{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T17:13:26Z","timestamp":1789665206024,"version":"4.0.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,11,15]],"date-time":"2024-11-15T00:00:00Z","timestamp":1731628800000},"content-version":"vor","delay-in-days":319,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India","award":["BT\/IC-06\/003\/91 and BT\/PR40151\/BTIS\/137\/5\/2021"],"award-info":[{"award-number":["BT\/IC-06\/003\/91 and BT\/PR40151\/BTIS\/137\/5\/2021"]}]},{"name":"Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India","award":["BT\/IC-06\/003\/91 and BT\/PR40151\/BTIS\/137\/5\/2021"],"award-info":[{"award-number":["BT\/IC-06\/003\/91 and BT\/PR40151\/BTIS\/137\/5\/2021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The global population surge demands increased food production and nutrient-rich options to combat rising food insecurity. Climate-resilient crops are vital, with millets emerging as superfoods due to nutritional richness and stress tolerance. Given limited genomic information, a comprehensive genetic resource is crucial to advance millet research. Whole-genome sequencing provides an unprecedented opportunity, and molecular genetic methodologies, particularly simple sequence repeats (SSRs), play a pivotal role in DNA fingerprinting, constructing linkage maps, and conducting population genetic studies. SSRs are composed of repetitive DNA sequences where one to six nucleotides are repeated in tandem and distributed throughout the genome. Different millet species exhibit genomic variations attributed to the presence of SSRs. While SSRs have been identified in a few millet species, the existing information only covers some of the sequenced genomes. Moreover, there is an absence of complete gene annotation and visualization features for SSRs. Addressing this disparity and leveraging the de-novo millet genome assembly available from the NCBI, we have developed the Genomic SSR Millets Database (GSMDB; https:\/\/bioinfo.icgeb.res.in\/gsmdb\/). This open-access repository provides a web-based tool offering search functionalities and comprehensive details on 6.747645 million SSRs mined from the genomic sequences of seven millet species. The database, featuring unrestricted public access and JBrowse visualization, is a pioneering resource for the research community dedicated to advancing millet cultivars and related species. GSMDB holds immense potential to support myriad studies, including genetic diversity assessments, genetic mapping, marker-assisted selection, and comparative population investigations aiming to facilitate the millet breeding programs geared toward ensuring global food security.<\/jats:p>\n                  <jats:p>Database URL: https:\/\/bioinfo.icgeb.res.in\/gsmdb\/<\/jats:p>","DOI":"10.1093\/database\/baae114","type":"journal-article","created":{"date-parts":[[2024,11,11]],"date-time":"2024-11-11T23:23:53Z","timestamp":1731367433000},"source":"Crossref","is-referenced-by-count":8,"title":["The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture"],"prefix":"10.1093","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-2978-3012","authenticated-orcid":false,"given":"Sonu","family":"Kumar","sequence":"first","affiliation":[{"name":"Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , New Delhi, Delhi 110067,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3600-9982","authenticated-orcid":false,"given":"Sangeeta","family":"Singh","sequence":"additional","affiliation":[{"name":"Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , New Delhi, Delhi 110067,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rakesh","family":"Kumar","sequence":"additional","affiliation":[{"name":"Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , New Delhi, Delhi 110067,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7548-8835","authenticated-orcid":false,"given":"Dinesh","family":"Gupta","sequence":"additional","affiliation":[{"name":"Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , New Delhi, Delhi 110067,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,15]]},"reference":[{"key":"2025030713434971800_R1","doi-asserted-by":"publisher","DOI":"10.3390\/genes12050739","article-title":"Alternative strategies for multi-stress tolerance and yield improvement in millets","volume":"12","author":"Numan","year":"2021","journal-title":"Genes"},{"key":"2025030713434971800_R2","doi-asserted-by":"publisher","first-page":"5147","DOI":"10.1007\/s13197-014-1617-y","article-title":"Comparative study on nutritional and sensory quality of barnyard and foxtail millet food products with traditional rice products","volume":"52","author":"Verma","year":"2015","journal-title":"J Food Sci Technol"},{"key":"2025030713434971800_R3","first-page":"1577","article-title":"Millets: nutritional composition, production and significance: a review","volume":"11","author":"Bhatt","year":"2022","journal-title":"J Pharm Innov"},{"key":"2025030713434971800_R4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40066-020-00282-6","article-title":"The nutritional use of millet grain for food and feed: a review","volume":"10","author":"Hassan","year":"2021","journal-title":"Agri Food Sec"},{"key":"2025030713434971800_R5","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.781524","article-title":"Breeding drought-tolerant pearl millet using conventional and genomic approaches: achievements and prospects","volume":"13","author":"Srivastava","year":"2022","journal-title":"Front Plant Sci"},{"key":"2025030713434971800_R6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-021-07888-5","article-title":"Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage","volume":"22","author":"Zhang","year":"2021","journal-title":"BMC Genomics"},{"key":"2025030713434971800_R7","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.fcr.2014.11.005","article-title":"Seed set variability under high temperatures during flowering period in pearl millet (Pennisetum glaucum L.(R.) Br.)","volume":"171","author":"Gupta","year":"2015","journal-title":"Field Crops Res"},{"key":"2025030713434971800_R8","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.711429","article-title":"The alkali tolerance of broomcorn millet (Panicum miliaceum L.) at the germination and seedling stage: the case of 296 broomcorn millet genotypes","volume":"12","author":"Ma","year":"2021","journal-title":"Front Plant Sci"},{"key":"2025030713434971800_R9","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1111\/1541-4337.12012","article-title":"Millet grains: nutritional quality, processing, and potential health benefits","volume":"12","author":"Saleh","year":"2013","journal-title":"Compr Rev Food Sci Food Saf"},{"key":"2025030713434971800_R10","doi-asserted-by":"publisher","DOI":"10.3390\/foods11162442","article-title":"The role of amaranth, quinoa, and millets for the development of healthy, sustainable food products\u2014a concise review","volume":"11","author":"Balakrishnan","year":"2022","journal-title":"Foods"},{"key":"2025030713434971800_R11","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1007\/s13197-011-0584-9","article-title":"Health benefits of finger millet (Eleusine coracana L.) polyphenols and dietary fiber: a review","volume":"51","author":"Devi","year":"2014","journal-title":"J Food Sci Technol"},{"key":"2025030713434971800_R12","article-title":"Millets: nutritional importance, health benefits, and bioavailability: a review","volume":"329","author":"Anagha","year":"2023","journal-title":"Energy"},{"key":"2025030713434971800_R13","doi-asserted-by":"publisher","first-page":"4127","DOI":"10.1093\/nar\/12.10.4127","article-title":"Simple sequences are ubiquitous repetitive components of eukaryotic genomes","volume":"12","author":"Tautz","year":"1984","journal-title":"Nucleic Acids Res"},{"key":"2025030713434971800_R14","first-page":"45","article-title":"Microsatellites in plants: a new class of molecular markers","volume":"70","author":"Gupta","year":"1996","journal-title":"Curr Sci"},{"key":"2025030713434971800_R15","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1007\/BF00564200","article-title":"The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis","volume":"2","author":"Powell","year":"1996","journal-title":"Mol Breed"},{"key":"2025030713434971800_R16","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-00100-4","article-title":"Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing","volume":"11","author":"Desai","year":"2021","journal-title":"Sci Rep"},{"key":"2025030713434971800_R17","doi-asserted-by":"publisher","first-page":"160","DOI":"10.2174\/2211550109999200908090745","article-title":"Microsatellite marker: importance and implications of cross-genome analysis for finger millet (Eleusine coracana (L.) Gaertn)","volume":"9","author":"Krishna","year":"2020","journal-title":"Curr Biotechnol"},{"key":"2025030713434971800_R18","doi-asserted-by":"publisher","DOI":"10.3390\/agronomy13102514","article-title":"Microsatellite-based genetic diversity analysis and population structure of Proso Millet (Panicum miliaceum L.) in Kazakhstan","volume":"13","author":"Zargar","year":"2023","journal-title":"Agronomy"},{"key":"2025030713434971800_R19","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1016\/j.gpb.2019.01.001","article-title":"Rice genomics: over the past two decades and into the future","volume":"16","author":"Song","year":"2018","journal-title":"Genom Proteom Bioinform"},{"key":"2025030713434971800_R20","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1007\/978-981-13-0535-1_29","volume-title":"Biotechnological Approaches for Medicinal and Aromatic Plants: Conservation, Genetic Improvement and Utilization","author":"Kumar","year":"2018"},{"key":"2025030713434971800_R21","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1007\/978-981-10-9029-5_14","volume-title":"Biotic and Abiotic Stress Tolerance in Plants","author":"Kumar","year":"2018"},{"key":"2025030713434971800_R22","doi-asserted-by":"crossref","first-page":"20","DOI":"10.2174\/9789811433788120010007","volume-title":"Contemporary Research on Bryophytes","author":"Kumar","year":"2020"},{"key":"2025030713434971800_R23","doi-asserted-by":"publisher","first-page":"6343","DOI":"10.1007\/s11033-014-3574-y","article-title":"FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets","volume":"41","author":"Bonthala","year":"2014","journal-title":"Mol Biol Rep"},{"key":"2025030713434971800_R24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0071418","article-title":"FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research","volume":"8","author":"Muthamilarasan","year":"2013","journal-title":"PLoS One"},{"key":"2025030713434971800_R25","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1106104","article-title":"LMTdb: a comprehensive transcriptome database for climate-resilient, nutritionally rich little millet (Panicum sumatrense)","volume":"14","author":"Shekhar","year":"2023","journal-title":"Front Plant Sci"},{"key":"2025030713434971800_R26","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-21560-1","article-title":"Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources","volume":"8","author":"Jaiswal","year":"2018","journal-title":"Sci Rep"},{"key":"2025030713434971800_R27","doi-asserted-by":"publisher","DOI":"10.1186\/s13104-021-05599-4","article-title":"TGIF-DB: terse genomics interface for developing botany","volume":"14","author":"Tsugama","year":"2021","journal-title":"BMC Res Notes"},{"key":"2025030713434971800_R28","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.57","article-title":"Predicting genes in single genomes with AUGUSTUS","volume":"65","author":"Hoff","year":"2019","journal-title":"Curr Protoc Bioinform"},{"key":"2025030713434971800_R29","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025030713434971800_R30","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025030713434971800_R31","doi-asserted-by":"publisher","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","article-title":"MISA-web: a web server for microsatellite prediction","volume":"33","author":"Beier","year":"2017","journal-title":"Bioinformatics"},{"key":"2025030713434971800_R32","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1007\/s00122-002-1031-0","article-title":"Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)","volume":"106","author":"Thiel","year":"2003","journal-title":"Theor Appl Genet"},{"key":"2025030713434971800_R33","doi-asserted-by":"publisher","first-page":"1937","DOI":"10.1093\/bioinformatics\/bty036","article-title":"Primer3_masker: integrating masking of template sequence with primer design software","volume":"34","author":"K\u00f5ressaar","year":"2018","journal-title":"Bioinformatics"},{"key":"2025030713434971800_R34","first-page":"425","article-title":"The BLAST sequence analysis tool","volume":"2","author":"Madden","year":"2013","journal-title":"NCBI Handbook"},{"key":"2025030713434971800_R35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0205286","article-title":"BlasterJS: a novel interactive JavaScript visualisation component for BLAST alignment results","volume":"13","author":"Blanco-M\u00edguez","year":"2018","journal-title":"PLoS One"},{"key":"2025030713434971800_R36","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02914-z","article-title":"JBrowse 2: a modular genome browser with views of synteny and structural variation","volume":"24","author":"Diesh","year":"2023","journal-title":"Genome Biol"},{"key":"2025030713434971800_R37","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/nbt.2195","article-title":"Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential","volume":"30","author":"Zhang","year":"2012","journal-title":"Nat Biotechnol"},{"key":"2025030713434971800_R38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004915","article-title":"Transposable elements contribute to activation of maize genes in response to abiotic stress","volume":"11","author":"Makarevitch","year":"2015","journal-title":"PLoS Genetics"},{"key":"2025030713434971800_R39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12863-021-01003-z","article-title":"Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline","volume":"22","author":"Xu","year":"2021","journal-title":"BMC Genomic Data"},{"key":"2025030713434971800_R40","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-023-09156-0","article-title":"Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding","volume":"24","author":"Zhao","year":"2023","journal-title":"BMC Genomics"},{"key":"2025030713434971800_R41","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/S1672-0229(04)02004-2","article-title":"Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes","volume":"2","author":"Li","year":"2004","journal-title":"Genom Proteom Bioinform"},{"key":"2025030713434971800_R42","first-page":"536","article-title":"Identification, distribution and comparative analysis of microsatellites in the chloroplast genome of Oryza species","volume":"79","author":"Tripathy","year":"2019","journal-title":"Indian J Genet Plant Breed"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae114\/60685444\/baae114.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baae114\/60685444\/baae114.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T08:44:22Z","timestamp":1741337062000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baae114\/7901189"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"references-count":42,"URL":"https:\/\/doi.org\/10.1093\/database\/baae114","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024]]},"published":{"date-parts":[[2024]]},"article-number":"baae114"}}