FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets

Bonthala, Venkata Suresh; Muthamilarasan, Mehanathan; Roy, Rajarshi

doi:10.1007/s11033-014-3574-y

Cited by 23 publications

(12 citation statements)

References 22 publications

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“…Genes Si030514m, Si036615m and Si036647m comprised of one alternate transcript Si030506m, Si036606m and Si036938m, respectively. The number conforms with the number of AP2/ERFs reported in Foxtail millet Transcription Factor Database [55] . Of note, the identification of pseudogenes among these 171 AP2/ERFs require further experimentations.…”

Section: Resultssupporting

confidence: 77%

Genome-Wide Investigation and Expression Profiling of AP2/ERF Transcription Factor Superfamily in Foxtail Millet (Setaria italica L.)

et al. 2014

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The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

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Section: Resultssupporting

confidence: 77%

Genome-Wide Investigation and Expression Profiling of AP2/ERF Transcription Factor Superfamily in Foxtail Millet (Setaria italica L.)

et al. 2014

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“…The HMM search showed the presence of 229 MYB genes in foxtail millet genome ( Table S2 ). The result was then confirmed by comparing the data with Foxtail millet Transcription Factor Database (FmTFDb; http://59.163.192.91/FmTFDb/ ) [31] . Further, all 229 SiMYB genes were BLAST searched against foxtail millet genome in Phytozome to identify alternate transcripts and chromosomal location.…”

Section: Resultsmentioning

confidence: 74%

“…The Hidden Markov Model (HMM) profile of MYB DNA-binding domain (PF00249) downloaded from Pfam v27.0 ( http://pfam.sanger.ac.uk/family/PF00249 ) [30] was queried against Phytozome v9.1 ( www.phytozome.net ) of Setaria italica . All hits with expected values less than 1.0 were retrieved and compared with MYB protein dataset available in Foxtail millet Transcription Factor Database ( http://59.163.192.91/FmTFDb/ ) [31] . In addition, S. italica MYB (SiMYB) proteins were examined using CDD search ( http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ) for presence of one or more MYB DNA-binding domains.…”

Section: Methodsmentioning

confidence: 99%

Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)

et al. 2014

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MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I - X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.

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“…The re-sequencing of diverse foxtail millet germplasm should continue as a strategy to aid marker-assisted breeding efforts. Much work has also been accomplished in the behavior of transcription factors in foxtail millet under a variety of stressful conditions, details of which have been conveniently compiled in the database “FmTFDb” (Bonthala et al, 2014 ). The availability of this data is expected to greatly accelerate functional genomics in all small millet species.…”

Section: Diversity Of the Small Milletsmentioning

confidence: 99%

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

2015

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Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed “orphan cereals.” Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa.

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FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets

Cited by 23 publications

References 22 publications

Genome-Wide Investigation and Expression Profiling of AP2/ERF Transcription Factor Superfamily in Foxtail Millet (Setaria italica L.)

Genome-Wide Investigation and Expression Profiling of AP2/ERF Transcription Factor Superfamily in Foxtail Millet (Setaria italica L.)

Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

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