Transcriptome profiling reveals differentially expressed genes associated with flowering time in contrasting switchgrass genotypes

Abstract

Switchgrass (Panicum virgatum L.) has become an important biofuel crop. The experiment was designed to identify differentially expressed genes (DEGs) for flowering time in switchgrass genotypes contrasting in heading and anthesis dates. Phytomers of early-(S041) and late-flowering (B901) parents and early-(7071) and late-flowering (7055) F 2 genotypes were collected on two sampling dates of vegetative stages, and transcriptome profiling was completed to identify DEGs involved in flowering time using RNA sequencing. Across two sampling dates, the comparison between S041 and B901 identified six upregulated (TOC1, FKF1, two PHYA, and two PFT1) and five downregulated flowering DEGs (FT, GASA, COP1, and two CHS) in S041, but one upregulated FT and one downregulated GASA in B901. When comparing two F 2 genotypes, three DEGs (PFT1 and two FT) were upregulated in 7071, and six DEGs (PRR7, PRR5, PHYB, TOC1, and two CKB4) were upregulated and one DEG (COP1) was downregulated in 7055 genotype. The upregulation of PRR5 and FKF1 and downregulation of GASA and COP1 were found in both early-flowering genotypes, whereas FKF1, PRR5, PRR7, and PHYB were upregulated and two GASA were downregulated in both late-flowering genotypes. Across both early-flowering genotypes, seven upregulated and 12 downregulated transcription factors (TFs) from nine families related to flowering were differentially expressed, whereas eight upregulated and 30 downregulated flowering related TFs from 16 families were differentially expressed across both late-flowering genotypes. The identification of key genes involved in the flowering pathways could facilitate the development of desirable flowering phenotypes of switchgrass.Abbreviations: cDNA, complementary DNA; DAVID, the database for annotation, visualization, and integrated discovery; DEG, differentially expressed gene; FPKM, fragments per kilobase pair of exon model per million fragments mapped; GA, gibberellin; KEGG, Kyoto Encyclopedia of Genes and Genomes; PCA, principal component analysis; qRT-PCR, quantitative reverse transcription polymerase chain reaction; TF, transcription factor.

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

“…In switchgrass, overexpression of an FT ortholog, P. virgatum FLOWERING LOCUS T1 ( PvFT1 ), in the lowland switchgrass accession Alamo (2 n =4 x =36) led to earlier flowering, implying that transcript level differences, caused either by differential expression or copy number variation, of FT orthologs between the ecotypes could be a driver of differential flowering time ( Niu et al , 2016 ). This was supported by the finding of Taylor and colleagues that FT was expressed more highly in an early-flowering F 2 progeny carrying an upland FT allele than in a later-flowering F 2 progeny carrying a lowland allele ( Taylor et al , 2020 ). Another flowering-inducing gene, an ortholog of the Myb transcription factor gene LUX ARRHYTHMO ( LUX ) in Arabidopsis, has also been shown to be expressed more highly in uplands throughout development in both leaf and SAM tissues.…”

“…One strategy to meet the industrial demand for short hydrocarbons is to increase the biomass production of lignocellulosic feedstocks, including switchgrass. Because enhancing biomass accumulation in switchgrass can be achieved by delaying flowering time ( van Esbroeck et al , 1998 ), identifying the genetic loci contributing to the differential floral transition between the early-flowering upland accessions and the later-flowering lowland accessions has been the focus of multiple studies ( Grabowski et al , 2016 ; Milano et al , 2016 ; Tornqvist et al , 2017 , 2018 ; Taylor et al , 2018 , 2020 ; Lowry et al , 2019 ). Flowering time QTLs on Chr04K have been mapped in several upland–lowland segregating mapping populations, including in our study ( Tornqvist et al , 2018 ; Lowry et al , 2019 ).…”