Abstract
Foxtail millet is very a drought-tolerant crop. Basic helix–loop–helix (bHLH) transcription factors are involved in many drought-stress responses, but foxtail millet bHLH genes have been scarcely examined. We identified 149 foxtail millet bHLH genes in a genome-wide analysis and performed Swiss-Prot, GO, and KEGG pathway analyses for these genes. Phylogenetic analyses placed the genes into 25 clades, with some remaining orphans. We identified homologs based on gene trees and Swiss-Prot annotation. We also inferred that some homologs underwent positive selection in foxtail millet ancestors, and selected motifs differed among homologs. Expression of eight foxtail millet bHLH genes varied with drought stress. One of these genes was localized to a QTL that contributes to drought tolerance in foxtail millet. We also perform a cis-acting regulatory element analysis on foxtail millet bHLH genes and some drought-induced genes. Foxtail millet bHLH genes were inferred to have a possible key role in drought tolerance. This study clarifies both the function of foxtail millet bHLH genes and drought tolerance in foxtail millet.
Highlights
The basic helix–loop–helix transcription factor family is a large gene super-family found in plant and animal genomes [1], and its members play very key roles in a wide range of metabolic, physiological, and developmental processes [2,3,4,5]. bHLH family members have many different functions [6], and they each contain a core bHLH domain of approximately 60 amino acids, including a basic region and a HLH region [7,8]. bHLH proteins can interact with each other and form homo-dimers or hetero-dimers that are promoted by the bHLH domains [1, 9]
QTLs for drought tolerance were identified from previous research by Qie et al [37], and the physical locations of foxtail millet bHLH genes were collected from the foxtail millet genome database
We identified 149 bHLH family members distributed among all nine chromosomes
Summary
The basic helix–loop–helix (bHLH) transcription factor family is a large gene super-family found in plant and animal genomes [1], and its members play very key roles in a wide range of metabolic, physiological, and developmental processes [2,3,4,5]. bHLH family members have many different functions [6], and they each contain a core bHLH domain of approximately 60 amino acids, including a basic region (at the N-terminus) and a HLH region [7,8]. bHLH proteins can interact with each other and form homo-dimers or hetero-dimers that are promoted by the bHLH domains [1, 9]. We identified the foxtail millet bHLH transcription factors in a genome-wide survey and studied the expression of bHLH genes in foxtail millet in various tissues under drought stress conditions. Identification of foxtail millet bHLH genes within drought tolerance QTLs
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