Genomic organization, phylogenetic comparison, and expression profiles of the SPL family genes and their regulation in soybean

Abstract

SQUAMOSA Promoter-Binding Protein-Like (SPL) genes form a major family of plant-specific transcription factors and play an important role in plant growth and development. In this study, we report the identification of 41 SPL genes (GmSPLs) in the soybean genome. Phylogenetic analysis revealed that these genes were divided into five groups (groups 1-5). Further, exon/intron structure and motif composition revealed that the GmSPL genes are conserved within their same group. The N-terminal zinc finger 1 (Zn1) of the SBP domain was a CCCH (Cys3His1) and the C terminus zinc finger 2 (Zn2) was a CCHC (Cys2HisCys) type. The 41 GmSPL genes were distributed unevenly on 17 of the 20 chromosomes, with tandem and segmental duplication events. We found that segmental duplication has made an important contribution to soybean SPL gene family expansion. The Ka/Ks ratios revealed that the duplicated GmSPL genes evolved under the effect of purifying selection. In addition, 17 of the 41 GmSPLs were found as targets of miR156; these might be involved in their posttranscriptional regulation through miR156. Importantly, RLM-RACE analysis confirmed the GmmiR156-mediated cleavage of GmSPL2a transcript in 2-4 mm stage of soybean seed. Alternative splicing events in 9 GmSPLs were detected which produces transcripts and proteins of different lengths that may modulate protein signaling, binding, localization, stability, and other properties. Expression analysis of the soybean SPL genes in various tissues and different developmental stages of seed suggested distinct spatiotemporal patterns. Differences in the expression patterns of miR156-targeted and miR156-non-targeted soybean SPL genes suggest that miR156 plays key functions in soybean development. Our results provide an important foundation for further uncovering the crucial roles of GmSPLs in the development of soybean and other biological processes.

Cloning and expression analysis of SPL8 homolog from pak choi (Brassica rapa subsp. chinensis)

“…The trend in BrcSPL8 expression was consistent with the expression of BrcLFY [1]. GmSPL8a and GmSPL8b are highly expressed in flowers and young leaves, whereas their expression is reduced in roots and seeds [27], which indicates that GmSPL8a and GmSPL8b play an important role during floral development in soybean. These results suggest that BrcSPL8 plays a role during flower development in pak choi.…”

Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton

“…The number of SPLs varies from species to species. For instance, there are 15 SPLs in potato, pepper, peanut, citrus, Prunus mume , danshen, castor bean and tomato 10 , 13 , 14 , 16 – 19 , 23 , 17–20 in grape, rice and Arabidopsis 22 , 24 , 27–30 in Chinese cabbage, Populus and apple 15 , 20 , 21 , 41 in soybean 11 , and 58 in oilseed rape 12 . However, no genome-wide identification of SPL gene family has been reported in cotton although there are four cotton species sequenced.…”

“…Among 17 SPLs in Arabidopsis , 10 were putative targets of miR156/157 4 , 44 . 11 of 19 SPLs in rice 45 , 18 of 28 SPLs in Populus 20 , 17 of 41 SPLs in soybean 11 were reported to be potential targeted by certain miR156. In this study, we also found that 31 of 59 identified SPLs were potentially targeted by miR156 in upland cotton, which are from 6 different orthologs ( GhSPL2 , GhSPL6 , GhSPL9 , GhSPL10 and GhSPL13 ).…”

“…Genome-wide identification of SPL/SBP-box gene family have been characterized in many plant species, including potato 10 , soybean 11 , oilseed rape 12 , pepper 13 , peanut 14 , Chinese cabbage 15 , citrus 16 , Prunus mume 17 , Salvia miltiorrhiza (Danshen) 18 , castor bean 19 , Populus trichocarpa 20 , apple 21 , grape 22 , tomato 23 , Arabidopsis and rice 24 . Guo et al .…”

Selection pressure causes differentiation of the SPL gene family in the Juglandaceae

“…Another study revealed that several cis-acting elements in the Gossypium arboreum and H. vulgare SPL promoter regions are associated with responses to light, stresses, and phytohormones (Cai et al 2018;Tripathi et al 2018). The numbers, structures, and functions of the SPL genes have also been studied in other major crops and in some model plant species, such as Glycine max, Lycopersicon esculentum, Malus pumila, O. sativa, Petunia hybrida, and Salvia miltiorrhiza (Tripathi et al 2017;Manning et al 2006;Miura et al 2010;Li et al 2013;Preston et al 2016;Zhang et al 2014). For example, in O. sativa, high expression of the SPL genes leads to grain yield enhancement and increases in crop production (Jiao et al 2010;Miura et al 2010).…”