Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica)

Abstract

Background Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA gene family in foxtail millet (Setaria italica). The release of the foxtail millet reference genome presents an opportunity for the genome-wide characterization of these GATA genes. Results In this study, we identified 28 GATA genes in foxtail millet distributed on seven chromosomes. According to the classification method of GATA members in Arabidopsis, SiGATA was divided into four subfamilies, namely subfamilies I, II, III, and IV. Structural analysis of the SiGATA genes showed that subfamily III had more introns than other subfamilies, and a large number of cis-acting elements were abundant in the promoter region of the SiGATA genes. Three tandem duplications and five segmental duplications were found among SiGATA genes. Tissue-specific results showed that the SiGATA genes were mainly expressed in foxtail millet leaves, followed by peels and seeds. Many genes were significantly induced under the eight abiotic stresses, such as SiGATA10, SiGATA16, SiGATA18, and SiGATA25, which deserve further attention. Conclusions Collectively, these findings will be helpful for further in-depth studies of the biological function of SiGATA, and will provide a reference for the future molecular breeding of foxtail millet.

Genome-Wide Identification, Evolution, and Expression Pattern Analysis of the GATA Gene Family in Tartary Buckwheat (Fagopyrum tataricum)

“…The pI of 16/28 (57.14%) FtGATA genes was under seven ( Table S2 ), indicating that most FtGATA genes were rich in acidic amino acids. However, this was contrary to the results of some GATA transcription factors [ 35 , 37 , 38 ], and the findings for different protein families in Tartary buckwheat were consistent [ 39 ]. This indicated that the pI of the same gene family is different for different species, and the pI of the same species may be the same for different gene families.…”

“…The tissues were rapidly placed in liquid nitrogen and stored at −80 °C [ 2 , 44 ]. In addition, the root, stem, young leaf, mature leaf, flower, fruit, and husk were taken from growing Tartary buckwheat to the grain-filling period; the fruits and husks were taken during the early, middle, and late grain-filling periods, and the samples were stored at −80 °C [ 35 ].…”

“…The fruit is rich in amino acids, and it has a higher total protein content than major grain crops; thus, it can be developed as a healthcare product to relieve various diseases [ 29 , 30 ]. The GATA gene family is found in Arabidopsis [ 31 ], rice [ 32 ], Brachypodium [ 33 ], soybean [ 34 ], millet [ 35 ], and other crops. However, the Tartary buckwheat GATA gene family is not identified, and related studies of this gene family under stress and hormone treatment are rarely reported.…”

Genome-wide identification of GATA transcription factors in tetraploid potato and expression analysis in differently colored potato flesh

“…The GATA gene family has been reported in many different plants. For example, previous reports revealed 30 GATA family members in Arabidopsis thaliana ( Reyes et al., 2004 ; Bi et al., 2005 ), 28 in rice ( Reyes et al., 2004 ; Gupta et al., 2017 ), 28 in foxtail millet ( Lai et al., 2022 ), 64 in soybean ( Zhang et al., 2015 ), and 79 in wheat ( Feng et al., 2022 ). However, primarily because commonly cultivated potato varieties are autotetraploids with highly heterozygous genomes, complicated genetic analysis and relatively scarce gene databases, the genome-wide investigation of the GATA gene family has not been performed in tetraploid potato.…”

Genome‐wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato

“…The GATA transcription factor family is actively involved in light response and abiotic stress mechanisms, exhibiting high conservation across eukaryotes. Identified by a characteristic type IV zinc finger domain (CX 2 CX 17‐20 CX 2 C, where C represents cysteine and X is any amino acid) and a nearby basic region, GATA factors were first identified in tobacco (Daniel‐Vedele & Caboche, 1993 ) and have been extensively studied in various plant species, Arabidopsis thaliana (Kim, Xi, & Park, 2021 ; Teakle & Gilmartin, 1998 ), rice (Reyes et al, 2004 ), poplar (An et al, 2014 ), Noccaea caerulescens (Milner et al, 2014 ), soybean (Zhang et al, 2015 ), apple (Chen et al, 2017 ), grape (Zhang et al, 2018 ), Moso bamboo (Wang et al, 2019 ), Brachypodium distachyon (Peng et al, 2021 ), poplar (Kim, Xi, Park, Yun, & Park, 2021 ), cucumber (Zhang et al, 2021 ), potato (Yu, Chang, et al, 2021 ), wheat (Du et al, 2022 ; Feng et al, 2022 ), and foxtail millet (Lai et al, 2022 ). The GATA transcription factor‐binding cis ‐elements are commonly found in the promoters of genes associated with light and circadian rhythms, which are crucial for plant growth and development (Argüello‐Astorga & Herrera‐Estrella, 1998 ; Manfield et al, 2007 ).…”