Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis

Abstract

The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensis Ghd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A. The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus.

1. Introduction

The genus Miscanthus is a rhizomatous, self-incompatible, C4 perennial grass that has a natural distribution from the tropics to ~50° N in East Asia and Oceania [1], including Miscanthus sinensis, Miscanthus floridulus and Miscanthus sacchariflorus, and is closely related to sugarcane (Saccharum officinarum) and sorghum (Sorghum bicolor). Owing to its environmental adaptability, Miscanthus is used as forage for livestock feed, as an ornamental for landscapes, and as a bioenergy crop that provides high yields with low nutrient requirements [2,3]. For Miscanthus production, optimization of flowering time is essential to obtain high biomass yield under different environments [4,5], and may also impact biomass quality [6]. Controlling flowering also assists intra- and interspecific hybridizations between Miscanthus and Saccharum to facilitate the introgression of genes for disease resistance and abiotic stress tolerance from Miscanthus to sugarcane [7]. Additionally, to develop seed-based hybrid cultivars of Miscanthus, uniform flowering of the parental genotypes will be needed, and this has the potential to reduce the cost of establishment and accelerate domestication relative to the current standard approach of vegetatively propagating rhizomes of Miscanthus× giganteus, which is a hybrid between M. sacchariflorus and M. sinensis, and has recently attracted considerable attention as a feedstock crop for bioenergy [8,9].

Miscanthus has a long life span, exceeding 15 years, and it typically flowers annually [10], indicating that it has a complex mechanism for renewed vegetative growth after flower initiation. Initially, M. sinensis was described as a day neutral plant by Deuter [11], whereas Jensen et al. [8] demonstrated that flowering regulation in M. sinensis was complex, operated by thermal time/degree days but also a photoperiod sensitivity mechanism. In their latest study, Dong et al. [7] reported that M. sinensis was a facultative short-day (SD) plant, and photoperiod strongly affected Miscanthus flowering. Thus, it would be desirable to study the photoperiod regulation of flowering time in M. sinensis. The major regulatory genes for photoperiod control of flowering have been evolutionarily conserved in flowering plants but their specific effects can vary greatly among genera and species [12]. To date, the photoperiod regulation of flowering has been extensively investigated in the SD plant rice (Oryza sativa), and two independent genetic pathways have been identified [12]. One is the rice OsGI-Hd1-Hd3a pathway, which has been conserved in the SD plant sorghum [13], and is orthologous with the GI-CO-FT pathway in the long-day (LD) plant Arabidopsis [12]. In rice, GIGANTEA (GI) upregulates HEADING DATE 1 (Hd1), the ortholog of CONSTANS (CO), which regulates the expression of HEADING DATE 3a (Hd3a) to promote flowering in SD and delay flowering in LD [14,15,16]. Another flowering time pathway is Ghd7-Ehd1-Hd3a, which has been found in rice, sorghum and maize (Zea mays) but is absent from Arabidopsis thaliana [12,17,18,19,20]. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (Ghd7) is a grass-specific regulator of flowering and related traits. In rice, Ghd7 represses flowering under LD by down-regulating EARLY HEADING DATE 1 (Ehd1) and Hd3a [19]. In SD, Ehd1 activates Hd3a expression and induces floral transition [17,21]. Ehd1 is regulated by many genes, including Hd1, GI, Ghd7, PSEUDORESPONSE REGULATOR PROTEIN 37 (PRR37), and GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) [19,22,23,24,25]. In sorghum, there is a similar but not identical flowering time pathway. Sorghum CENTRORADIALIS 15 (SbCN15), the sorghum ortholog of rice Hd3a (FLOWERING LOCUS T, FT), may modify flowering time in a photoperiod-insensitive manner [18,26,27]. SbCO acts as an activator of flowering in SD by inducing the expression of SbEhd1, SbCN8 and SbCN12 (FT-like genes), whereas in LD, SbCO activity is inhibited by SbPRR37 [13]. SbPRR37 [Maturity1(Ma1)] and SbGhd7 (Ma6), which are promoted by sorghum PHYTOCHROME B (SbPhyB), inhibit flowering by decreasing the expression of SbEhd1, SbCN8 and SbCN12 under LD [18,26,27]. Ma2 delayed flowering in LD by selectively enhancing the expression of SbPRR37 and SbCO [28].

To date, information on the genetics of flowering regulation in Miscanthus is in its infancy [4,7,8]. Genetic linkage maps revealed fourteen flowering time quantitative trait loci (QTLs) in Miscanthus [29,30,31]. Dong et al. [29] found one Miscanthus flowering QTL on LG02 that corresponded to sorghum maturity gene Ma3 (PhyB) [26] and another located on LG01 that corresponded to the ASYMMETRIC LEAVES-like1 gene, which controls proximal–distal patterning in Arabidopsis petals [32]. Gifford et al. [30] found a Miscanthus QTL that corresponded to sorghum maturity gene Ma5 (PHYTOCHROME C, PhyC). Jensen et al. [31] reported eleven flowering QTLs on LG04 in M. sinensis, three of which were robust QTLs related to the age-dependent flowering pathway (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE and MADS-box SEPELLATA2) and the gibberellin pathway (gibberellin-responsive bHLH137). However, the functions of these candidate flowering time genes in the Miscanthus QTLs have yet to be verified, and allelic sequence variation for these genes has yet to be described. At present, Hd1/CO is the only candidate flowering time gene that has been screened in Miscanthus for sequence diversity and its geographic distribution, with large differences found among accessions from the Asian mainland relative to those from the Japanese archipelago [33].

Recently, Ghd8 (DTH8/LHD1/Hd5/LH8) has been found to be a key regulator of the Ghd7-Ehd1-Hd3a pathway in rice [34]. Ghd8 was initially identified as HAP3b in Arabidopsis, which can promote flowering in Arabidopsis by enhancing the expression of key flowering time genes, such as FT and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), under LD [35]. In rice, Ghd8 has a dual function to inhibit flowering under LD and promote flowering under SD by regulating Ghd7, Ehd1, RICE FLOWERING LOCUS T 1 (RFT1) and Hd3a [22,23]. In particular, Ghd8 encodes a protein transcription factor, heme activator protein 3 (HAP3)/ nuclear factor-YB (NF-YB), that in rice binds to CCAAT motif in the promoter region of Ghd7, as part of a complex with HD1 and OsHAP5b [34]. In rice, a 19 bp deletion in Ghd8 causes a loss-of-function that confers early flowering and thus adaptation to high latitudes; this allele is widely distributed among cultivars from Northern China and Japan [36,37], and has been selected and used widely for breeding early heading varieties in Hokkaido [37]. Therefore, Ghd8 plays a key role in the domestication and adaptation of rice in Hokkaido. It is worthwhile to investigate if a similar process occurred in Miscanthus during its migration northward after the last glacial maximum. Ehd1 in rice is induced by blue light in the morning, and Ghd7 suppression of Ehd1 is induced by red light in the morning under LD, thereby suppressing flowering, whereas under SD, the peak of Ghd7 expression shifts to night, and this misaligned timing allows Ehd1 to induce Hd3a and promote flowering [12]. Genomic synteny and collinearity are common features in the Poaceae [38,39], and have also been confirmed among rice, sorghum, switchgrass and M. sinensis genomes [29,31,40,41,42,43]. Previous studies have identified genes/QTLs under parallel evolution across grass species [31,33,44,45,46,47,48]. To date, there have been no reports of Ghd8 in C4 bioenergy crops such as sorghum, switchgrass and Miscanthus. Thus, a key question this study seeks to answer is the following: does M. sinensis have a functional Ghd8 that contributes to the regulation of flowering time? Moreover, we expect that if Ghd8 regulates flowering in M. sinensis, the gene’s expression in the day will follow a pattern of differential flowering times under LD relative to SD. In this study, we cloned the ortholog of OsGhd8 in a mini-core collection of M. sinensis with the aim to 1) characterize allelic and deduced amino acid sequence diversity and geographic distribution, and 2) determine expression patterns in response to photoperiod and relate these to previously obtained data on days to first flower under LD and SD.

2. Materials and Methods

2.1. Plant Materials and Growth Conditions

Twelve Miscanthus accessions (clones maintained by vegetative propagation) were studied for gene sequence variation and expression over time in response to two photoperiod treatments (15 h, LD; 12.5 h, SD) (Table 1). The twelve accessions included eleven M. sinensis from known locations in China and Japan, representing latitudes ranging from 18° N to 45° N, and one M. floridulus from 20.9° S in New Caledonia (we consider M. floridulus conspecific with M. sinensis [49,50] and hereafter refer to the entire panel as M. sinensis). The M. sinensis accessions represent six genetic groups that were previously identified by Clark et al. [49,50]. Dong et al. [7] previously evaluated the same twelve accessions for days to first flowering under day lengths of 15, 12.5 and 10 h in controlled environment chambers, and observed strong flowering time responses that varied by latitude of origin. In the current study, six pots of each accession were established by planting rhizomes in 2 L plastic pots containing soilless medium consisting of compost, vermiculite, calcined clay and peat moss (Forex Mori Sangyo Co., Ltd., Hokkaido, Japan) and growing these in a greenhouse at Hokkaido University in Sapporo, Japan (43.1° N, 141.3° E), with natural photoperiod.

After 40 d of establishment in the greenhouse, the Miscanthus plants were cut to 5 cm above the soil surface and moved into growth chambers (BioTRON LH-350S, NK Systems, Nippon Medical & Chemical Instruments Co., Ltd., Osaka, Japan) under constant long days (15 h). Pots were rotated randomly inside and between the chambers on a daily basis to minimize between-chamber and within-chamber environmental effects. The growth chambers provided 400 ± 50 μmol m⁻² s⁻¹ of photosynthetically active radiation with fluorescent lamps (Hitachi FLR40S-EX-N/M/36-A, Hitachi, Ltd., Tokyo, Japan), as measured with a quantum sensor (MIJ-14PARII, Environmental Measurement, Fukuoka, Japan). After 30 d of establishment in the chambers, the plants were subjected to one of two day-length treatments: LD (15 h light/9 h dark) and SD (12.5 h light/11.5 h dark), with three pots per accession given LD and three given SD. The temperature in the chambers was a constant 23 °C for the duration of the experiment. At planting and again at the start of each experiment, 15 g of 12-9-12 compound fertilizer (Kumiai Grassland No. 8; Hokkaido Fertilizer Co., Ltd., Japan) was added to each pot. Irrigation was provided to each pot each day. At day 38, one week after commencement of the LD or SD treatment, the three topmost leaves from each of the three pots per accession within each treatment were harvested and pooled at Zeitgeber times (ZT) of 3, 9, 15 and 21 h for one 24 hour light–dark cycle.

2.2. Genomic DNA Extraction and Isolation of Ghd8 in Miscanthus

Genomic DNA was isolated from young, healthy leaves by the modified cetyltrimethylammonium bromide (CTAB) [51] protocol using the DNeasy Plant Mini Kit (Qiagen, Tokyo, Japan) according to the manufacturer’s instructions. Gene-specific primers (Forward primer 1: 5′-GAAAGGCGATTAAGAGGAGAAT-3′; Forward primer 2: 5′-CACCATAAGCTAGCTGACTAGCT-3′; Reverse primer 1: 5′-GCAAGTATCGTTTGTCGTCGTCTT-3′) for Ghd8 were designed by aligning multiple sequences retrieved from the Miscanthus sinensis v7.1 genome [41] and its close relative sorghum using the Sorghum bicolor v3.1 genome from Phytozome v.13 (https://phytozome-next.jgi.doe.gov (accessed on 15 September 2019)). Amplification of Ghd8 was accomplished by polymerase chain reactions (PCRs) containing 30 ng of total genomic DNA as a template and LA Taq polymerase (TaKaRa Bio, Shiga, Japan). Amplification conditions were 1 min at 95 °C, followed by 30 cycles of 30 s at 95 °C, 30 s at suitable primer temperature and 1 m 30 s at 72 °C. PCR products were separated on 0.8% agarose gels by electrophoresis. Amplified bands of desired molecular weight were eluted from the agarose gel with the NucleoSpin^® Gel and PCR Clean-up kit (Macherey-Nager GmbH & Co. KG, Düren, Germany) and cloned into a pGEM-T Easy vector (Promega, Madison, WI, USA) using the TA-Blunt Ligation Kit (Nippon Gene Co., Ltd., Toyama, Japan) following the manufacturer’s instructions. Positively transformed colonies were selected on blue-white selection on ampicillin/IPTG/X-Gal LB plates, and plasmids were purified using a High Pure Plasmid Isolation Kit (Roche, Sigma-Aldrich, Tokyo, Japan). About 20 plasmid clones of each genotype were sequenced in both directions with a BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) via an ABI PRISM 3130 Genetic Analyzer (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. To identify true alleles and to limit the potential for misidentifying point mutations and indels resulting from PCR and sequencing errors as true alleles, we set a quality-control threshold of at least three colonies with the identical sequence for inclusion in further analysis and reporting.

2.3. RNA Isolation and Quantitative Reverse Transcription-PCR Analysis

Leaves were sampled from fully expanded healthy leaves at ZT 3, 9, 15 and 21 h in the growth chamber. All samples were immediately frozen in liquid nitrogen and stored at −80 °C until analysis. Total RNA was isolated from frozen leaves with a Favorgen^® Plant Total RNA Extraction Mini Kit (Favorgen Biotech Corp., Taiwan) and treated with DNase I (TaKaRa Bio, Shiga, Japan) to remove contaminating genomic DNA. cDNA was synthesized from purified RNA using an oligo (dT) 20 primer and random hexamer primers with Invitrogen™ M-MLV Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) according to Dwiyanti et al. [52]. The transcript levels for candidate genes were determined by quantitative real-time PCR (qRT-PCR). The PCR reactions (20 μL) contained 4.6 μL of the cDNA synthesis reaction mixture diluted to 1/15th of its original volume, 5 μL of 1.2 μM primer premix, 0.4 μL ROX Reference Dye (50×) and 10 μL of TB Green^® Premix Ex Taq™ II (Tli RNaseH Plus) (TaKaRa Bio, Shiga, Japan). Expression levels were determined on a StepOnePlus™ Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) with cycling conditions of 95 °C for 5 min, followed by 40 cycles of 95 °C for 10 s, 60 °C for 20 s and 72 °C for 30 s. Values were normalized to ACTIN (Misin17G008500) as an internal control. A reaction mixture without reverse transcriptase was also used as a control to confirm the absence of genomic DNA contamination. Amplification of a single DNA fragment was confirmed by melting-curve analysis of quantitative PCR and gel electrophoresis of the PCR products. Relative changes in gene expression were estimated following the 2^−ΔΔCt method [53]. Averages and standard errors of relative expression levels were calculated for three independently synthesized cDNAs. The forward primer used for ACTIN (Misin17G008500) gene expression was 5′-AGGGCTGTTTTCCCTAGCATCGT-3′, and the reverse primer was 5′-GGGTACTTGAGCGTGAGAATACCTC-3′. Primers were designed for MsiGhd8 based on the putative functional alleles. The forward primer used for MsiGhd8A (Misin13G040800) gene expression was 5′-CTCAACCGCTACCGCGAGGTC-3′, and the reverse primer was 5′- TCATCCGCCGCGCCATCT-3′. The forward primer used for MsiGhd8B (Misin07G127500) gene expression was 5′-ACGTCGGGCTCATGATGGGAGCA-3′, and the reverse primer was 5′-ATACGACTTCCGTGCTGCCGT-3′.

2.4. Data Analysis

The nucleotide sequences were assembled with ATGC v.6 software (GENETYX Co., Tokyo, Japan). O. sativa, S. bioclor, M. sinenesis genome sequences (Phytozome v.13, 100 kb) spanning Ghd8 gene were used for microsynteny /collinearity analysis, which was determined and visualized by Genome Evolution Analysis (GEvo) (http://genomevolution.org/CoGe/GEvo.pl (accessed on 2 January 2021)) and the high-resolution sequence analysis tool from the Accelerating Comparative Genomics (CoGe) toolkit (http://genomevolution.org/CoGe/ (accessed on 2 January 2021)). Multiple alignments of nucleotide and amino acid sequences were implemented in MEGA X [54,55,56], using ClustalW [57] with default settings. Phylogenetic trees were generated in MEGA X [54,55] using the Neighbor-Joining (NJ) method [58] with the substitutional model of Kimura 2-parameter [59]. The corresponding sequences of rice and sorghum were used as an out-group. Support for each node was tested with 1000 bootstrap repetitions [60]. The trees were edited and visualized in FigTree ver.1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 5 September 2020)). Relative changes in mean ± standard error of the mean (SE) gene expression were analyzed in Microsoft Excel (Microsoft Office 2016, Microsoft Inc., Seattle, WA, USA) and then exported to GraphPad Prism 9 software (GraphPad Software, San Diego, CA, USA) for visualization. Statistical tests for differences among means were conducted by a Student’s t-test or analyses of variances (ANOVAs) using GraphPad Prism 9 software (GraphPad Software, San Diego, CA, USA). The DNA sequences obtained are available from DDBJ (http://www.ddbj.nig.ac.jp/index-e.html (accessed on 21 December 2020)) with the accession numbers LC598392 to LC598437.

3. Results

3.1. Characterization of M. sinensis Ghd8

In M. sinensis, two homoeologous Ghd8 loci, MsiGhd8A located on chromosome 13 (Chr.13) and MsiGhd8B on chromosome 7 (Chr.07), were identified, with one on each of this paleo-allotetraploid species’ subgenomes (Figure 1). A total of 46 MsiGhd8 alleles were identified from the 12 wild-collected M. sinensis accessions (Figure 2 and Table S1). Sequence alignment indicated that the ORF lengths of M. sinensis Ghd8 ranged from 813 to 831 nucleotides, and contained one exon that coded for 270 to 276 amino acid residues (Figure 1). Multiple sequence blasting in Phytozome v13 (https://phytozome-next.jgi.doe.gov (accessed on 20 March 2020)) revealed that the nucleotide sequences of M. sinensis Ghd8 were highly similar to those in other plant species, such as S. bicolor (Sobic.007G059500, 88.6–92.3%), O. sativa (LOC_Os08g07740, 72.2–73.3%), Z. mays (Zm0001d049485, 82.7–86.3%) and A. thaliana (AT5G47640, 32.0–32.9%). A microsynteny assessment of genomic regions adjacent to Ghd8 in rice, sorghum and M. sinensis identified four colinear genes, including Ghd8, aligned with the same relative genomic order in a 100 kbp region, which was consistent with the identification of LOC_Os08g07740 as an ortholog of rice Ghd8 [22] (Figure S1 and Table S2). Therefore, based on sequence similarity and gene collinearity, two homoeologous Ghd8 loci in M. sinensis were designated as orthologs of Ghd8 in rice and sorghum, and probable orthologs of HAP3b in A. thaliana. Neighbor-Joining (NJ) phylogenetic trees revealed a robust separation of clades representing MsiGhd8A (22 alleles) and MsiGhd8B (24 alleles) (Figure 2). The phylogenetic trees indicated that the sorghum Ghd8 was more similar to MsiGhd8B than MsiGhd8A. Two accessions (Onna-1a and PMS-375, 16.7%) were homozygous at the MsiGhd8A locus, and all accessions were heterozygous at the MsiGhd8B locus (Table 1). Pairwise DNA sequence comparisons showed that the similarity of MsiGhd8A open reading frame (ORFs) ranged from 98.7% (Teshio -Func2 vs. PMS-226 -Func2, Teshio -Func2 vs. PMS-382 -Func2, Teshio -Func2 vs. US56-0022-03 -Func2) to 100% (Sugadaira -Func1 vs. PMS-436 -Func1, PMS-164 -Func1 vs. PMS-306 -Func1, PMS-375 -Func1 vs. PMS-382 -Func1) (Table S1). Similarly, the nucleotide sequence similarity of MsiGhd8B ORFs varied from 97.9% (Sugadaira -Func4 vs. US56-0022-03 -Func4) to 100% (PMS-164 -Func3 vs. PMS-306 -Func3, PMS-164 -Func4 vs. PMS-436 -Func4, PMS-226 -Func3 vs. PMS-375 -Func3) (Table S1).

Comparison of the 46 MsiGhd8 alleles derived from the 12 wild-collected M. sinensis accessions in this study with the alleles in the Miscanthus sinensis v7.1 genome [41] revealed 35 non-synonymous single nucleotide variants (nsSNVs), 36 synonymous single nucleotide variants (sSNVs) and two 3-bp insertions in ORFs, with some accessions having more than one SNV per allele (Table S1). Considering the fact that the nucleotide diversity cannot exactly represent the protein diversity owing to synonymous SNVs in ORFs, Ghd8 protein variant types were analyzed in the present study (Table 1 and Table S1, Figure 2 and Figure 3). Accounting for nsSNVs, 13 predicted amino acid sequence types of MsiGhd8A and 15 of MsiGhd8B (28 total) were identified from the 12 M. sinensis accessions (Table 1 and Table S1, Figure 2 and Figure 3). The amino acid sequence similarity of putatively functional MsiGhd8A and MsiGhd8B variants ranged from 92.1% to 94.2%. Notably, the deduced amino acid sequence of Ghd8 in M. sinensis indicated that the gene products contain a HAP3/NF-YB DNA-binding domain located from position 53 to 146 (Figure 1b), which is critical for the transcription factor function of Ghd8 gene products. Though no putatively non-functional alleles were detected, four nsSNVs in the HAP3/NF-YB DNA-binding domain of MsiGhd8 (two in MsiGhd8A and two in MsiGhd8B) were observed in five accessions, with one nsSNV of MsiGhd8A found in each of two accessions (Sugadaira and PMS-436), one nsSNV of MsiGhd8A found in Teshio and one nsSNV of MsiGhd8B in PMS-226 and another nsSNV of MsiGhd8B found in US56-0022-03 (Table S1).

3.2. Geographical Distribution of Naturally Occurring MsiGhd8 Protein Variants

Some of the MsiGhd8 protein variants were found over a broad geographic range, whereas others had restricted patterns of occurrence (Table 1, Figure 2, Figure 3 and Figure S1). In the A subgenome, variant A1 was the most broadly distributed, with occurrence in accessions that originated from the mid and highest latitudes in this study (PMS-226 from Sichuan basin and Teshio from northern Hokkaido Japan), but it was infrequently observed (16.7% of accessions). In contrast, A7 was distributed widely and the second-most frequently observed variant (25% of accessions). A3 was limited to two accessions, one in Northern China and one in Central Japan; however, DNA sequence analysis indicated that A3 and A7 are closely related (Table S1) and thus represent a broadly distributed group in mainland Asia and Japan. A11 had a restricted distribution from New Caledonia to Guangdong China with a latitude ranging from 20.9° S to 22.9° N and was the most frequent variant (33.3% of accessions) but was absent from mid and high latitudes in mainland Asia and Japan. However, phylogenetic analysis of the DNA sequence revealed that A11 and A1 protein variants were closely related and thus represented a widely distributed group from east to west and from north to south. A8 was limited to mid latitudes in mainland Asia. The other eight variants were each observed in only one accession. A2 and A3, which encode one additional amino acid resulting from the same 3-bp insertion in the nucleotide sequence, were limited to Northern Japan and China.

In the B subgenome, variant B1 was observed from Hainan to Hokkaido but infrequently (16.7% of accessions). In mainland Asia, B8 was also broadly distributed from low to high latitude and frequent (25% of accessions). B9 was observed in two accessions, one in Sichuan Basin and one in Southern China. The other twelve variants were each observed in only one accession. Phylogenetic analyses of DNA sequence indicated the following closely related protein variant groups: B7 and B8; B9 and B10; B1, B4 and B13; B3, B6, B11 and B12 (Figure 2 and Figure 3).

3.3. Expressions Patterns of M. sinensis Ghd8

For each of the M. sinensis accessions, expression of Ghd8 (assessed as the ratio of Ghd8/ACTIN mRNA transcript abundance) from the B subgenome was one to two orders of magnitude greater than for the A subgenome (Figure 4 and Figure 5). Within each subgenome, large differences among the accessions for Ghd8 expression were observed (Figure 4 and Figure 5). The two accessions with the highest morning-expression of MsiGhd8B under LD (Teshio and Onna-1a) also had the highest expression of MsiGhd8A (Figure 5). Interestingly, under LD, Onna-1a was the latest flowering of the accessions, but Teshio was the earliest flowering, and neither flowered under SD. Three patterns of diurnal MsiGhd8 expression were observed: day peak, night peak and no clear peak (Figure 5). The most common diurnal MsiGhd8 expression pattern observed was a day peak at ZT9 or ZT15 (Figure 5), which is later than the dawn peak that has been reported for rice, suggesting that optimal timing may differ between M. sinensis and rice. For the B subgenome, the LD/SD ratio of Ghd8 expression at ZT9, was >1 for three accessions, <1 for five accessions and ~1 for four accessions (Figure 5). Notably, two of the accessions with MsiGhd8B LD/SD ratios ~1 also had a relatively low expression, were from the tropics (PMS-382 and US56-0022-03) and were among the only three accessions in the panel that did not flower under LD (Figure 5, Table 1); the third accession (PMS-375) was similar, with a small but significantly lower expression under LD than SD at ZT9. In contrast to the B subgenome, the A subgenome LD/SD ratio of Ghd8 expression at ZT9 was >1 for only one accession (PMS-436) and ~1 for eleven accessions.

4. Discussion

The results of the current study demonstrate that Ghd8 is present in M. sinensis, and likely contributes to a regulatory function for flowering time in this species in a manner that is similar to that in rice. Firstly, collinearity analysis revealed that two homoeologous Ghd8 loci (Misin13G040800 and Misin07G127500), one each in the two M. sinensis subgenomes (MsA and MsB), corresponded to the same genomic region on rice Chr.08 (LOC_Os08g07740) and sorghum Chr.07 (Sobic.007g059500) (Figure S1 and Table S2), which was consistent with the known paleo-duplications (rice Chr.08- sorghum Chr.07, sorghum Chr.07- Miscanthus Chr.13 and Chr.07) from the ancestral grass chromosomal groups [29,40,41]. Additionally, at each of the two homoeologous Ghd8 loci in M. sinensis, each accession in this study had at least one putatively functional full-length allelic copy containing a highly conserved HAP3/NF-YB DNA-binding domain that is required for the transcription factor function of Ghd8 in rice [22] and A. thaliana [61]. Moreover, the two homoeologous Ghd8 loci in M. sinensis expressed and may have a conserved function to regulate flowering time. If the M. sinensis Ghd8 genes were non-functional, we would expect a high frequency of accessions to have no functional alleles due to a lack of selection pressure, but this was not observed. Moreover, the M. sinensis Ghd8 genes were highly expressed (especially from the B subgenome), which is a necessary requirement for function.

Perhaps the strongest evidence for Ghd8 having a role in regulating the photoperiod-sensitive induction of flowering in M. sinensis comes from the observed differences in the gene’s expression under LD relative to SD during the day and its relationship to observed days to first flower among the accessions. If the critical time for Ghd8 to suppress Ehd1 via Ghd7 is in the morning, as was reported for rice [34], or at ZT9 for M. sinensis, as evidenced by a frequent peak at that time, then an LD/SD Ghd8 expression ratio >1 would be expected to delay or prevent flowering under LD and hasten flowering under SD, whereas a LD/SD ratio <1 would be expected to do the opposite (i.e., hasten flowering under LD and delay or prevent flowering under SD). A value of one for the day LD/SD Ghd8 expression ratio would indicate that Ghd8 did not regulate flowering time in that accession, and that other genes conferred any observed differences in flowering time associated with day length. For the M. sinensis B subgenome, four of the eight accessions with ZT9 LD/SD Ghd8 expression ratios differing from ~1 had values that were consistent with their observed flowering times (Table 1, Figure 5). Two of these four accessions (Miyazaki and PMS-306) had ZT9 LD/SD MsiGhd8B expression ratios >1 and flowered substantially earlier under 12.5 than 15 h day length, similar to the short-day (SD) response reported for rice [22,23]. The other two accessions (PMS-436 and PMS-164) had ZT9 LD/SD MsiGhd8B expression ratios <1 and flowered early under 15 h but failed to flower under 12.5 h day lengths; at ZT 3, both accessions also had LD/SD MsiGhd8B expression ratios <1 and a third accession, Sugadaira, performed similarly with an LD/SD ratio <1 at ZT3 but not at ZT9. Notably, the five accessions with day LD/SD MsiGhd8B expression ratios that were consistent with their flowering times were among the six most northerly accessions (≥29.9° N) in the panel (only Teshio was not included), suggesting that MsiGhd8B regulation of flowering time may predominate in M. sinensis from high latitudes. The three tropical accessions with Ghd8 expression ratios ~1 uniquely did not flower under 15 h but did flower under 12.5 h day length, suggesting that this adaptation was conferred not by Ghd8 but some other, yet to be determined gene(s). Given that grasses have multiple pathways to regulate flowering time, including two known major pathways for photoperiod regulation of flowering time that each has multiple modifiers, we would not expect every accession in the panel to have its flowering time predominantly conferred by any one gene, including Ghd8. Nevertheless, we identified a signal of Ghd8 regulation of flowering time from nearly half of the M. sinensis accessions in the panel.

In contrast to the B genome, two lines of evidence suggest that the M. sinensis A genome homoeolog of Ghd8 does not substantially contribute to the photoperiod regulation of flowering time. First, eleven of the twelve accessions in the panel had ZT9 LD/SD MsiGhd8A expression ratios ~1, yet all the accessions studied had different flowering time responses to LD or SD. Second, the expression of MsiGhd8A was substantially lower than the expression of MsiGhd8B for each accession. The lower expression observed for MsiGhd8A than MsiGhd8B was consistent with a previously observed M. sinensis genome-wide expression bias in favor of the B subgenome, with ~10% more pairs of genes having higher expression in the B subgenome [41]. Thus, MsiGhd8A may be a case of reduced or neo-functionalization, which is common in organisms with duplicated genomes [62].

The four nsSNVs identified in the HAP3/NF-YB domain of MsiGhd8 from five accessions (Table S1) could have an important effect on protein stability and function. Though the sample size is limited, it is worthwhile to consider what role these variants might have in regulating the flowering time of M. sinensis. If the M. sinensis Ghd8 functions similarly to the rice Ghd8, by regulating Ghd7 as part of a complex with HD1 and HAP5b [34], then there is the potential for reduced stability of the complex to affect the phenotype. Complex formation, such as Ghd8-OsHAP5b-Hd1, and DNA-binding are stochastic processes that can be affected by the concentration of the molecules involved. For example, if expressed copies of Ghd8 that have a non-functional or reduced-functioning DNA binding site produce protein molecules that remain able to form a complex with the products of HD1 and HAP5b, then they may compete with copies of Ghd8 that have fully functional DNA binding sites, thereby reducing the quantity of functional complex and consequently reducing the transcription of Ghd7 and promoting flowering. Similarly, copies of Ghd8 that have a conserved DNA binding site, but which can form a complex that has an unstable conformation, may not be able to promote Ghd7 transcription, yet may compete for Ghd7 binding sites with molecules of the complex that can act as a functional transcription factor. In domesticated rice, non-functional alleles of Ghd7, Ghd8 and Hd1 enabled early flowering and thus the expansion of cultivation to high latitudes for food production [63], whereas for undomesticated M. sinensis, natural selection appears to have resulted in functional alleles Ghd8 and Hd1 [33], conferring adaptation to high latitudes. For M. sinensis Hd1, a high frequency of non-functional alleles differentiated accessions from the Japanese archipelago and with those from mainland Asia [33], which is different from what we observed for Ghd8 in the current study.

Further research is needed to quantify the effects of individual putative functional MsiGhd8 alleles with nsSNVs and/or sSNVs on flowering time in response to day length. These studies can evaluate segregating populations derived from controlled biparental crosses, or be achieved by gene editing. The current study provides information on which alleles are present in different accessions that can be used to conduct genetics studies of segregating biparental populations. Additionally, the sequence data obtained by the current study for many different natural MsiGhd8 alleles can be used to plan gene-editing studies in Miscanthus, rice or other species to dissect function while controlling for genetic background.

Dong et al. [7] observed that short days (<12.5 h) were also a signal for M. sinensis from high latitude plants to induce a short-internode dormancy response, which is an adaptation to protect apical meristems from damaging low temperatures during winter in high latitudes, and this dormancy response was epistatic to flowering. Similar dormancy responses to short days have been found in several quantitative short-day, perennial, C4 grasses, including M. sacchariflorus [4], switchgrass (Panicum virgatum) [64] and big bluestem (Andropogon gerardii) [65]. Additional research is needed to determine whether MsiGhd8 also mediates dormancy directly or indirectly.

In Arabidopsis and rice, extensive studies have revealed the underlying genetic mechanisms for regulating heading date. Using yeast and animal systems, it has been demonstrated that HAPs, a CCAAT-box-binding transcription factor, form a heterotetramer or heterotrimer for transcription activation. In A. thaliana, HAP3b subunits can directly interact with Hd1/CO through its CCT-domain, forming CCAAT-binding CBF complexes that bind to FT promoters and activate transcription to promote flowering under LD [66,67]. In rice, the grass-specific gene Ghd7 is upregulated by a Ghd8-OsHAP5b-Hd1 complex under LD, enabling Ghd7 to suppress Ehd1 and delay flowering [36,63,68,69,70,71,72]. However, Hd1/CO also competes with the complexes to promote Hd3a/RFT1 expression, creating a tradeoff relationship for photoperiod sensitive flowering under SD conditions. Thus, the regulatory network controlling flowering time is complex and quantitative, which likely accounts for the great plasticity of this trait in diverse populations. Whether MsiGhd8 protein can bind these flowering-related gene products (Hd1/CO and Ghd7) forming NF-Y complexes as described in rice remains to be confirmed in future studies, but the results of the current study suggest it is likely.

In addition to flowering time, Ghd8 has been found to regulate multiple developmental and physiological processes in rice. In previous studies, OsGhd8 has been associated with stress tolerance and regulation of photosynthesis [23,73,74]. OsGhd8 up-regulated MONOCULM 1 (MOC1), a key gene controlling tillering and branching; this increased the number of tillers and primary and secondary branches [23]. Wang et al. [73] found a cis-regulatory variation in the Ghd8 promoter, associated with cold tolerance, thus contributing significantly to the ecological adaptation of rice varieties to high latitudes. Adachi et al. [74] indicated that CARBON ASSIMILATION RATE 8 (CAR8), identical to DTH8/Ghd8/LHD1, affected multiple physiological aspects relating to photosynthesis in rice, such as CO₂ assimilation rate and hydraulic conductivity. Given the great allelic diversity observed for M. sinenesis Ghd8 in the current study, it would be desirable to determine if this gene also regulates a range of important physiological and developmental traits of Miscanthus.

In summary, this study identified two homoeologous loci of MsiGhd8 among a mini-core collection of M. sinensis, with one on each of this paleo-allotetraploid species’ subgenomes. Several alleles and predicted amino acid sequence variants of MsiGhd8 showed a geographic and latitudinal distribution. The gene expression of MsiGhd8 correlated with the flowering date for some accessions in response to the photoperiod. The diverse MsiGhd8 expression patterns illustrated the complicated flowering regulatory network in Miscanthus. Further studies will be necessary to clarify the molecular mechanism of regulatory networks of flowering-related genes in Miscanthus, and to potentially improve biomass yield and quality by the regulation of the reproductive phase.

Supplementary Materials

The following are available online at https://www.mdpi.com/2073-4425/12/2/288/s1. Figure S1: Chromosome organization of Ghd8 gene orthologous regions (100 kbp) from Oryza sativa, Sorghum bicolor and Miscanthus sinensis. Figure S2: Geographical distribution of MsiGhd8A and MsiGhd8B alleles in Miscanthus sinensis. Table S1: A summary of polymorphic sites in MsiGhd8 open reading frames (ORFs) from 12 Miscanthus sinensis accessions. Table S2: Colinear genes near orthologs of Ghd8 in Miscanthus sinensis, Sorghum bicolor, and Oryza sativa.

Author Contributions

Conceptualization, T.Y. and E.J.S.; methodology, M.X. and H.N.; formal analysis, Z.G.; investigation, Z.G.; resources, T.Y., E.J.S. and L.V.C.; data curation, Z.G. and M.X.; writing—original draft preparation, Z.G.; writing—review and editing, Z.G., M.X., T.Y. and E.J.S.; supervision, T.Y. and E.J.S.; funding acquisition, T.Y. and E.J.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant nos. DE-SC0012379 and DE-SC0016264, and DE-SC0018420 (Center for Advanced Bioenergy and Bioproducts Innovation). This work was partially supported by Grants-in-Aid for Scientific Research (No. 17H04615 to T.Y.) from the Japanese Ministry of Education, Science, Sports and Culture. E.J.S. gratefully acknowledges support from Hokkaido University’s visiting professor program. Z.G. gratefully acknowledges the China Scholarship Council to pursue her doctoral research at the Hokkaido University, Japan.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data necessary for confirming the conclusions of the article are present within the article, Figures and Tables, and within Supplementary Tables and Figures.

Acknowledgments

We thank Yoichiro Hoshino for providing greenhouse space in Hokkaido University and Sarah J Lipps for preparing divisions of the Miscanthus entries at the University of Illinois, Urbana-Champaign, Urbana, IL.

Conflicts of Interest

The authors declare no conflict of interest.

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures and Table

Figure 1. Gene structure and multiple alignment analysis of Miscanthus sinensis Ghd8 homoeologs and their comparison with orthologs from four other plant species. (a) Gene structure of MsiGhd8A and MsiGhd8B. F, forward primer; R, reverse primer; the primer pairs F1/R1 and/or F2/R1 were used to detect open reading frames (ORFs) for Ghd8. The start codon (ATG) and stop codon (TGA) are highlighted in black. The yellow box represents the HAP3/NF-YB domain. (b) Multiple amino acid sequence alignments for Ghd8 from M. sinensis (this study), Sorghum bicolor (Sobic.007g059500), Oryza sativa (LOC_Os08g07740), Zea mays (Zm0001d049485) and Arabidopsis thaliana (AT5G47640). The HAP3/NF-YB domain is boxed in red. The M. sinensis sequence used for alignment was from accession PMS-382.

Figure 2. Phylogenetic tree inferred by neighbor-joining method for nucleotide sequences of 42 Ghd8 alleles from 11 accessions of Miscanthus sinensis and four alleles from one Miscanthus floridulus accession. Sorghum bicolor (Sobic.007g059500) and Oryza sativa (LOC_Os08g07740) were used as an out-group. The phylogenetic tree was divided into two clusters, which were classified as MsiGhd8A and MsiGhd8B, one for each of the two subgenomes. Bootstrap values for nodes supported in >50% of 1000 bootstrap replicates are shown. Allele names with A or B prefix indicate putatively functional alleles types based on predicted amino acid sequence variants, which are named in parentheses and correspond to the names in Figure 3 and Figure S2, Table 1 and Table S1.

Figure 3. Geographical distribution of MsiGhd8A and MsiGhd8B predicted amino acid sequence variant types in Miscanthus sinensis. Pie charts with one to two sections represent the number of detected alleles. A or B prefix indicates putatively functional alleles types based on predicted amino acid sequence variants, corresponding to the names in Figure 2, Table 1 and Table S1. Different colors in pie charts represent different variant types that occurred in more than one accession; variant types that were observed only once have a gray background, corresponding to Table S1. Accessions’ names were colored to represent M. sinensis genetic groups previously described by Clark et al. [49,50]; Sugadaira and Miyazaki were changed from yellow to black for making the map clear.

Figure 4. Expression of MsiGhd8 at Zeitgeber time 9 for 12 Miscanthus sinensis accessions under long days (15 h). Grey and black represent MsiGhd8A and MsiGhd8B, respectively. Relative mRNA levels are expressed as the ratios to ACTIN transcript levels. Mean ± 1SE for three replications are given for each data point. A different letter on top of a bar indicates significant difference between accessions within each subgenome according to the Tukey HSD (95% family-wise confidence level) multiple comparison tests. *** shown between the two subgenomes indicates a significant difference at p < 0.001 according to the Student’s t-test.

Figure 5. Diurnal expression of MsiGhd8 in 12 Miscanthus sinensis genotypes under long days (15 h, long-day (LD); solid black lines) and short days (12.5 h, short-day (SD); red dashed line). (a) MsiGhd8A and (b) MsiGhd8B. Relative mRNA levels are expressed as the ratios to ACTIN transcript levels. The numbers below the x-axis indicate Zeitgeber times (ZT) of the day. The white bar at the bottom of each graph indicates the light period and the black bar indicates the dark period. Mean ± 1SE for three replications are given for each data point. Asterisks indicate significant difference between the two means under LD and SD at the same ZT of the day (Student’s t-test, * p < 0.05, ** p < 0.01, *** p < 0.001). No asterisk indicates the difference between the two means is not statistically significant (p < 0.05).

Table 1

Provenance, flowering time under short or long days and amino acid sequence diversity for two homoeologous Ghd8 loci in a mini-core panel of 11 Miscanthus sinensis and one Miscanthus floridulus accessions.

Genotypes	Ploidy	Lat	Long	Genetic Group †	Genetic Group Color Code †	Days to First Flowering ‡		Variant Types Classified by Predicted Protein in Ghd8 Homoeologs
						12.5 h	15 h	MsiGhd8A		MsiGhd8B
M. sinensis “Teshio”	2x	44.9	141.9	Northern Japan	Blue		66	A1	A2	B1	B2
M. sinensis “Sugadaira”	2x	36.0	138.1	Southern Japan	Yellow		96	A3	A4	B3	B4
M. sinensis “Miyazaki”	2x	31.8	131.4	Southern Japan	Yellow	61	167	A5	A6	B5	B6
M. sinensis “PMS-436”	2x	41.3	123.7	Korea/North China	Red		115	A3	A7	B7	B8
M. sinensis “PMS-164”	2x	37.3	114.3	Yangtze-Qinling	Green		130	A8	A8	B8	B8
M. sinensis “PMS-306”	2x	29.9	118.8	Yangtze-Qinling	Green	84	173	A8	A9	B8	B8
M. sinensis “PMS-226”	2x	26.6	106.8	Sichuan Basin	Orange	76	189	A1	A7	B9	B10
M. sinensis “Onna-1a”	2x	26.5	126.8	SE China plus tropical	Purple		274	A10		B11	B12
M. sinensis “PMS-359”	2x	22.9	112.3	SE China plus tropical	Purple	81	179	A11	A7	B8	B13
M. sinensis “PMS-375”	2x	19.6	110.3	SE China plus tropical	Purple	142		A11		B9	B9
M. sinensis “PMS-382”	2x	18.9	109.5	SE China plus tropical	Purple	184		A11	A12	B1	B1
M. floridulus “US56-0022-03”	2x	−20.9	165.3	SE China plus tropical	Purple	114		A11	A13	B14	B15

† M. sinensis genetic groups determined by Clark et al. [49,50]. ‡ Days to first flowering under short days (12.5 h) or long days (15 h) by Dong et al. [7]; empty cells indicate flowering did not occur. A or B prefix indicates putatively functional alleles types based on predicted amino acid sequence variants in the A and B subgenomes, respectively, corresponding to Figures 2 and 3, Table S1. Empty cells of MsiGhd8A indicated that only one allele type was detected in Onna-1a and PMS-375, and therefore, these two accessions were homozygous at MsiGhd8A.