Taejoong contributed significantly to the spike length QTLs.
Article
Plant Sciences
Jae-Sung Lee, Dmytro Chebotarov, Kenneth L. McNally, Valerien Pede, Tri Deri Setiyono, Rency Raquid, Woong-Jo Hyun, Ji-Ung Jeung, Ajay Kohli, Youngjun Mo
Summary: Pre-harvest sprouting (PHS) poses a serious threat to rice production, especially in regions cultivating japonica varieties like California, Japan, and Korea. Promising rice germplasm with strong resistance to PHS has been identified from a diverse rice panel at the International Rice Genebank. A genome-wide association analysis revealed two major loci on chromosomes 1 and 4 associated with PHS resistance in certain japonica accessions. Gene networks suggest a key resistance mechanism related to abscisic acid (ABA), gibberellic acid (GA), and auxin signaling pathways.
Article
Biotechnology & Applied Microbiology
Jing Luo, Matthew N. Rouse, Lei Hua, Hongna Li, Boshu Li, Tianya Li, Wenjun Zhang, Caixia Gao, Yanpeng Wang, Jorge Dubcovsky, Shisheng Chen
Summary: The identification of the Ug99-effective SrTm5 gene from diploid wheat and its successful introgression into hexaploid wheat opens up new possibilities for developing more effective strategies to combat wheat stem rust. The rare insertion of a large retrotransposon into the Sr22b gene indicates the complexity of genetic resistance mechanisms in wheat, highlighting the importance of exploring diverse sources of resistance for breeding programmes aimed at controlling this devastating disease. The use of a diagnostic molecular marker and biolistic transformation techniques demonstrate the potential for rapid deployment of Sr22b and its combination with other resistance genes to enhance resistance in wheat.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Genetics & Heredity
Katherine W. Jordan, Peter J. Bradbury, Zachary R. Miller, Moses Nyine, Fei He, Max Fraser, Jim Anderson, Esten Mason, Andrew Katz, Stephen Pearce, Arron H. Carter, Samuel Prather, Michael Pumphrey, Jianli Chen, Jason Cook, Shuyu Liu, Jackie C. Rudd, Zhen Wang, Chenggen Chu, Amir M. H. Ibrahim, Jonathan Turkus, Eric Olson, Ragupathi Nagarajan, Brett Carver, Liuling Yan, Ellie Taagen, Mark Sorrells, Brian Ward, Jie Ren, Alina Akhunova, Guihua Bai, Robert Bowden, Jason Fiedler, Justin Faris, Jorge Dubcovsky, Mary Guttieri, Gina Brown-Guedira, Ed Buckler, Jean-Luc Jannink, Eduard D. Akhunov
Summary: In this study, we used the Practical Haplotype Graph (PHG) tool to improve the efficiency of high-density genotype data storage and imputation in bread wheat. The Wheat PHG database was constructed using whole-exome capture sequencing data from a diverse set of wheat accessions. We found that imputation accuracy varied depending on the sequencing method and coverage depth, with higher accuracy obtained using exome capture. We also demonstrated that genetic mapping based on genotypes imputed using PHG can identify SNPs that explain a larger proportion of genetic variance for heading date and meiotic crossover rate.
G3-GENES GENOMES GENETICS
(2022)
Article
Agronomy
Andrew Katz, Patrick Byrne, Scott Reid, Sarah Bratschun, Scott Haley, Stephen Pearce
Summary: To ensure food security for the growing global population, it is crucial to increase the yield of staple crops like wheat. This study identified and validated a quantitative trait locus (QTL) on chromosome 6BL that controls spikelet number in wheat. Despite the presence of genetic interactions with other loci, genotypes with more superior alleles consistently showed higher spikelet numbers. This research lays the groundwork for the positional cloning of the genetic variant underlying the QTL, enhancing our understanding of spikelet number determination in wheat.
MOLECULAR BREEDING
(2022)
Article
Agronomy
Rocio Alarcon-Reverte, Yucong Xie, John Stromberger, Jennifer D. Cotter, Richard Esten Mason, Stephen Pearce
Summary: This study successfully reduced dietary acrylamide exposure by developing wheat varieties with low asparagine content. Field trials showed that these genetically modified wheat lines exhibited no significant differences in quality and agronomic traits compared to wildtype, while effectively reducing the concentration of asparagine.
Article
Biology
Yedomon Ange Bovys Zoclanclounon, Michael Rostas, Nam-Jin Chung, Youngjun Mo, Petr Karlovsky, Komivi Dossa
Summary: This study conducted a comprehensive investigation of peroxidase and laccase genes in the emerging oil crop sesame. Potential (+)-pinoresinol synthase genes were identified and their expression patterns matched the accumulation of (+)-pinoresinol in seeds. These findings have wide potential applications in food, health, and medicinal domains.
Article
Multidisciplinary Sciences
Carl VanGessel, James Hamilton, Facundo Tabbita, Jorge Dubcovsky, Stephen Pearce
Summary: In order to maintain global food security, it is important to increase wheat yield. This study analyzed the gene regulatory networks associated with wheat inflorescence development using a temporal wheat spike transcriptome dataset. The findings further our understanding of wheat inflorescence development.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Gilad Gabay, Hanchao Wang, Junli Zhang, Jorge I. Moriconi, German F. Burguener, Leonardo D. Gualano, Tyson Howell, Adam Lukaszewski, Brian Staskawicz, Myeong-Je Cho, Jaclyn Tanaka, Tzion Fahima, Haiyan Ke, Katayoon Dehesh, Guo-Liang Zhang, Jin-Ying Gou, Mats Hamberg, Guillermo E. Santa-Maria, Jorge Dubcovsky
Summary: This study reveals that dosage differences in monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes play a crucial role in shaping root architecture in wheat. Increasing the dosage or introducing these genes through transgenic methods results in inhibition of root development, early lateral root growth, and elevated levels of jasmonic acid (JA and JA-Ile). The findings suggest that jasmonic acid is involved in regulating root length differences. These OPRIII genes can be used as a starting point for engineering root architecture in wheat and other cereals.
NATURE COMMUNICATIONS
(2023)
Article
Agronomy
Seung Young Lee, Hyun-Sook Lee, Chang-Min Lee, Su-Kyung Ha, Hyang-Mi Park, So-Myeong Lee, Youngho Kwon, Ji-Ung Jeung, Youngjun Mo
Summary: This study used multi-environment trials to evaluate the grain yield and yield-related traits of 276 Korean rice cultivars. The results showed that the performance of rice is significantly influenced by the differences in planting seasons and regions. By using GGE biplot analysis and stability index, suitable rice cultivars for different types were identified, and recommendations were made for the development of regional specialty cultivars and climate-resilient parents.
Article
Agronomy
Su-Kyung Ha, Hyun-Sook Lee, Seung Young Lee, Chang-Min Lee, Youngjun Mo, Ji-Ung Jeung
Summary: We developed a floury endosperm mutant line, SK-flo3, derived from the chemical mutagenesis of an elite Korean japonica rice cultivar, Samkwang. SK-flo3 showed significantly lower grain hardness, making it suitable for producing dry-milled rice flour without the need for soaking and drying processes. The dry-milled flour of SK-flo3 exhibited excellent physicochemical properties with less damaged starch and finer flour particles. A molecular marker for the causative mutation in SK-flo3 was developed for efficient transfer to commercial rice cultivars. Our results provide valuable genetic resources and information for developing specialty rice cultivars for high-quality rice flour production with reduced milling costs.
Article
Microbiology
Andrew Chen, Jiaman Sun, Altus Viljoen, Diane Mostert, Yucong Xie, Leroy Mangila, Sheryl Bothma, Rebecca Lyons, Eva Hribova, Pavla Christelova, Brigitte Uwimana, Delphine Amah, Stephen Pearce, Ning Chen, Jacqueline Batley, David Edwards, Jaroslav Dolezel, Peter Crisp, Allan F. Brown, Guillaume Martin, Nabila Yahiaoui, Angelique D'Hont, Lachlan Coin, Rony Swennen, Elizabeth A. B. Aitken
Summary: Fusarium wilt of banana is a destructive disease that has caused significant damage to banana production worldwide. In this study, the genetic basis of host resistance to the causal agent Fusarium oxysporum f. sp. Cubense (Foc) is dissected using two segregating populations. Marker loci and trait association analysis revealed a specific genetic interval associated with resistance on chromosome 3. The expression of pattern recognition receptors was found to be rapidly upregulated in resistant progenies, suggesting their involvement in resistance. The developed markers can aid breeding programs in selecting for resistance to Foc.
Article
Plant Sciences
Paula Berman, Luis Alejandro de Haro, Adam Jozwiak, Sayantan Panda, Zoe Pinkas, Younghui Dong, Jelena Cveticanin, Ranjit Barbole, Rotem Livne, Tali Scherf, Eyal Shimoni, Smadar Levin-Zaidman, Nili Dezorella, Ekaterina Petrovich-Kopitman, Sagit Meir, Ilana Rogachev, Prashant D. Sonawane, Asaph Aharoni
Summary: This study uncovers a pathway for cannabinoid production in Helichrysum umbraculigerum, a plant that is genetically distinct from Cannabis. This provides a potential source of new cannabinoids and tools for metabolic engineering.
Article
Plant Sciences
Rency Raquid, Ajay Kohli, Russell Reinke, Maribel Dionisio-Sese, Jieun Kwak, Dmytro Chebotarov, Youngjun Mo, Jae-Sung Lee
Summary: Seed longevity is crucial for maintaining seed viability and vigor under changing climates, with previous studies focusing on QTL for temperate japonica rice but not tropical japonica rice. Through QTL mapping and candidate gene identification, this study highlights potential mechanisms for enhancing seed longevity in tropical japonica rice varieties.
CURRENT PLANT BIOLOGY
(2021)