Milletdb: a multi‐omics database to accelerate the research of functional genomics and molecular breeding of millets

Abstract

SummaryMillets 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.

Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet (Pennisetum glaucum)

“…To provide an overview of the expression patterns of PgERF genes, we extracted the relevant transcriptome data from a public data repository as described in [ 34 ]. Of the 167 PgERF genes, 57 were preferentially expressed in the imbibed seeds, and 30 were preferentially expressed in the stems during the tilling stage ( Figure 4 and Table S6 ).…”

“…The whole genomic data of pearl millet cv. PI537069 was acquired from of public genome sequencing database (Milletdb, http://milletdb.novogene.com, accessed on 30 July 2023) [34]. The Hidden Markov Model (HMM) profile of AP2/ERF conserved domains (PF00847) [55] was downloaded from the Pfam database v35.0 [56] and employed to identify the pearl millet AP2/ERF (PgERF) protein sequences using the HMMER 3.0 program [57].…”

Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits

“…6 Comparative analysis of putative promoters of five grain-specific genes across six pearl millet genotypes. The cis -element analysis was conducted on the promoters of five grain-specific phospholipase genes, namely ( A ) PgPLD-alpha1-1 , ( B ) PgPLD-alpha1-5 , ( C ) PgPLD-delta1-7a , ( D ) PgPLA1-II-1a , and ( E ) PgPLD-delta1-2a , along with their corresponding homologous sequences from six different genotypes of pearl millet [ 107 ]. The analysis revealed the presence of various variations, such as single-nucleotide polymorphisms, deletions, and insertions within these sequences.…”

Finger millet: a hero in the making to combat food insecurity

“…2 ), as well as trait data and molecular marker data. Milletdb ( http://milletdb.novogene.com/ ) focuses on millets and has capabilities to conduct a range of genomic analyses on the genomes housed by the database (Sun et al 2023 ). At the time of writing, only the PR202 finger millet genome (Hatakeyama et al 2017 ) was present in Milletdb.…”