Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

Abstract

Background Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. Results In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. Conclusions In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.

Genome-wide analysis of SPL/miR156 module and their expression analysis in vegetative and reproductive organs of oil palm (Elaeis guineensis)

“…Phylogenetic analysis of 24 oil palm SPLs with Arabidopsis and rice SPLs suggested the diversi cation of oil palm SPL members among model-to-crop plants during evolution process. The uneven distribution of 24 SPL genes on 16 chromosomes of oil palm also coinciding with the previous reports on SPL gene family distribution on sweet cherry, Alfalfa and foxtail millet genomes [12,13,14]. SPL genes encode plant-speci c transcription factors that play important roles in ower development, including vegetative to reproductive growth [48] .…”

“…The motifs related to the SBP domain are found in all the identi ed EgSPL proteins. Conserved motif analysis revealed the occurrence of 10 motifs in oil palm SPL genes as reported in other plants including foxtail millet [14], Alfalfa [13] and Quinoa [37]. The post transcriptional regulation of SPLs by miR156 determines ne-tune functions of SPLs [45].…”

“…In this study, we identi ed a total of 24 SPL genes in oil palm genome through bioinformatics approach and dissected the expression of 14 SPLs in male and female in orescences of oil palm plants through experimental approach. The number of identi ed SPLs (24) in this study are fewer than the number of SPLs identi ed in sweet cherry (16SPLs) [12], alfalfa (23SPLs) [13], foxtail millet (18 SPLs) [14], jatropha (15 SPLs) [16] and lesser than the number of SPLs identi ed in soybean(41 SPLs) [40], owering cherry (32 SPLs) [43], wheat(56 SPLs) [38], populus (33 SPLs) [41], trifolium(37 SPLs) [15] genomes. Present information on oil palm SPLs would elucidate the evolutionary process of SPLs across various plants.…”

“…SPLs are plant-speci c transcription factors with highly conserved SBP domain and involved in regulating growth and development of plants. Various number of SPL genes were identi ed and characterized their expression in various crops including sweet cherry [12], alfalfa [13], Quinoa [37], Foxtail millet [14], wheat [38], pecan [39] , soybean [40], populas [41], Jatropha [16]. However, some of the studies were carried out to characterize SPL gene expression during reproductive tissue development in various crops including Pecan [39], Tartary Buckwheat [20], Rice [42], owering cherry [43], Trifolium [15] and Petunia [44].…”

“…The NLS overlaps with the zinc nger structure to direct the SBP proteins into nucleus for transcriptional regulation of downstream genes [11]. In recent years, various genome-wide studies identi ed the occurrence of SPL gene members in various plants including 16 in sweet cherry [12], 23 in alfalfa [13], 18 in foxtail millet [14], 37 in trifolium [15], 15 in jatropha [16], 17 in Arabidopsis [17,18], 19 in rice [9], 56 in wheat [19], 24 in tartary buckwheat [20], 15 in Pomegranate [21], 15 in tomato [22,28 in poplar [23], 27 in apple [24], 18 in grape [25], 17 in orchardgrass genome [26]. However, none of the genome wide studies are carried out for identifying the SPL genes in oil palm genome.…”