Genome-wide identification and characterization of GRAS genes in soybean (Glycine max)

Abstract

Background: GRAS proteins are crucial transcription factors, which are plant-specific and participate in various plant biological processes. Thanks to the rapid progress of the whole genome sequencing technologies, the GRAS gene families in different plants have been broadly explored and studied. However, comprehensive research on the soybean (Glycine max) GRAS gene family is relatively lagging. Results: In this study, 117 Glycine max GRAS genes (GmGRAS) were identified. Further phylogenetic analyses showed that the GmGRAS genes could be categorized into nine gene subfamilies: DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR. Gene structure analyses turned out that the GmGRAS genes lacked introns and were relatively conserved. Conserved domains and motif patterns of the GmGRAS members in the same subfamily or clade exhibited similarities. Notably, the expansion of the GmGRAS gene family was driven both by gene tandem and segmental duplication events. Whereas, segmental duplications took the major role in generating new GmGRAS genes. Moreover, the synteny and evolutionary constraints analyses of the GRAS proteins among soybean and distinct species (two monocots and four dicots) provided more detailed evidence for GmGRAS gene evolution. Cis-element analyses indicated that the GmGRAS genes may be responsive to diverse environmental stresses and regulate distinct biological processes. Besides, the expression patterns of the GmGRAS genes were varied in various tissues, during saline and dehydration stresses and during seed germination processes. Conclusions: We conducted a systematic investigation of the GRAS genes in soybean, which may be valuable in paving the way for future GmGRAS gene studies and soybean breeding.

QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a genotyped RIL population by using RAD-seq based high-density linkage map

“…Soybean is a crucial crop abundant with healthy protein and oil, and high yield is one of the most important targets in soybean breeding [ 25 , 57 ]. Early studies turned out that the soybean leaf chlorophyll contents could be positively correlated to soybean yield [ 6 , 7 ].…”

Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean (Glycine max L.)

“…Despite these studies, our understanding of TALE superfamily members in soybean is still very limited. With the rapid developments of the whole genome sequencing technologies, distinct soybean gene families like GRAS [ 22 ], HD-ZIP [ 23 ], WOX [ 24 ], WRKY [ 25 ], NAC [ 26 ], MYB [ 27 ] and ARF [ 28 ], were reported and systematically characterized. However, investigations on the Glycine max TALE (GmTALE) superfamily genes are still lacking.…”

Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

“…GRAS is a transcription factor family that has been identified in many plant species ( Huang et al, 2015 ; Liu & Widmer, 2014 ; Tian et al, 2004 ; Xu et al, 2016 ). In soybean ( Glycine max ), 117 GRAS genes were identified, and these GmGRAS genes might have been under strong purifying selective pressures during evolution ( Wang et al, 2020 ). Sixty-two GRAS members were observed in barley ( Hordeum vulgare L.), and 74.2% of them were intron-free ( To et al, 2020 ).…”

“…Initially, GRAS proteins were divided into eight subfamilies in Arabidopsis , including LS, LISCL, HAM, PAT1, SCL3, SHR, SCR and DELLA ( Tian et al, 2004 ). However, 117 GmGRAS genes were divided into nine subfamilies in soybean ( Glycine max ), including DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR ( Wang et al, 2020 ). Brachypodium distachyon included another subfamilies: DLT ( Niu et al, 2019 ).…”