Field‐grown soybean transcriptome shows diurnal patterns in photosynthesis‐related processes

Abstract

Many plant physiological processes have diurnal patterns regulated by diurnal environmental changes and circadian rhythms, but the transcriptional underpinnings of many of these cycles have not been studied in major crop species under field conditions. Here, we monitored the transcriptome of field‐grown soybean ( Glycine max ) during daylight hours in the middle of the growing season with RNA ‐seq. The analysis revealed 21% of soybean genes were differentially expressed over the course of the day. Expression of some circadian‐related genes in field‐grown soybean differed from previously reported expression patterns measured in controlled environments. Many genes in functional groups contributing to and/or depending on photosynthesis showed differential expression, with patterns particularly evident in the chlorophyll synthesis pathway. Gene regulatory network inference also revealed seven diurnally sensitive gene nodes involved with circadian rhythm, transcription regulation, cellular processes, and water transport. This study provides a diurnal overview of the transcriptome for an economically important field‐grown crop and a basis for identifying pathways that could eventually be tailored to optimize diurnal regulation of carbon gain.

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

“…LCL2 ( Glyma.03G261800 ), PRR3 ( Glyma.U034500 ), PRR7 ( Glyma.10G048100 ), and TOC1 ( Glyma.04G166300 ) showed diurnal variation only in the leaves, whereas LCL2 belonged to pattern 5, PRR3/7 belonged to pattern 3, and TOC1 belonged to pattern 8 (Figure 2). These gene expressions in the leaves exhibited the same trends as previous studies (Marcolino-Gomes et al, 2014; Locke, Slattery, and Ort, 2018). The diurnal fluctuation of the gene expressions for LCL2, PRR3/7, and TOC1 in the roots showed the same pattern as in the leaves, although statistically insignificant.…”

“…The diurnal fluctuation of the gene expressions for LCL2, PRR3/7, and TOC1 in the roots showed the same pattern as in the leaves, although statistically insignificant. The genes encoding transcription factors GIGANTEA (GI) ( Glyma.20G170000 ), Jumonji ( Glyma.11G130600 ), ZEITLUPE (ZTL) ( Glyma.09G056100 ), LUX ARRHYTHMO (LUX) ( Glyma.12G060200 ), and Early flowering 4 (ELF4) ( Glyma.18G027500 ) did not fall within the 12 expression patterns but displayed a similar expression tendency as observed in previous studies (Marcolino-Gomes et al, 2014; Locke et al, 2018) (Figure 2).…”

“…The expression of key genes related to the circadian clock in soybeans (Locke et al, 2018) showed divergent diurnal changes both in the leaves and roots. Late elongated hypocotyl/circadian clock associated 1-like 1 (LCL1, Glyma07G048500 ) belonged to pattern 5 in both the leaves and roots (Figure 2).…”

Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots

“…For each sample, color corresponds to the z-score given by the sample's TPM. ZT, hours after dawn.TPM, transcripts per million et al, 2013;Liew et al, 2017;Locke et al, 2018;Marcolino-Gomes et al, 2014;Wang et al, 2020) (Figure 2).…”

Advances in Transcriptome Analyses Using RNA Sequencing Technology in Soybean Plants [Glycine max]

“…Their work provides novel insights in the complex molecular mechanisms of photoperiodic flowering control in soybean. Locke et al (2018) examined the diurnal patterns of genes involved in photosynthesis-related processes in field-grown soybean transcriptomes and reported 21% of genes were differentially expressed over the course of the day.…”