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MaizeGDB 2018: the maize multi-genome genetics and genomics database

John L Portwood, Margaret R Woodhouse, Ethalinda K Cannon, Jack M Gardiner, Lisa C Harper, Mary L Schaeffer, Jesse R Walsh, Taner Z Sen, Kyoung Tak Cho, David A Schott, Bremen L Braun, Miranda Dietze (+9 others)
2018 Nucleic Acids Research  
Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in addition to the B73 reference genome assembly.  ...  MaizeGDB also continues to be the community hub for maize research, coordinating activities and providing technical support to the maize research community.  ...  We would like to give a special thank you to Ed Coe as not only the founder of the original Maize Genetics Database and continued contributor to the database, but also for his contribution to the generation  ... 
doi:10.1093/nar/gky1046 pmid:30407532 fatcat:4kigm7hldzfxpmy6zpwwxsqki4

MaizeDIG: Maize Database of Images and Genomes

Kyoung Tak Cho, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Carolyn J. Lawrence-Dill, Iddo Friedberg, Carson M. Andorf
2019 Frontiers in Plant Science  
The code is free and open source and can be found at  ...  The maize genetics and genomics database (MaizeGDB, provides an array of useful resources for diverse data types including thousands of images related to mutant phenotypes in Zea mays  ...  ACKNOWLEDGMENT We would like to acknowledge the MaizeGDB team for testing and providing feedback for MaizeDIG, Dr.  ... 
doi:10.3389/fpls.2019.01050 pmid:31555312 pmcid:PMC6724615 fatcat:c3bno4adzvahjnxukki7kuiq4y

A pan-genomic approach to genome databases using maize as a model system

Margaret R. Woodhouse, Ethalinda K. Cannon, John L. Portwood, Lisa C. Harper, Jack M. Gardiner, Mary L. Schaeffer, Carson M. Andorf
2021 BMC Plant Biology  
MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models  ...  We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.  ...  MaizeGDB is the maize community database, providing data curation and informatics resources to support maize genetics, genomics, and breeding research for maize scientists.  ... 
doi:10.1186/s12870-021-03173-5 pmid:34416864 pmcid:PMC8377966 fatcat:bshsrovtofd67lgnookuowuox4

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

Songtao Gui, Linfeng Yang, Jianbo Li, Jingyun Luo, Xiaokai Xu, Jianyu Yuan, Lu Chen, Wenqiang Li, Xin Yang, Shenshen Wu, Shuyan Li, Yuebin Wang (+4 others)
2020 iScience  
Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits.  ...  With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte.  ...  Several maize genomics and functional genomics databases have been developed, including the Maize Genetics and Genomics Database (MaizeGDB) (, which collects maize reference sequences  ... 
doi:10.1016/j.isci.2020.101241 pmid:32629608 pmcid:PMC7306594 fatcat:6j5ihsfuf5c2hkfoave3cgrcci

Applications of Multi-Omics Technologies for Crop Improvement

Yaodong Yang, Mumtaz Ali Saand, Liyun Huang, Walid Badawy Abdelaal, Jun Zhang, Yi Wu, Jing Li, Muzafar Hussain Sirohi, Fuyou Wang
2021 Frontiers in Plant Science  
genetics and breeding science.  ...  The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions.  ...  , and SFGD/ metabolic pathways 26 SoyNet Soybean Functional genomics and transcriptomics 27 MaizeGDB Maize Multi-omics 28 MaizeDIG Maize Phenomics  ... 
doi:10.3389/fpls.2021.563953 pmid:34539683 pmcid:PMC8446515 fatcat:dk4kvn6qxfe4xoz266tquokway

Genome-Wide Association Mapping of Starch Pasting Properties in Maize Using Single-Locus and Multi-Locus Models

Yang Xu, Tiantian Yang, Yao Zhou, Shuangyi Yin, Pengcheng Li, Jun Liu, Shuhui Xu, Zefeng Yang, Chenwu Xu
2018 Frontiers in Plant Science  
The results suggest that the multi-locus method is more powerful than the single-locus method and a combination of these multi-locus methods could help improve the detection power of GWAS.  ...  ), and three multi-locus methods, FASTmrEMMA, FarmCPU, and LASSO.  ...  To mine candidate genes based on the detected QTNs for the pasting properties, we used gene annotation and ontology information available in maizeGDB 2 and Phytozome database 3 .  ... 
doi:10.3389/fpls.2018.01311 pmid:30233634 pmcid:PMC6134291 fatcat:ruaonjin5zf2peduk53gv7fsim

Genomic resources in plant breeding for sustainable agriculture

Mahendar Thudi, Ramesh Palakurthi, James C. Schnable, Annapurna Chitikineni, Susanne Dreisigacker, Emma Mace, Rakesh K. Srivastava, C. Tara Satyavathi, Damaris Odeny, Vijay K. Tiwari, Hon-Ming Lam, Yan Bin Hong (+11 others)
2020 Journal of plant physiology  
The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.  ...  In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants  ...  multi-location trials in India (Taunk et al., 2018) .  ... 
doi:10.1016/j.jplph.2020.153351 pmid:33412425 pmcid:PMC7903322 fatcat:xujybmnnbrdnfnueet55wsb25i

Identifying inbred lines with resistance to endemic diseases in exotic maize germplasm

Ezequiel A. Rossi, Marcos Ruiz, Natalia C. Bonamico, Mónica G. Balzarini
2020 Crop science  
A multi-trait mixed linear model was used to identify the lines with the best performance for both diseases and estimate genetic parameters.  ...  A multi-environment trial was performed to phenotypically assess a diverse panel of inbred lines from the International Maize and Wheat Improvement Center (CIMMYT).  ...  The genomic database used in this work is available from  ... 
doi:10.1002/csc2.20275 fatcat:4xjivenw7rho7aqtt5vmxohxyu

Genetic Diversity and Genome-Wide Association Study of Major Ear Quantitative Traits Using High-Density SNPs in Maize

Xiao-Mei Zhu, Xiao-Yu Shao, Yu-He Pei, Xin-Mei Guo, Jun Li, Xi-Yun Song, Mei-Ai Zhao
2018 Frontiers in Plant Science  
Combining with the genotype obtained from Maize SNP50 chip, genetic diversity and association mapping in a set of 292 inbred lines were performed.  ...  Genomewide association study (GWAS) uses the linkage disequilibrium (LD) in the whole genome to determine the genes affecting certain phenotype.  ...  AUTHOR CONTRIBUTIONS X-YSo and M-AZ conceived and designed the study. M-AZ, X-MZ, X-YSh, Y-HP, X-MG, and JL performed the experiments, phenotyped the populations and field work.  ... 
doi:10.3389/fpls.2018.00966 pmid:30038634 pmcid:PMC6046616 fatcat:3gakdcbspjblnermoo5l5umc2m

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize

Ji Huang, Juefei Zheng, Hui Yuan, Karen McGinnis
2018 BMC Plant Biology  
Conclusions: By combining publicly available genome-wide expression data and network analysis, we can uncover GRNs at tissue-level resolution in maize.  ...  We also present a publicly available database, maize tissue-specific GRN (mGRN, mgrn/), for easy querying.  ...  Acknowledgements We thank Alexander Study and Joshua M. McCoy from Computer Support Facility in Department of Biological Science for setting up computing and web server environment.  ... 
doi:10.1186/s12870-018-1329-y pmid:29879919 pmcid:PMC6040155 fatcat:e73cco2sjzaunavrokq65nv3uq

A comprehensive review of web-based resources of non-coding RNAs for plant science research

Peiran Liao, Shipeng Li, Xiuming Cui, Yun Zheng
2018 International Journal of Biological Sciences  
Acknowledgements The research was supported in part by two grants (No. 31460295 and 31760314) of National Natural Science Foundation of China ( and a grant (No.  ...  / A resource for rice genome information [9, 10] MaizeGDB A database for Maize genetics and genomics [25, 26] SoyBase A database for the USDA-ARS  ...  Database [9, 10] , MaizeGDB [25, 26] , SoyBase [27] are databases for Arabidopsis, wheat, rice, maize, and soybean genome, respectively.  ... 
doi:10.7150/ijbs.24593 pmid:29989090 pmcid:PMC6036741 fatcat:ega4utdykbap5m4zgavecnprli

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies [article]

Jose Arcadio Valdes Franco, Joseph L Gage, Lynn C. Johnson, Peter Bradbury, Zachary R. Miller, Edward S. Buckler, M. Cinta Romay
2020 bioRxiv   pre-print
Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database.  ...  As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome,  ...  Because maize is both a powerful system for genetics and evolutionary research, along with being a major crop worldwide, accounting for over 38% of the world's cereal production (FAO, 2018) , it has been  ... 
doi:10.1101/2020.08.31.268425 fatcat:kl4rtu7tobgsdb7z7rdo5zyguq

Map-based cloning and characterization of Zea mays male sterility33 (ZmMs33) gene, encoding a glycerol-3-phosphate acyltransferase

Ke Xie, Suowei Wu, Ziwen Li, Yan Zhou, Danfeng Zhang, Zhenying Dong, Xueli An, Taotao Zhu, Simiao Zhang, Shuangshuang Liu, Jinping Li, Xiangyuan Wan
2018 Theoretical and Applied Genetics  
This study reveals that the monocot-specific GPAT3 protein plays an important role in male fertility in maize, and ZmMs33 and mutants in this gene may have value in maize male-sterile line breeding and  ...  Key message Map-based cloning of maize ms33 gene showed that ZmMs33 encodes a sn-2 glycerol-3-phosphate acyltransferase, the ortholog of rice OsGPAT3, and it is essential for male fertility in maize.  ...  Information (NCBI), Rice Genome Annotation Project (RGAP) and Maize Genetics and Genomics Database (MaizeGDB) websites.  ... 
doi:10.1007/s00122-018-3083-9 pmid:29546443 pmcid:PMC5945757 fatcat:x723i3x755hu5ap5atw6iggpve

Discovery and validation of genomic regions associated with resistance to maize lethal necrosis in four biparental populations

Manje Gowda, Yoseph Beyene, Dan Makumbi, Kassa Semagn, Michael S. Olsen, Jumbo M. Bright, Biswanath Das, Stephen Mugo, L. M. Suresh, Boddupalli M. Prasanna
2018 Molecular breeding  
The sudden outbreak of maize lethal necrosis (MLN) disease is seriously threatening the maize production in the region. Understanding the genetic basis of MLN resistance is crucial.  ...  In this study, we used four biparental populations applied linkage mapping and joint linkage mapping approaches to identify and validate the MLN resistanceassociated genomic regions.  ...  database that links the genetic positions of the proprietary SNP markers with public markers.  ... 
doi:10.1007/s11032-018-0829-7 pmid:29773962 pmcid:PMC5945787 fatcat:n3vfgr6cmzbjnijqxqu46xrjua

Maize Combined Insect Resistance Genomic Regions and Their Co-localization With Cell Wall Constituents Revealed by Tissue-Specific QTL Meta-Analyses

Arfang Badji, Michael Otim, Lewis Machida, Thomas Odong, Daniel Bomet Kwemoi, Dennis Okii, Symphorien Agbahoungba, Natasha Mwila, Frank Kumi, Angele Ibanda, Stephen Mugo, Samuel Kyamanywa (+1 others)
2018 Frontiers in Plant Science  
Our results highlight the existence of combined-insect resistance genomic regions in maize and set the basis of multiple-pests resistance breeding.  ...  generated 24 leaf (LIR), 42 stem (SIR), and 20 kernel (KIR) insect resistance meta-QTL (MQTL) of a diverse genetic and geographical background.  ...  However, the genome coverage based on the physical coordinates of the MQTL is higher than that based on the genetic map reaching around 17, 21, and 25% of the total maize genome for LIR, KIR, and SIR,  ... 
doi:10.3389/fpls.2018.00895 pmid:30026746 pmcid:PMC6041972 fatcat:nxwdsapn6jaqnexgd7h33dk2ca
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