Comparing Early Transcriptomic Responses of 18 Soybean (Glycine max) Genotypes to Iron Stress

Abstract

Iron deficiency chlorosis (IDC) is an abiotic stress that negatively affects soybean (Glycine max [L.] Merr.) production. Much of our knowledge of IDC stress responses is derived from model plant species. Gene expression, quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS) performed in soybean suggest that stress response differences exist between model and crop species. Our current understanding of the molecular response to IDC in soybeans is largely derived from gene expression studies using near-isogenic lines differing in iron efficiency. To improve iron efficiency in soybeans and other crops, we need to expand gene expression studies to include the diversity present in germplasm collections. Therefore, we collected 216 purified RNA samples (18 genotypes, two tissue types [leaves and roots], two iron treatments [sufficient and deficient], three replicates) and used RNA sequencing to examine the expression differences of 18 diverse soybean genotypes in response to iron deficiency. We found a rapid response to iron deficiency across genotypes, most responding within 60 min of stress. There was little evidence of an overlap of specific differentially expressed genes, and comparisons of gene ontology terms and transcription factor families suggest the utilization of different pathways in the stress response. These initial findings suggest an untapped genetic potential within the soybean germplasm collection that could be used for the continued improvement of iron efficiency in soybean.

Soybean PHR1-regulated low phosphorus-responsiveGmRALF22increases uptake of phosphate via stimulatingGmPTs expression

“…Soybean genome has 27 GmRALFs. GmRALF5,GmRALF6,and GmRALF10,GmRALF11,GmRALF22 and GmRALF25 are published RNA-seq data (Belamkar et al, 2014;Zhao et al, 2020;Kohlhase et al, 2021;Wang et al, 2012;Mo et al, 2019;Zeng et al, 2018;Zeng et al, 2019), and the heatmap was drawn with TBtools (Chen et al,2023). subtilis inoculated with GmRALF22 and empty carrier were grown in HP and LP soil, respectively.…”

“…We date-mined and obtained the expression levels of GmRALF genes under drought, salt (Belamkar et al, 2014), Al toxicity (Zhao et al, 2020), Fe deficiency (Kohlhase et al, 2021), potassium deficiency (K) (Wang et al, 2012), P deficiency (Mo et al, 2019;Zeng et al, 2018) and Zn deficiency (Zeng et al, 2019). Under drought conditions, the expression levels of GmRALF4 and GmRALF24 are down-regulated and that of GmRALF6 is up-regulated in soybean leaves.…”

GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean

“…SPAD measurements have been used to map IDC QTLs and confirm the identification of IDC QTLs visual scores ( Lin et al., 1997 , Lin et al., 2000 ; Assefa et al., 2020 ). In addition, SPAD measurements have been used in IDC gene expression analyses ( O’Rourke et al., 2007 , O’Rourke et al., 2009 ; Atencio et al., 2021 ; Kohlhase et al., 2021 ) and to phenotype VIGS plants in terms of response to iron stress ( Atwood et al., 2014 ; O’Rourke et al., 2021 ). The average of six SPAD readings per trifoliolate, two readings per leaflet, was calculated for the first and second trifoliolates for eight plants per construct.…”

“…Collectively, these studies identified the hallmarks of the iron stress response, regulation of genes involved in defense and stress, iron homeostasis, and DNA replication/methylation in Clark. Kohlhase et al. (2021) conducted RNA-seq analyses of leaves and roots from nine IDC-tolerant and nine IDC-susceptible lines (members of the Assefa et al.…”

“…Collectively, these studies identified the hallmarks of the iron stress response, regulation of genes involved in defense and stress, iron homeostasis, and DNA replication/methylation in Clark. Kohlhase et al (2021) conducted RNA-seq analyses of leaves and roots from nine IDC-tolerant and nine IDC-susceptible lines (members of the Assefa et al (2020) GWA panel) at 1 hour after iron stress. Little overlap in differentially expressed genes (DEGs) was found between the nine IDC-tolerant lines, confirming that multiple IDC tolerance responses are present within the soybean germplasm collection.…”