Abstract
HD-Zip proteins represent the major transcription factors in higher plants, playing essential roles in plant development and stress responses. Foxtail millet is a crop to investigate the systems biology of millet and biofuel grasses and the HD-Zip gene family has not been studied in foxtail millet. For further investigation of the expression profile of the HD-Zip gene family in foxtail millet, a comprehensive genome-wide expression analysis was conducted in this study. We found 47 protein-encoding genes in foxtail millet using BLAST search tools; the putative proteins were classified into four subfamilies, namely, subfamilies I, II, III, and IV. Gene structure and motif analysis indicate that the genes in one subfamily were conserved. Promotor analysis showed that HD-Zip gene was involved in abiotic stress. Duplication analysis revealed that 8 (~17%) hdz genes were tandemly duplicated and 28 (58%) were segmentally duplicated; purifying duplication plays important roles in gene expansion. Microsynteny analysis revealed the maximum relationship in foxtail millet-sorghum and foxtail millet-rice. Expression profiling upon the abiotic stresses of drought and high salinity and the biotic stress of ABA revealed that some genes regulated responses to drought and salinity stresses via an ABA-dependent process, especially sihdz29 and sihdz45. Our study provides new insight into evolutionary and functional analyses of HD-Zip genes involved in environmental stress responses in foxtail millet.
Highlights
The homeodomain leucine zipper (HD-Zip) gene family is a major group of transcription factors in the higher plants, which include a DNA-binding domain (HD) at the Cterminal and a leucine-zipper domain that can interact with other proteins [1, 2]
The Hidden Markov Model (HMM) sequence was used here to search for the foxtail millet HD-Zip genes in Phytozome
Promotor analysis showed that HD-ZIP gene was involved in abiotic stress
Summary
The homeodomain leucine zipper (HD-Zip) gene family is a major group of transcription factors in the higher plants, which include a DNA-binding domain (HD) at the Cterminal and a leucine-zipper domain (bZIP known as LZ domain) that can interact with other proteins [1, 2]. Plants with an HD-Zip transgene exhibited improved morphological features when subjected to different stressful environmental conditions. The HD-Zip gene family can be divided into four classes (HD-Zip I–IV) according to their sequence similarity and structures of their different domains [5, 6]. A structural comparison found that all four classes contained the conserved HD and LZ domains, which promote dimerization, a prerequisite for DNA binding [6]. A minor distinction among the groups was found; namely, HD-Zip I and HD-Zip
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