The rice varieties Hokkaiwase, Kitaake, and Hoshinoyume were used for the gene expression analysis. The genotypes of qLTG3-1 in Hokkaiwase, Kitaake, and Hoshinoyume were the wild type, single amino acid substitute type, and loss-of-function type, respectively (Fujino and Iwata, 2011; Fujino and Sekiguchi, 2011). These varieties were cultivated in an experimental paddy field at Hokkaido Agricultural Research Center, Sapporo, Japan, 43°00′N latitude, in 2013. Seeds were harvested at the maturing stage and were then maintained at room temperature. These seeds were used in experiments 4 months after harvesting. Seeds were incubated at 15 and 30°C in dark conditions (Fujino et al., 2004). After being incubated, seed samples from each time point were frozen immediately in liquid nitrogen and stored at −80°C for RNA extraction.

In the analysis of the sequence diversity of Os10g0554800, a paralogous gene of qLTG3-1, a set of 58 genetically diverse varieties was used, which represents the wide genetic diversity among cultivated rice varieties termed world rice core collection (WRC) (Kojima et al., 2005). Seeds were provided by the Local Independent Administrative Agency Hokkaido Research Organization and National Institute of Agrobiological Sciences, Japan.

To identify the HyP/GRP gene family in the rice genome, we employed BlastP searches of RAP-DB (http://rapdb.dna.affrc.go.jp/) and MSU-RGAP (http://rice.plantbiology.msu.edu/) using the protein sequence of qLTG3-1 as a query. The HyP/GRP gene family in monocots was searched by BlastP programs. The protein sequences in maize, sorghum, and Brachypodium were retrieved from Phytozome version 10 (http://phytozome.jgi.doe.gov/pz/portal.html). Barley gene sequences were retrieved from the IPT Barley blast server (http://webblast.ipk-gatersleben.de/barley/). The 1 kb upstream region from the transcription start site on each gene was also retrieved from databases as the promoter sequence.

Multiple sequence alignment of the HyP/GRP protein sequences was performed using the ClustalW method with MEGA version 6 built in with a default setting (http://www.megasoftware.net/). A phylogenic tree was constructed by the neighbor-joining method considering 1000 replications with bootstrap analyses. The similarity of the amino acid sequences and identities of the promoter sequences among the HyP/GRP gene family were calculated using alignment data by the SIAS program with a default setting (http://imed.med.ucm.es/Tools/sias.html). The cis-acting elements in the promoter region were analyzed using the MEME suite (http://meme.nbcr.net/meme/) with the following parameters. The optimum width of each motif was between 6 and 20 bp. The number of differential motifs was 20, while that of the minimum motif site was 5. E = 1.1e⁺⁴ was used as a threshold for shuffle sequences.

Syntenic dotplots for the chromosomal regions around qLTG3-1 orthologous genes were generated using PipMaker (http://pipmaker.bx.psu.edu/pipmaker/). The orthologous genomic regions were identified through comparative genomics analysis of the putative highly conserved gene pairs in monocots. The 163 kb in rice chromosome 3 including 22 genes, the 117 kb in Brachypodium chromosome 1 including 21 genes, the 200 kb in sorghum chromosome 1 including 15 genes, the 383 kb in maize chromosome 1 including 17 genes, and the 209 kb in barley chromosome 4 including 12 genes were used for the initial analysis. The CDSs in these orthologous genomic regions were then used to analyze collinearity among the monocots.

Total DNA was isolated from young leaves using the CTAB method (Murray and Thompson, 1980). PCR, electrophoresis, and sequencing were performed as described previously (Fujino et al., 2004, 2005, 2010). The 1128-bp Os10g0554800 region was sequenced, including the 364-bp 5′ upstream region, 504-bp coding region, and 260-bp 3′ downstream region. PCR products were sequenced directly using cycle sequencing with BigDye terminators (Applied Biosystems) on a Prism 3700 automated sequencer (Applied Biosystems). The sequences of four Os10g0554800 alleles were deposited in GenBank as Accession Nos. AB973302–AB973304.

RNA extraction and semi-quantitative RT-PCR analysis were performed as described previously (Fujino et al., 2008a,b; Fujino and Matsuda, 2010). Total RNA was extracted from 10 embryos of seeds during seed germination because qLTG3-1 was specifically expressed in the embryos of germinating seeds (Fujino et al., 2008b). In addition, total RNA from the roots of 4-day-old seedlings and the 3rd leaf blades of 3-week-old seedlings were used. In semi-quantitative RT-PCR, each PCR reaction (10 μl) contained 1 μl of a five-fold-diluted cDNA template. The gene-specific primer sets and PCR conditions are listed in Supplemental Table S1. PCR was performed under the same conditions as those for RT-PCR using RNA without reverse transcription to determine contamination with genomic DNA. To validate the results obtained, each PCR experiment was repeated three times.

To identify members of the HyP/GRP gene family in rice, the reference Nipponbare genome sequence was searched using the qLTG3-1 proteins as queries. A total of 21 genes were identified as putative HyP/GRP genes (Table 1). Amino acid alignments ranged between 124 and 184 amino acids. We renamed them OsHyPRP01 to OsHyPRP21 based on their order on the chromosome. OsHyPRP05 was qLTG3-1, which controlled low-temperature tolerance at the seed germination stage (Fujino et al., 2004, 2008b). OsHyPRP01 and OsHyPRP13 were RCc3 and RCc2, respectively, which were root-specific proteins (Xu et al., 1995). The amino acid alignments of OsHyPRP revealed three conserved regions: an N-terminal region (region A), variable P/GRD region (region B), and conserved 8CM region (region C) (Figure 1). All genes, except for OsHyPRP21, were clustered in five regions spanning 9573–38,960 bp intervals on four chromosomes. OsHyPRP21 was located on chromosome 10 apart from the 89,260 bp of OsHyPRP20. Clusters derived by tandem duplication on chromosomes 2 and 4 and chromosomes 3 and 10 were paralogous chromosomal regions. These two pairs were previously shown to be involved in 10 major chromosome-to-chromosome duplication relationships in the rice genome (Throude et al., 2009).

The OsHyPRP genes showed high similarity to each other at amino acid alignments, 0.442–0.985 (Supplemental Table S2). The highest and lowest similarities occurred between OsHyPRP06 and OsHyPRP07 and between OsHyPRP05 and OsHyPRP19, respectively. All, except for OsHyPRP05 and OsHyPRP21, showed higher similarity, a mean of 0.730 ranging 0.641–0.985. These two OsHyPRP genes, OsHyPRP05 and OsHyPRP21, had GRD and showed lower similarity with other members of the OsHyPRP genes, 0.498 and 0.539, respectively.

The phylogenic tree of the OsHyPRP genes corresponded to tandem duplications and chromosome duplications (Figure 2). The differentiation of OsHyPRPs was mainly caused by amino acid substitutions within regions A and B. In contrast to the high similarity in region C, 0.920, those in regions A and B were 0.783 and 0.586, respectively. P/GRDs characterized each member of the OsHyP/GRP gene family.

To determine the expression specificity of the HyP/GRP gene family in rice, semi-quantitative RT-PCR analysis was conducted using the RNA of Hokkaiwase extracted from various tissues: embryos during seed germination at different times, the tips and bases of the roots of 4-day-old seedlings, and the 3rd leaf blades of 3-week-old seedlings (Figure 2). Seventeen of the 21 members were expressed in the different tissues of Hokkaiwase. The expression of four genes, OsHyPRP08, 11, 12, and 18, was negligible in these tissues. Gene expression levels varied among different tissues and times. OsHyPRP01 showed a similar expression profile to OsHyPRP03, specifically to that in the root. OsHyPRP06 showed a similar expression profile to OsHyPRP07, 13, 19, and 20, specifically in the tip of the root. The gene expression of OsHyPRP05 was detected after 12-h and 2-day incubations at 30 and 15°C during seed germination. The expression of eight genes, OsHyPRP04, 09, 10, 14, 15, 16, 17, and 21, was detected during seed germination. These were located on chromosomes 3 and 10, suggesting that paralogous genes have similar gene expression patterns. The gene expression of OsHyPRP21 was higher and earlier than that of OsHyPRP05. The overlapped and different gene expression patterns of the OsHyPRP genes suggested that OsHyPRP has redundant and different roles at the developmental stages in rice.

In contrast to the high similarity of amino acid alignments, sequence identity in 1 kb of the 5′ upstream regions from UTR was low, with a mean of 0.330 ranging 0.262–0.410 (Supplemental Table S3). Due to this low identity in the 5′ upstream regions, similar expression patterns may be controlled by a small number of cis-regulatory elements.

Similar expression patterns, but lower expression levels were detected in Kitaake and Hoshinoyume (Supplemental Figure S1). Since these varieties have different qLTG3-1 alleles, they exhibited different growth stages from the start of the incubation. The results strongly suggested that the expression of these OsHyPRP genes is dependent on the developmental stage based on qLTG3-1.

Based on chromosomal locations and the glycine-rich motif, OsHyPRP21 was considered to be a paralogous gene to OsHyPRP05. A total of 1128 nucleotides in the OsHyPRP21 (Os10g0554800) gene were sequenced among 58 varieties in WRC. Compared with the sequence of Nipponbare as a reference allele (allele A), nine mutation events at nine sites, including deletions and substitutions, were detected (Supplemental Figure S2). Only three mutation events were detected in the coding region; two deletions at positions +95 and +193 and a single nonsynonymous substitution at position +139. These deletions occurred in-frame in the GRD, which contained Gly repeats with a Ser residue. As a result of the mutation events of these deletions, the repeat number varied. The A–G substitution at position +139 generated the amino acid substitution, Ser to Gly.

Based on these mutations, 4 different alleles were detected among WRC (Supplemental Figure S2, Table S4). Allele B, which was found in a single variety, was generated from intragenic recombinations between alleles A and C. Allele A included 30 varieties, while alleles C and D included 17 and 10 varieties, respectively. A clear relationship was observed between the allele types of OsHyPRP21 and the cultivar group classification. Varieties of japonica and aus had allele A, while varieties of indica had alleles C and D.

Similar to qLTG3-1 (OsHyPRP05) (Fujino and Sekiguchi, 2011), the almost completely conserved protein alignment of OsHyPRP21 was identified. These results suggested that the function of OsHyPRP21 is critical at least for seed germination, during which gene expression was detected.

The sequences of four genome-sequenced species, barley, maize, Brachypodium, and sorghum, were analyzed to determine the evolutional relationships among the HyP/GRP gene family in monocots. The results of a BLAST search with qLTG3-1 as the query identified 12 genes in barley, 20 genes in maize, 10 genes in Brachypodium, and 28 genes in sorghum (Supplemental Figure S3, Table S4). All these species contained the HyP/GRP gene family, with predicted amino acid alignments ranging from 120 aa in barley to 325 aa in sorghum. Two HyP/GRP genes with a glycine rich motif was detected in barley, maize, and Brachypodium, while five were identified in sorghum. Species-specific tandem duplications occurred. In maize, four members of ZmHyPRP05-08 and four members of ZmHyPRP16-19 were tandem duplicated within the 52 kb region on chromosome 1 and the 197 kb region on chromosome 9, respectively. In Brachypodium, four members of BdHyPRP02-05 were tandem duplicated within the 16 kb region on chromosomes 1. In sorghum, three members of SbHyPRP02-04, 11 members of SbHyPRP08-18, three members of SbHyPRP20-22, and four members of SbHyPRP23-26 were tandem duplicated within the 22 kb region on chromosome 1, the 101 kb region on chromosome 4, the 19 kb region on chromosome 6, and the 52 kb region on chromosome 8, respectively.

Phylogenetic analysis revealed that a total of 91 HyP/GRPs in these five monocots appeared to be divided into seven distinct groups (Figure 3). The main difference in the amino acid alignments in each group was the alignment of the proline/glycine-rich motif (Supplemental Figure S4). The nine members of OsHyPRP, which were tandem located on chromosome 10, formed a distinct group, group V, while HyP/GRPs from other groups were clustered together in each species.

In the phylogenic tree, qLTG3-1 belonged to group VI with eight orthologous genes in monocots with marked similarity to qLTG3-1, with a mean of 0.738 and range of 0.568–1.000 (Supplemental Table S5). All members in group VI had GRD. Three genes with GRD, OsHyPRP21, ZmHyPRP04, and SbHyPRP01, formed a subcluster in group I. These results suggested that genes with a glycine-rich motif in group VI are the ancestor type, while those in group I are the paralogous type and diversified from the ancestor type. In the common ancestor of these monocots, qLTG3-1 orthologous HyP/GRP genes with GRD may be generated and at least a single duplication may have occurred.

Ten conserved amino acids, LLALNLLFFT, were previously identified at the N-termini from a comparison of qLTG3–1-like proteins in plants (Fujino et al., 2008b). An allelic variation with a single amino acid substitution, LLALNLHFFT, was then identified, which had weak function on seed germination (Hori et al., 2010; Fujino and Iwata, 2011). The LLALNLL_F_ alignment was completely conserved in the nine genes for orthologous qLTG3-1 (Supplemental Figure S5), suggesting that this alignment plays a significant role in the molecular function of qLTG3-1.

In contrast to the marked similarity of amino acid alignments among the qLTG3-1 orthologous genes, sequence identity in 1 kb of the 5′ upstream regions from UTR among rice, Brachypodium, maize, and sorghum was low, with a mean of 0.422 and range of 0.274–0.756 (Supplemental Table S6). Among the three conserved motifs expected, two conserved motifs were identified as a cis-regulatory motif, AGCT repeat, and ATGC repeat (Supplemental Figures S6, S7). The ATGC repeat had a CATGCA sequence, called the RY element, which was previously shown to be crucial for transactivation through ABI3/VP1-like B3-domain proteins (Ezcurra et al., 2000; Reidt et al., 2000) and has been predominantly detected in seed-specific promoters (Lelievre et al., 1992). Therefore, the RY element was found in Brachypodium, maize, and sorghum, but not in rice.

Phylogenetic analysis of the HyP/GRP genes in monocots strongly suggested that the expansion of the HyP/GRP gene family occurred from the latest common ancestor of the monocots of these five species. These results indicated that orthologous HyP/GRP genes have the same function in each species. Whole genome duplications and tandem duplications after the differentiation of these species may contribute to the expansion of HyP/GRP genes as a gene family.

To clarify whether the genes in group VI originated from a common ancestral gene, we compared the chromosomal locations of these genes. OsHyPRP05/qLTG3-1 was located on rice chromosome 3. Others were BrHyPRP03 on Brachypodium chromosome 1, HvHyPRP07 on barley chromosome 4, ZmHyPRP01 on maize chromosome 1, and SbHyPRP06 on sorghum chromosome 1. A previous study reported that these chromosomes had homologous relationships (Abrouk et al., 2010). These genes among monocots were orthologous to rice qLTG3-1, indicating that these genes within group VI were evolutionary related through a common ancestral gene on chromosome A7 from a putative ancestor in the proposed angiosperm evolutionary models (Abrouk et al., 2010).

Orthologous chromosomal regions were aligned and compared to identify the conservation of micro-synteny around qLTG3-1 and its orthologous genes (Supplemental Figure S8). However, only a small region was conserved among the monocots. The coding regions (CDSs) were then aligned and compared. Conserved gene alignments were detected among these species, except for barley, and high homology was detected between homologous CDSs (Figures 4, 5). Although the number of tandem duplicated HyP/GRP genes differed, the gene order was highly conserved among maize, sorghum, and Brachypodium.

Marked genomic collinearity was observed among Brachypodium, sorghum, and maize, while collinearity could not be detected in barley. The gene order in the ancestor genome was proposed based on collinearity (Figure 6). According to the gene order, rearrangements including duplications, deletions, and insertions were involved in each monocot genome, which occurred in similar chromosomal regions.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.