Global analysis of SBP gene family in Brachypodium distachyon reveals its association with spike development

Abstract

SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B.distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1,BdSBP3,BdSBP8,BdSBP9,BdSBP14,BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein–protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.

Differential expression and global analysis of miR156/SQUAMOSA promoter binding-like proteins (SPL) module in oat

“…7 B,G). The barley HvSPL3 and Brachypodium distachyon BdSBP3 also expressed differentially between the vegetative and early reproductive stages 13 , 14 . Moreover, the knockout mutants of OsSPL3 and OsSPL4 lead to changes in the heading date, suggesting the conserved role of group 4 SPLs in the flowering 47 .…”

“…The SBP domain consists of three essential motifs i.e., two zinc-binding fingers, Cys3His1 (Zn1) and Cys2HisCys (Zn2), and a bipartite nuclear localization signal (NLS) that moderately protrude over the Zn2 motif, which lies at the C-terminal of the domain 8 , 10 . So far, 16 AtSPLs in Arabidopsis thaliana 9 , 56 TaSPLs in wheat 11 , 19 OsSPLs in rice 12 , 17 HvSPLs in barley 13 and 18 BdSBPs in Brachypodium distachyon 14 have been reported. SPL genes regulate various developmental processes, including panicle architecture 15 , vegetative to reproductive phase change 16 , embryogenesis 17 , fertility 18 , hormonal signalling 19 , flowering 20 , copper homeostasis 21 and germination and starch debranching 22 .…”

Highly Efficient and Reproducible Genetic Transformation in Pea for Targeted Trait Improvement

“…Amplification conditions were an initial denaturation step at 95 °C for 2 min, followed by 40 cycles of 95 °C for 5 s, 60 °C for 30 s, and 72 °C for 30 s, with a final melting curve analysis step of 95 °C for 1 min, 60 °C for 30 s, and 95 °C for 30 s. The qRTPCR data were automatically collected and analyzed. The relative level of gene expression was analyzed using the 2 –ΔΔ C q method . Expression values were represented as the average values of three biological repeats and error bars represented standard deviations.…”

“…The relative level of gene expression was analyzed using the 2 –ΔΔ C q method. 29 Expression values were represented as the average values of three biological repeats and error bars represented standard deviations. Asterisks indicated significant differences revealed by the Student’s t -test using JMPpro 16 software.…”

Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor

“…The SQUAMOSA-promoter binding like (SPL) transcription factors are regulated by miR156 and involved in various biological pathways and growth phase transitions in plants [35] , [36] . The highly conserved SBP domain of SPL, which contains two zinc-binding motifs and a nuclear localization signal (NLS) sequence, is required for binding to a cis -regulatory element with a GTAC core motif [21] .…”