Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.
abiotic stress
database
functional genomics
millet
multi-omics
Journal
Plant biotechnology journal
ISSN: 1467-7652
Titre abrégé: Plant Biotechnol J
Pays: England
ID NLM: 101201889
Informations de publication
Date de publication:
11 2023
11 2023
Historique:
revised:
01
07
2023
received:
07
02
2023
accepted:
17
07
2023
medline:
23
10
2023
pubmed:
2
8
2023
entrez:
2
8
2023
Statut:
ppublish
Résumé
Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
Identifiants
pubmed: 37530223
doi: 10.1111/pbi.14136
pmc: PMC10579705
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2348-2357Informations de copyright
© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Références
Exp Parasitol. 2017 Sep;180:2-12
pubmed: 28286326
Crit Rev Food Sci Nutr. 2018 Feb 11;58(3):463-474
pubmed: 27246820
J Agric Food Chem. 2019 Jul 24;67(29):8085-8095
pubmed: 31265279
J Biosci. 2007 Apr;32(3):621-8
pubmed: 17536181
Plant Physiol Biochem. 2006 Jul-Sep;44(7-9):483-93
pubmed: 17023166
Adv Genet. 2019;103:1-38
pubmed: 30904092
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Nat Genet. 2012 Jun 17;44(7):821-4
pubmed: 22706312
BMC Genomics. 2014 Jul 09;15:581
pubmed: 25007843
Trends Genet. 2021 Dec;37(12):1124-1136
pubmed: 34531040
BMC Plant Biol. 2020 Jun 15;20(1):274
pubmed: 32539796
Front Plant Sci. 2015 Mar 24;6:157
pubmed: 25852710
BMC Res Notes. 2021 Jan 14;14(1):24
pubmed: 33446233
Front Plant Sci. 2022 Jun 10;13:890550
pubmed: 35755691
FEMS Microbiol Lett. 1999 May 15;174(2):247-50
pubmed: 10339815
Gigascience. 2021 Mar 12;10(3):
pubmed: 33710327
Mol Ecol Resour. 2021 Feb;21(2):526-542
pubmed: 33040437
Genes (Basel). 2021 Oct 28;12(11):
pubmed: 34828322
Biotechnol Biofuels. 2021 Apr 11;14(1):94
pubmed: 33840392
PLoS One. 2015 Nov 23;10(11):e0143344
pubmed: 26600014
Bioinformatics. 2020 Aug 1;36(15):4269-4275
pubmed: 32415954
Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4736-41
pubmed: 11930019
Nat Protoc. 2012 Sep;7(9):1728-40
pubmed: 22936215
Trends Plant Sci. 2015 Jun;20(6):388-97
pubmed: 25914086
BMC Genomics. 2021 Jul 23;22(1):568
pubmed: 34301177
Nat Commun. 2017 Oct 18;8(1):1031
pubmed: 29044108
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Nat Commun. 2019 Jan 25;10(1):436
pubmed: 30683860
Annu Rev Plant Biol. 2005;56:435-66
pubmed: 15862103
Nat Commun. 2022 Feb 3;13(1):689
pubmed: 35115514
Nat Biotechnol. 2018 Oct;36(9):875-879
pubmed: 30125266
J Environ Manage. 2021 Oct 15;296:113216
pubmed: 34237674
Int J Mol Sci. 2020 Jul 16;21(14):
pubmed: 32708737
Nat Biotechnol. 2017 Oct;35(10):969-976
pubmed: 28922347
Plant J. 2020 Mar;101(5):1170-1184
pubmed: 31651067
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Genome Biol. 2016 Apr 12;17:66
pubmed: 27072794
Trends Plant Sci. 2021 Jun;26(6):631-649
pubmed: 33893045
Trends Plant Sci. 2021 Jan;26(1):33-40
pubmed: 32900620
Int J Mol Sci. 2020 Nov 25;21(23):
pubmed: 33255649
Front Plant Sci. 2013 May 31;4:169
pubmed: 23755060
Int J Mol Sci. 2020 Nov 12;21(22):
pubmed: 33198267
Int J Mol Sci. 2021 Sep 02;22(17):
pubmed: 34502461
Curr Protoc Bioinformatics. 2003 Feb;Chapter 10:Unit 10.3
pubmed: 18428693
Food Res Int. 2021 Apr;142:110197
pubmed: 33773674
J Exp Bot. 2013 Jan;64(2):433-43
pubmed: 23162122
Mol Plant. 2014 Feb;7(2):264-76
pubmed: 24285094
PLoS One. 2020 Jun 2;15(6):e0234029
pubmed: 32484836
Nat Biotechnol. 2012 May 13;30(6):555-61
pubmed: 22580951
Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5232-41
pubmed: 27551092
Front Plant Sci. 2022 Mar 28;13:849618
pubmed: 35419021
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
Nat Genet. 2023 Mar;55(3):507-518
pubmed: 36864101
Mol Ecol Resour. 2022 Aug;22(6):2363-2378
pubmed: 35347881
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
DNA Res. 2018 Feb 1;25(1):39-47
pubmed: 28985356
Sci Rep. 2020 Aug 12;10(1):13660
pubmed: 32788682
Genes (Basel). 2021 Dec 15;12(12):
pubmed: 34946937