Skip to main content
Browse Subject Areas

Click through the PLOS taxonomy to find articles in your field.

For more information about PLOS Subject Areas, click here.

  • Loading metrics

Mapped Clone and Functional Analysis of Leaf-Color Gene Ygl7 in a Rice Hybrid (Oryza sativa L. ssp. indica)

  • Xiao-juan Deng,

    Affiliations College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China, Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, Hunan, China

  • Hai-qing Zhang ,

    Affiliations College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China, State Key Laboratory of Hybrid Rice, Hunan, China

  • Yue Wang,

    Affiliations College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China, Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, Hunan, China

  • Feng He,

    Affiliations College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China

  • Jin-ling Liu,

    Affiliation College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China

  • Xiao Xiao,

    Affiliation College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China

  • Zhi-feng Shu,

    Affiliation College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China

  • Wei Li,

    Affiliation College of Plant Preservation, Hunan Agricultural University, Changsha, Hunan, China

  • Guo-huai Wang,

    Affiliation College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China

  • Guo-liang Wang

    Affiliations College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China, Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, Hunan, China, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China, Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America


Leaf-color is an effective marker to identify the hybridization of rice. Leaf-color related genes function in chloroplast development and the photosynthetic pigment biosynthesis of higher plants. The ygl7 (yellow-green leaf 7) is a mutant with spontaneous yellow-green leaf phenotype across the whole lifespan but with no change to its yield traits. We cloned gene Ygl7 (Os03g59640) which encodes a magnesium-chelatase ChlD protein. Expression of ygl7 turns green-leaves to yellow, whereas RNAi-mediated silence of Ygl7 causes a lethal phenotype of the transgenic plants. This indicates the importance of the gene for rice plant. On the other hand, it corroborates that ygl7 is a non-null mutants. The content of photosynthetic pigment is lower in Ygl7 than the wild type, but its light efficiency was comparatively high. All these results indicated that the mutational YGL7 protein does not cause a complete loss of original function but instead acts as a new protein performing a new function. This new function partially includes its preceding function and possesses an additional feature to promote photosynthesis. Chl1, Ygl98, and Ygl3 are three alleles of the OsChlD gene that have been documented previously. However, mutational sites of OsChlD mutant gene and their encoded protein products were different in the three mutants. The three mutants have suppressed grain output. In our experiment, plant materials of three mutants (ygl7, chl1, and ygl98) all exhibited mutational leaf-color during the whole growth period. This result was somewhat different from previous studies. We used ygl7 as female crossed with chl1 and ygl98, respectively. Both the F1 and F2 generation display yellow-green leaf phenotype with their chlorophyll and carotenoid content falling between the values of their parents. Moreover, we noted an important phenomenon: ygl7-NIL's leaf-color is yellow, not yellowy-green, and this is also true of all back-crossed offspring with ygl7.


Genetic purity of crop plants, which has a critical impact on increasing crop yields, is gradually becoming the focus in hybrid rice production [1]. Molecular markers can be used to rapidly identify seed purity yet are not useful for identifying off-type plants. Plants with a distinct color phenotype can be easily identified and removed, so leaf-color has become a suitable marker for maintaining the genetic purity of hybrid rice [2]. In addition, study of the genetic mechanism of leaf-color mutations would further our understanding of chlorophyll biosynthesis and degradation, chloroplast development, tetrapyrrole synthesis, and photosynthesis.

The colors of leaf-color mutants include albino, chlorosis, thermo-color, light green, maintaining green, stripes and zebra, green-revertible albino, dark-green, and purple [3]. As of 2013, at least 208 leaf-color mutants have been identified in rice. Of those, 175 mutants have been analyzed and 154 genes have been mapped to all 12 chromosomes. However, only 53 leaf-color genes of rice have been cloned (14 of them had alleles). Among them, 14 genes function directly in chlorophyll biosynthesis and catabolism (DCBC) [4][11], while 6 genes indirectly take part in those two processes (ICBC) [12][15]. Sixteen genes are directly involved in the developmental regulation of chloroplast (DDC) [16][21], while another 3 genes are involved indirectly (IDC) [22]. Four genes take part in the metabolism of carotenoids (CBM) [23][26]. One gene influences anthocyanin biosynthesis and catabolism (ABC). Three genes influence rice leaf-color via other pathways (OP) [27]. The functions of the remaining 6 genes are not yet defined (NDF) [28][32]. Details are provided in Table S1.

Mg-chelatase, which was first discovered in photosynthetic bacteria, is the first enzyme catalyzing the committed step of chlorophyll synthesis. Mg-chelatase consists of three subunits: I (40-kDa), D (70-kDa), and H (140-kDa) [33]. Only one copy of all the three subunits exists in rice. However, there is more than one subunit I in some species, such as Arabidopsis [34]. Mg-chelatase activity can only be detected when all three subunits are present [35]. Subunit I of Mg-chelatase belongs to the functionally diverse superfamily of AAA proteins and has the ATPase activity which is associated with various cellular activities [36]. Subunit D of Mg-chelatase has three consecutive regions: an N-terminal domain homologous to the AAA module of subunit I but without ATPase activity, a central acidic and Pro-rich region, and an integrin I domain with an unknown function at the C-terminus [37]. ATP combines with subunit I, subunit D, and Mg2+ to form the I-D-Mg-ATP complex. Subunit H combines with Protoporphyrin IX to form the H- Protoporphyrin IX complex. Then, I-D-Mg-ATP and H-protoporphyrin IX are combined together to hydrolyze ATP. Simultaneously, Mg2+ is added to Protoporphyrin IX to form Mg-Protoporphyrin IX [38].

Using the map-based cloning method and T-DNA insertion mutants, the five genes Chl1 [39], Chl9 [39], Ygl9 [40], Ygl3 [9], and ChlH [41] have been cloned in rice. Chl1, Ygl98, and Ygl3 code for OsChlD, and they are alleles. Chl9 codes for OsChlI and ChlH codes for OsChlH. Plants with ch11 exhibit yellowish-green leaves at the seedling stage, and then the color turns to a normal green at maturity. The mutational allele of Chl1 has a single base change from G to A at position 1176 bp which is located at the 8th exon. This nucleotide change leads to one aa conversion from Arg (R) to Gln (Q) at position 393 aa [39]. The ygl98 mutant exhibits a yellow-green leaf phenotype throughout the growing season and lower grain output. Mutational Yg198 has a single base change from G to A at position 1522 bp which is located at the 10th exon. This conversion results in an amino acid change from Ala (A) to Thr (T) at position 508 aa [40]. The ygl3 mutant displays a yellowy-green leaf-color throughout the growth cycle, lower plant height, and lower grain yield. The mutational Yg13 has a single base change from G to C at position 1009 bp which is located at 6th exon. This mutation leads to an amino acid change from Ala (A) to Thr (T) at position 337 aa [9].

The rice variety An Nong Biao 810S is a natural, yellowy-green leaf mutant selected from the PTGMS (photo- and thermo-sensitive genetic male sterile) rice line An Nong 810S maintained by Huaihua Vocational and Technical College of Hunan [42]. This plant leaf displays a permanent yellowy-green color throughout its life. Several studies reported no remarkable differences between wild type and the mutant in other primary agronomic traits [43], [44]. Compared to the wild type An Nong 810S, the mutant has a sharp drop in chlorophyll content. This variety as a visual marker is useful for testing the varietal purity of hybrid rice seeds. The leaf-color phenotype in this mutant is controlled by the single recessive nuclear gene Ygl7 which encodes a magnesium-chelatase ChlD. In this study, a single-nucleotide mutation from T to C at position 1883 bp of gene Ygl7 which leads to a change in the protein (Leu to Ser at position 628 aa)is identified by genetic sequencing. The RNAi assay of normal Ygl7 has been conducted in Nipponbare. Interestingly, back-crosses between the mutant ygl7 and other varieties displayed yellow-leaves. This research is significant for the application of a leaf-color marker gene in hybrid rice production and for exploration of the chlorophyll synthesis mechanism.

Materials and Methods

Plant materials

These experiments were conducted at Hunan Changsha and Hainan Sanya in April 2009 to October 2013. We used the following varieties.

The mutant ygl7 was a spontaneous yellow-green leaf mutant derived from multiplication of the PTGMS rice variety An Nong 810S (810S) (Oryza sativa L. ssp. indica) [42]. For genetic analysis, we used three combinations derived from crossing ygl7 with two indica cultivars (353 and 9311) and a japonica variety termed Nipponbare (NPB). The F2 population derived from crossing ygl7 with NPB was used to map Ygl7. The ygl7's near-isogenic line ygl7-NIL was used as a genetic complement. We constructed the near -isogenic line ygl7-NIL to function as acceptor material of the genetic transformation. Nipponbare was the acceptor parent back-crossed with the donor parent, ygl7. The yellow plants' population from BC4F2 is ygl7-NIL. The Chl1 mutant (obtained from Professor Nam-Chon Paek, College of Agriculture and Life Sciences, Seoul National University) and the ygl98 mutant (obtained from Professor Wang Ping-rong, Sichuan Agriculture University) are the OsChlD allele's mutant. All plant materials were planted under a standard management.

Genetic analysis and mapping

The leaf-color phenotype in the F1 and F2 populations were designated as the wild type (normal green leaf) and the yellowy-green leaf phenotype was considered the mutant. The F2 segregation ratios were analyzed with a χ2 goodness of fit test using the Excel software.

DNA was extracted from leaves using the improved CTAB method [45]. A total of 1199 molecular markers were used in this study, including 1130 SSRs (simple sequence repeat), 67 SFPs (single feature polymorphism), and 2 STSs (sequence tagged site). The SSR markers were obtained from Gramene ( The SFP and STS markers were designed using the Primer 5.0 software (Table S2). First, we used 1100 SSRs and 67 SFPs to select polymorphic markers from Ygl7 and NPB. Then, we used the entire gene pool to obtain potential linked markers. We used those markers in primary mapping of F2 individuals with the yellowy-green leaf phenotype that were selected from the cross of Ygl7 and NPB. To fine map the Ygl7 locus, we selected an additional 30 SSRs, 4 SNPs, and 2 STSs. Six molecular markers were used to screen recombination events from 2,849 F2 individuals for fine-mapping. Linkage analysis was conducted with MAPMAKER3.0, and the linkage map was constructed with MapDraw V2.1.

Sequence analysis

Within the fine mapped chromosome region, candidate genes were screened according to the annotation database of the NCBI. Specific primers were designed according to the genome sequences of NPB. These primers were used to amplify the candidate genes from the ygl7 mutant and its wild type parent 810S. The amplified products from DNA and RNA were sequenced and structurally analyzed to determine the target gene and the mutation site within the target gene. Total RNA was extracted using the TRIZOL method [46].

Genetic complementation and RNAi suppression of YGL7

The PCR products of a full-length YGL7 cDNA (primer D-18, Table S2) were digested with BamHI and KpnI and then inserted into the vector pLYL18, which was derived from pCAMBIA1300 using an ubiquitin promoter (Figure S1). Because callus of the ygl7 mutant (an indica variety) was difficult to obtain, the recombinant plasmid designated as pLYL18-YGL7 was introduced into Agrobacterium tumefaciens EHA105. It was then used to infect calli of individuals with the homozygous ygl7 allele in japonica genetic background selected from one NPB/ygl7 BC4F2 population (ygl7-NIL). Transformation was conducted according to a published protocol [47].

The pFGC5941 with a 35S promoter and a petunia CHSA (chalconesynthase A) intron was used as an RNAi vector. The PCR product is 592 bp conserved segments of cDNA YGL7 (primers DXJRNAi II, Table S2). The sense segment link to pFGC5941 was accomplished using NcoI and AscI, and BamHI and XbaI were used to link the anti-sense segment (Figure S1), which was then transformed into NPB as described above.

Gene Expression Analysis

For quantitative real-time PCR (qRT-PCR) analysis, total RNA was extracted from young leaves of ygl7, 810S and ygl7-NIL using an RNA Prep Pure Plant kit (Tiangen Co., Beijing, China). RNA was reverse transcribed using a SuperScript II kit (TaKaRa). Real-time PCR was performed using a SYBR Premix Ex Taq™ kit (TaKaRa) on an ABI prism 7900 Real-Time PCR System. We selected two types of genes for analysis. The first type are associated with chlorophyll biosynthesis and includes ChlD (YGL7), ChlI, ChlH, YGL1, HEMA1, and PoPA [32]. The second type are associated with photosynthesis, including the genes Cab1R, Cab2R, PsaA, PsbA, and RbcL [32]. qRT-PCR primers come from Zhou KN's paper [32] (primers were DXJCHLD to DXJrbcL, Table S2).

Chlorophyll fluorescence and photosynthetic pigments

Chlorophyll fluorescence was determined through IMAGING-PAM at the early heading stage. Fo, Fv'/Fm', ETR, qN, and qP were used in our study.

The chlorophyll (Chl) and carotenoid (Car) contents were measured using a spectrophotometer according to the method described by Tang Yan-lin [48]. To summarize briefly, equal weights of freshly collected second top leaves from the heading stage were immersed in extracting solution for 12 h under dark conditions. The extraction solution had a volume ratio of acetone, ethanol, and distilled water of 4.5: 4.5: 1. Residual plant debris was removed by centrifugation. The supernatants were analyzed with a DU 1700 UV/Vis Spectrophotometer at 440 nm, 663 nm, and 645 nm using the following equations:

Chla(mg/g) = [(9.784OD663-0.990OD645)×V]/(M×1000)

Chlb(mg/g) = [(21.426OD645-4.650OD663)×V]/(M×1000)

Chl(mg/g) = [(5.134OD663+20.436OD645)×V]/(M×1000)

Car(mg/g) = [4.695OD440-0.268(Chla+Chlb)×V]/(M×1000)


Characterization of the ygl7 mutant and ygl7-NIL

The rice mutant ygl7 has a yellowy-green leaf under paddy field conditions; ygl7 exhibited a distinct and steady phenotype throughout its lifespan when grown in Hunan Province and Hainan Province from 2009 to 2013. The ygl7 plants showed an enduring yellow-green leaf phenotype that began when the first leaf completely unfolded (Figure 1 A, B). This color extended to the spikes, stalks, and other above-ground plant parts. Compared to 810S, there were no significant differences in main agronomic traits including the growth period, plant height, spike length, the spike number per plant, the grain number per spike, effective tiller, maturing rate, and 1000-grain weight (Table 1). Compared to same combinations which crossed with 810S, there were no significant differences in main agronomic traits, including the growth period, maturing rate, and 1000-grain weight (Table 2). These results suggested that this phenotype does not influence grain output and hybrid characteristics. The contents of Chl a, Chl b, and carotenoids were significantly reduced in ygl7 by about 50% compared to the wild-type parent 810S (Figure 1 C). These results suggested that the ygl7 mutant phenotype mainly resulted from reduced contents of photosynthetic pigments. In addition, the Chl a/b ratio of ygl7 increased compared to wild type, which indicated that the drop of Chl b was greater than Chl a in the ygl7 mutant.

Figure 1. Characterization of ygl7 and ygl7-NIL phenotypes and leaf pigments.

A. Phenotypes of wild type (WT) and ygl7 at seedling, booting, and heading stages. B. Leaf-color comparison between WT and ygl7. C. Leaf pigment contents of WT and ygl7 at booting and heading stages. D. Phenotypes of ygl7-NIL and its parents, NPB (acceptor) and ygl7 (donor). E. Comparison of leaf pigments contents of ygl7-NIL with its parents, NPB and ygl7 at booting and heading stages. Values are the mean ± SD of three replicates.

Table 1. The main agronomic traits of ygl7's propagation.

The ygl7-NIL is the ygl7's near isogenic line. To construct ygl7-NIL, the donor parent ygl7 was back-crossed with the receptor parent NPB. We found that ygl7-NIL displayed an abnormal leaf-color phenotype. The leaf-color of ygl7-NIL is yellow instead of yellow-green (Figure 1 D). The contents of Chl a, Chl b, and carotenoids were reduced in ygl7-NIL compared with ygl7 (Figure 1 E). The same phenomenon was observed when ygl7 was back-crossed with indica rice (data not shown). The situation is probably caused by an altered genetic background. It is also probably caused by the mutation of how YGL7 joins in other regulatory pathways. This phenotypic characterization improves the ability to cultivate better sterile lines and will facilitate hybrid seed production and purification for the growth of rice crops.

Single amino acid change in Ygl7

All F1 plants of the ygl7 mutant crossed with normal green rice varieties displayed normal green leaves. The F2 populations from ygl7/9311, ygl7/353, and ygl7/NPB showed a segregation ratio of 3∶1 (green: yellow-green plants, χ220.05 = 3.84, P>0.05; Table 3). These data indicated that the yellow-green leaf phenotype in the ygl7 mutant was controlled by a single recessive nuclear gene.

Table 3. Segregation of F1 and F2 populations from three crosses.

Locus mapping of the Ygl7 gene was performed using the F2 population from a ygl7×NPB mutant cross. A Bulked Segregant Analysis (BSA) suggested that the Ygl7 locus was possibly located on chromosome 3 or 12 (Table S3). The Ygl7 locus was initially mapped to within 3.9 cM between RM1308 and SFP-3-6 on the long arm of chromosome 3 based on 368 typical yellow-green leaf F2 individuals (Figure 2 A). With a total of 651 F2 homozygous mutant plants, we fine-mapped the Ygl7 locus to a 64.8 kb interval between SSR marker RM16106 and STS marker STS3-1 on BAC clones AC135595 and AC137507 (Figure 2 B, C). We found 12 ORFs were predicted within this region (Figure 2 D, Table S4). Among these ORFs, LOC_Os03g59640 was highly correlated with the ygl7 phenotype. The LOC_Os03g59640 ORF encodes the subunit CHLD of magnesium-chelatase. Comparison of sequences indicated that the single base change (T1883C) located in the 12th exon of Os03g59640 resulted in a missense mutation (L628S) in the encoded product (Figure 2 E, F). The cDNA sequenced from Os03g59640's was the same missense mutation as the sequenced DNA. For these reasons, this gene was identified as the candidate gene of Ygl7 that caused the phenotype of yellow-green leaves during the whole growth stage.

Figure 2. Map-based cloning of the Ygl7 locus.

A. Preliminary map of the Ygl7 locus between RM1038 and SFP-3-6 based on analysis of 368 F2 (ygl7/NPB) individuals. Numbers below indicate the genetic distance (cM) between the markers. B. Fine mapping of the Ygl7 locus, which was narrowed down to a 64.8 kb genomic DNA region between RM10106 (2 recombinants) and STS3-1 (6 recombinants) based on 651 F2 individuals. C. Ygl7 locus was covered by two BAC contigs AC135595 and AC137507. D. There were 12 expressed genes identified in the fine mapping of Ygl7's area. E. One candidate Ygl7 gene (Os03g59640) was found to contain one base replacement (1883, T→C) resulting in one amino acid mutation (628, Leu→Ser). F. PCR analysis of the F2 yellowy-green leaf plants from Ygl7 crossed with NPB. Marker, RM16108; P1, Ygl7; P2, NPB; M, 100 bp low ladder; others are individual yellowy-green leaf plants of the F2 from Ygl7 crossed with NPB.

Confirmation of Ygl7 function

To confirm whether the single base change in Ygl7 is responsible for the mutant phenotype, we performed a complementation analysis. Complementation analysis was performed by transforming ygl7-NIL with the YGL-cDNA transgene in pLYL18. The plasmids with YGL7 contained the bacterial hygromycin B phosphotransferase (HptII) gene as a selection marker (Figure 3 B). The positive transgenic plants were almost reverted to green leaf and their Chls and Cars contents approached the levels of wild type plants (Figure 3 A, C).

Figure 3. Expression analysis of Ygl7.

A. Leaf phenotypes in the complementation test. B. The PCR detection of HPT in some transgenic lines. CK1, H2O; CK2, normal plant of NPB; CK3, plasmid pLYL18; D16, the transgenic plant without the YGL7 gene; D5, D18, and D28 are the transgenic plants with the YGL7 gene. C. Pigment contents. Values are the mean ± SD of three replicates.

RNA interference was conducted by transforming NPB with a 594 bp conservative segment of cDNA transgene in pFGC5941. A total of 9 independent transgenic lines were obtained. The first three leaves of RNAi transformed plants were green, but over time all leaves gradually turned from pale-green (Figure 4 A, B) to yellowy-green, then to yellow, then to almost white, and then died (with about seven-to-eight leaves) (Figure 4 D, E). This data suggested that RNAi-mediated silencing of YGL7 causes a lethal phenotype of in the transgenic plants. Real-time PCR analysis showed that the magnitude of YGL7 expression in the transgenic lines was reduced compared to the NPB (Figure 4 C, F).

Figure 4. RNAi analysis of Ygl7.

A. and B. Phenotypes of leaf in the RNAi plants at 5 leaves. C. The expressions of ChlD (Ygl7) genes in tRNAi plants at 5 leaves. D. and E. Phenotypes of leaf in the RNAi plants at 7 leaves; old leaves were dead. F. The expressions of ChlD (Ygl7) genes in the RNAi plants at 7 leaves. Values are the mean ± SD of three replicates. Di1, Di2 and Di3 are the RNAi plants.

These results demonstrate that Os03g59640 corresponds to the Ygl7 gene. Moreover, silencing Ygl7 is a gradual process. Once the silencing is completely, rice is unable to synthesize chlorophyll which leads to the death of the plant. The combination of RNAi and complementation analysis shows that the mutation of YGL7 does not cause a loss of OsChlD's functions. The mutation instead endows the protein with a new function.

The ygl7 mutant uses light energy efficiently

Real-time PCR was performed to study the expression profile of ygl7. In ygl7, ChlD, ChlI, and ChlH (Mg-chelatase D, I and H subunit) are up-regulated compared in the ygl7 to the WT (810S). However, ChlD was much lower in ygl7 than ChlI and ChlH (Figure 5). This illustrates that the mutation ChlD led to an accumulation of the three subunits of Mg chelatase, especially ChlI and ChlH. This shows that the yellow-green leaf resulted from unusual chlorophyll biosynthesis controlled by the accumulation of ChlD, ChlI, and ChlH.

Figure 5. Real-time PCR expression analysis of genes associated with chlorophyll biosynthesis and photosynthesis in WT and ygl7.

Genes involved in chlorophyll biosynthesis included ChlD(YGL7), ChlI, ChlH, Hema1, PoRA, and Ygl1. Genes involved in photosynthesis included Cab1R, Cab2R, PsaA, PsbA, and RbcL. Values are the mean ± SD of three replicates.

Real-time PCR was performed to determine whether the Ygl7 gene has any relationship with other genes and to determine what kind of genes are related to Ygl7. Those genes associated with chlorophyll biosynthesis (including ChlD, ChlI, and ChlH), Hema1 (glutamyl tRNA reductase), and PoPA (NADPH-dependent protochlorophyllide oxidoreductase) were up-regulated in ygl7 compared with wild type. Similarly, those genes associated with photosynthesis, including Cab1R (light-harvesting Chl a/b-binding proteins of PSII), PsaA (reaction center polypeptides of PSI), PsbA (reaction center polypeptides of PSII), and RbcL (the large subunit of Rubisco), were also mostly up-regulated in ygl7. However, Ygl1 (Chl synthetase) and Cab2R (light-harvesting Chl a/b-binding proteins of PSII) were down-regulated in the ygl7 mutant (Figure 5). Thus, it seems that the ygl7 mutant affects transcription of not only the Ygl7 gene itself but also of genes associated with Chl biosynthesis and photosynthesis. The normal accumulation of ChlD might attract accumulation of other Chl biosynthesis-related genes that then destroys the chlorophyll biosynthetic pathway.

Interestingly, expression of these genes in Ygl7-NIL was at almost normal levels (Figure 5). Only a few Chl biosynthesis-related genes and photosynthesis-related genes were affected by Ygl7. We have no plausible explanation for this at present.

We performed Chlorophyll Fluorescence in ygl7, chl1, and ygl98. The Fo (minimal fluorescence) values from this chlorophyll fluorescence were consistent with the leaf chlorophyll content in ygl7, chl, and ygl98 (Figure 6). The data illustrated that the chlorophyll fluorescence detector is trustworthy. Fv'/Fm' (photochemical efficiency of PSII in the light), ETR (photosynthetic electron transport rate), and qP (photochemical quenching coefficient) were higher in ygl7 than WT, chl1, and ygl3 (Figure 6). This indicated that conversion efficiency of light energy and capture efficiency of solar energy in the PSII center is higher in ygl7. The transport number of photosynthetic quantum yield and the transport rate of acyclic electron from antenna pigments in PSII were also higher in ygl7. qN is a coefficient of non-photochemical quenching. It indicated that the absorbing light energy from antenna pigments in PS II is emitted as heat instead of being used for photosynthetic electron transport. When antenna pigment from PSII absorbs excess light energy, the inactivation and disruption of the photosynthetic apparatus will happen if not timely dissipated. So qN is a self-protection mechanism. There is no sharp difference in qN between ygl7 and WT (Figure 6). This demonstrates that ygl7 could protect the photosynthetic apparatus to a certain extent. The ygl98 and chl1 have not sufficient qN function. In general, the three leaf-color mutant ygl7 has high conversion efficiency of light energy, capture efficiency of solar energy, and protection of photosynthetic apparatus. The ygl7 is the only phenotype without influence upon grain output amongst the three mutants. Genes associated with photosynthesis were mostly up-regulated in ygl7. Ygl7 possessed a higher photosynthetic efficiency in earlier physiological and biochemical studies [43]. All this data suggests that photosynthesis-related genes might be up-regulated by the accumulation of ChlD. The mutation of YGL7 gives the protein a new function that can put up photosynthesis-related genes.

Figure 6. Chlorophyll Fluorescence in three leaf-color mutants.

Fo: immobilized fluorescent, Fo coincides chlorophyll content; Fv'/Fm': effective photochemical quantum yield from PSII; ETR: the electron-transfer; qP: photochemistry quenching; qN: non-photochemistry quenching.

Differences among ygl7, chl1, ygl3 and ygl98 mutants

We planted the three mutants, ygl7, chl1 and ygl3, at the field station under a standard management. In order to verify whether their mutations represent alleles, ygl7 as the female parent was crossed with chl1 and ygl98, respectively. Of the three mutants we planted under field conditions, all F1 and F2 plants had yellowy-green leaves (Figure 7, A). The content of chlorophyll and carotenoid in the F1 and F2 plants decreased to some extent (Figure 7, B). This established that the three mutants' genes are alleles. The Chl1's leaf-color was the most yellow of the three mutants, while ygl7 and ygl98 had a yellow-green leaf-color. However, there is some discrepancy in chl1's phenotype between populations in China and Korea. In our experiment, chl1 plants had sharp yellow leaves (Hunan and Hainan Provinces). In a prior study, the chl1 mutant displayed a yellowish-green leaf phenotype only at the seedling stage, and the abnormal leaf-color was first observed on the leaves of 2- to 3-week-old seedlings [39]. This difference will need further assessment in order to clearly understand the underlying causes.

Figure 7. Characterization of the OsChlD's alleles.

A. Phenotypes of the three mutants and their crossed offspring. The chl1 mutant is the most yellow of the three. B. Pigment contents of leaves. Values are the mean ± SD of three replicates. The chl has the lowest amount of pigment. All F1 and F2 offspring's pigment amounts fall between the amounts contained in their parents.

In four alleles, Ygl98 did not perform functional analysis [40]. Chl1 and Ygl3 did not perform functional complementation [9], [39]. Ygl3's transgenic plants of pCAMBIA1305(35S)-RNAi exhibited the same phenotype as the Ygl3 mutant [9]. Chl1's AtChlD-KO in Arabidopsis (T-DNA insertional AtchlD-knockout) was a lethal mutant [39]. Similarly, our transgenic plants of pFGC5941(35S)-RNAi were lethal mutants.


Plants with the ygl7 mutant maintained a yellowy-green leaf-color throughout their growth cycle, and had a sharp drop in chlorophyll content compared to WT (Figure 1). Previous studies showed that photoelectron utilization rate and photosynthetic rate are higher in ygl7 compared with WT [43], [49]. We also found that genes associated with photosynthesis were mostly up-regulated (Figure 4; Figure 6). The net photosynthesis and dark respiration rates of ygl7 were higher than WT [33], and the yellow-green phonotype did not negatively impact agronomic traits (Table 1). Thus, our analyses show that the ygl7 mutant is also highly efficient in its ability to use light energy (Figure 5, 6). In addition, seeds of hybrids crossed with ygl7 had the same grain output as the WT (Table 2). Thus, this mutant ygl7 is an ideal leaf-color marker. Interestingly, the leaf-color of ygl7's hybrids was significantly more yellow than ygl7 itself (Figure 1). New male sterile lines show a yellow-leaf-color when the Ygl7 gene is back-crossed to any male sterile with no associated negative agronomic traits (data not shown).

Overall, our genetic analyses of the ygl7 mutant showed that it was controlled by a base mutation of the magnesium chelatase subunit D. Mg-chelatase plays a decisive role in the synthesis of chlorophyll because it catalyzes the insertion of magnesium into Protoporphyrin IX [50]. This enzyme consists of the three subunits I, D, and H. The three subunits take part in the synthesis of chlorophyll via a complex substance and also act independently in other metabolic pathways. The H subunit plays a role in reverse signaling to the nucleus within the chloroplast [51], controlling the SigntaE factor in cyanobacteria [52], and acts in the ABA signal transduction pathway [53]. The I subunit is the target protein of thioredoxin. The D subunit acts in exhibiting the gun phenotype in Arabidopsis [54]. OsChlD has four alleles: Chl1 [39], Ygl98 [40], Ygl3 [9], and our gene Ygl7. The four alleles exhibit different phenotypes in the varieties in which they are found. Based on all of this evidence we can make several inferences. First, we surmise that different mutated proteins resulted in different leaf phenotypes. Second, we suggest that the D subunit may also play a role in other metabolic routes. However, these differences in leaf phenotype may simply be caused by variance in genetic backgrounds among the mutants. Of course, they may also be due to many other biological or ecological factors. A remaining question is what will happen to leaf-color when plants are grown with the same genetic background. Further study will be required to tease apart these different potential explanations.

More specific alleles continue to be identified with the continued study of rice genetics. At present, 14 genes have been shown to have alleles, amid the total of 53 cloned leaf-color genes. There has been little in-depth research on alleles, and this will be an ongoing focus of our research group. We crossed female ygl7 with chl1 and ygl98 mutants. They all expressed mutated leaf-color throughout their development. However, chl1 displayed an extreme yellowish-green leaf phenotype only at the seedling stage in Korea [39]. In China, however, chl1 had a yellow leaf-color, while ygl7 and ygl98 were yellowy-green. In our study, all F1 and F2 plants had the yellowy-green leaf, and the chlorophyll and carotenoid contents of leaves taken from F1 and F2 individuals fell between the values of their two parents. Heterozygotes exhibiting an intermediate phenotypeis what is a perplexing phenomenon. It may be due to genetic neutralization, interaction of the two mutated proteins, different genetic backgrounds, or some other mechanism. Further study will address these different possibilities.

The ygl7-NIL is the form that represents the ygl7 mutant's near isogenic lines. ygl7-NIL has the yellow leaf type instead of the yellowy-green leaf of ygl7 (Figure 1). The same outcome was observed in offspring crossed with ygl7. This striking result has not been documented in previous studies of rice-leaf-color mutations. The situation is probably caused by multiple copies of the mutant gene or perhaps by an altered genetic background. We speculate that Ygl7's magnesium chelatase function may be doubled by an amino acid mutation. It rapidly synthesizes magnesium protoporphyrin, but later steps in chlorophyll biosynthesis occur at normal speed thereby leading to an accumulation of magnesium protoporphyrin. Chloroplasts may send signals to the cell nucleus to regulate photosynthesis-related genes and improve the transfer rate of photoelectrons. However, feedback regulation occurs in the latter steps of chlorophyll synthesis so this may result in abnormal chlorophyll synthesis.

The fading leaf color and ultimate death of the leaves of RNAi-transformed plants (Figure 3) illustrates that rice can no longer synthesize chlorophyll once Ygl7 is completely silenced. Moreover, photosynthesis-related genes were mostly up-regulated in Ygl7 (Figure 4). These phenomena show that the mutational YGL7 protein has part of OsChlD's function and promotes photosynthesis. The YGL7 protein does not lose the function of OsChlD, but as a new protein possesses a new function. There has been some research showing that accumulation of magnesium protoporphyrin can lead to reverse signal transduction and influence photoelectron transfer via regulated photosynthesis genes [55], [56]. Further research will be required to confirm that Ygl7 plays a role in other metabolic pathways and to explore what those pathways and functions might be.

In conclusion, we have conducted a study on a yellowy-green leaf mutant of rice termed An Nong Biao 810S. This mutation was controlled by the mutational gene Ygl7 which encodes for a magnesium-chelatase ChlD. The mutational ygl7 had a single-nucleotide change from T to C at position 1883 bp which was located at the 12th exon. The base conversion led to a change of AA (Leu 628 Ser). The mutational YGL7 protein acts with partial of OsChlD's function, and it could promote photosynthesis. The phenotype is without influence upon grain output and hybrid characteristics. The ygl7 has a high light use efficiency, and the hybrid offspring from crosses between yg17 and some other varieties exhibited a yellow-leaf. All these results will improve the ability to cultivate better sterile lines, facilitate hybrid seed production, and promote the purification of rice crops.

Supporting Information

Figure S1.

The vectors in this experiment. A. Functional complementation vector pLYL18 which reformed from pCAMBIA1300 with an ubiquitin promoter. B. RNAi vector pEGC5941.


Table S1.

Cloned genes that control leaf-color in rice.


Table S3.

Polymorphic markers from screened gene-pool.


Table S4.

There are 12 expressed genes at the mapping locus.



We thank Mr. Song, Mr. Paek and Mr. Wang for providing rice seeds. We also appreciate helpful comments from anonymous academic editor and two reviewers of the manuscript.

We thank LetPub for its linguistic assistance during the preparation of this manuscript.

Author Contributions

Performed the experiments: HqZ GlW. Analyzed the data: XjD YW JlL. Contributed reagents/materials/analysis tools: XjD HqZ YW. Wrote the paper: XjD HqZ. Performed Real-time PCR experiments: FH. Contributed to the work in the field: XX. Participated in the extracting of DNA and RNA: ZfS. Contributed to design of the writing structure: WL. Contributed to modifying the manuscript: GhW.


  1. 1. Deng XJ, Chang JY, Xiao CL, Zhang HQ (2010) Main factors and strategies on purify of seed production of two-line hybrid rice. Crop Research(Chinese Version) 24: 46–51.
  2. 2. Shu QR, Liu GF, Xia YW (1996) Temperature-sensitve leaf color mutation in rice (Oryza SativaL.). Acta Agriculturae Nucleatae Sinica(Chinese Version) 10: 6.
  3. 3. Deng XJ, Zhang HQ, Wang Y, Shu ZF, Wang GH, et al. (2012) Research advances on rice leaf-color mutant genes. Hybrid Rice(Chinese Version) 27: 9–14.
  4. 4. Huang XQ, Wang PR, Zhao HX, Deng XJ (2008) Genetic analysis and molecular mapping of a novel chlorophyll-deficit mutant gene in rice. Rice Science 15: 7–12.
  5. 5. Wang PR, Gao JX, Wan CM, Zhang FT, Xu ZJ, et al. (2010) Divinyl chlorophyll (ide) a can be converted to monovinyl chlorophyll (ide) a by a divinyl reductase in rice. Plant Physiology 153: 994–1003.
  6. 6. Wang PR, Ma XZ, Li CM, Sun CH, Deng XJ (2013) Comparative analysis of three mutants of divinyl reductase gene in rice. Scientia Agricultura Sinica(Chinese Version) 46: 1305–1313.
  7. 7. Sakuraba Y, Rahman ML, Cho SH, Kim YS, Koh HJ, et al. (2013) The rice faded green leaf locus encodes protochlorophyllide oxidoreductase B and is essential for chlorophyll synthesis under high light conditions. The Plant Journal 74: 122–133.
  8. 8. Zhou Y, Gong ZY, Yang ZF, Yuan Y, Zhu JY, et al. (2013) Mutation of the light-induced yellow leaf 1 gene, which encodes a geranylgeranyl reductase, affects chlorophyll biosynthesis and light sensitivity in rice. PloS One 8: e75299.
  9. 9. Tian XQ, Ling YH, Fang LK, Du P, Sang XC, et al. (2013) Gene cloning and functional analysis of yellow green leaf 3(ygl3) gene during the whole-plant growth stage in rice. Genes and Genomics 35: 87–93.
  10. 10. Jiang HW, Li MR, Liang NT, Yan HB, Wei YB, et al. (2007) Molecular cloning and function analysis of the stay green gene in rice. The Plant Journal 52: 197–209.
  11. 11. Park SY, Yu JW, Park JS, Li J, Yoo SC, et al. (2007) The senescence-induced staygreen protein regulates chlorophyll degradation. The Plant Cell Online 19: 1649–1664.
  12. 12. Yang QS, He H, Li HY, Tian H, Zhang JJ, et al. (2011) NOA1 functions in a temperature-dependent manner to regulate chlorophyll biosynthesis and rubisco formation in rice. PloS One 6: e20015.
  13. 13. Liu WZ, Fu YP, Hu GC, Si HM, Zhu L, et al. (2007) Identification and fine mapping of a thermo-sensitive chlorophyll deficient mutant in rice (Oryza sativa L.). Planta 226: 785–795.
  14. 14. Wang PR, Wang B, Sun XQ, Sun CH, Wan CM, et al. (2013) Fine mapping and physiological aharacteristics of a green-revertible albino gene gra75 in rice. Scientia Agricultura Sinica (Chinese Version) 46: 225–232.
  15. 15. Huang JL, Qin F, Zang GC, Kang ZH, Zou HY, et al. (2013) Mutation of OsDET1increases chlorophyll content in rice. Plant Science 210: 241–249.
  16. 16. Gong XD, Jiang Q, Xu JL, Zhang JH, Teng S, et al. (2013) Disruption of the rice plastid ribosomal protein S20 leads to chloroplast developmental defects and seedling lethality. Genes Genomes Genetics 3: 1769–1777.
  17. 17. Peng Y, Zhang Y, Lv J, Zhang JH, Li P, et al. (2012) Characterization and fine mapping of a novel rice albino mutant low temperature albino1. Journal of Genetics and Genomics 39: 385–396.
  18. 18. Hu F, Kang ZH, Qiu SC, Wang Y, Qin F, et al. (2012) Overexpression of OsTLP27 in rice improves chloroplast function and photochemical efficiency. Plant Science 195: 125–134.
  19. 19. Gothandam KM, Kim ES, Cho H, Chung YY (2005) OsPPR1, a pentatricopeptide repeat protein of rice is essential for the chloroplast biogenesis. Plant Molecular Biology 58: 421–433.
  20. 20. Zhang FT, Luo XD, Hu BL, Wan Y, Xie JK (2013) YGL138(t), encoding a putative signal recognition particle 54 kDa protein, is involved in chloroplast development of rice. Rice 6: 1–10.
  21. 21. Su N, Hu ML, Wu DX, Wu FQ, Fei GL, et al. (2012) Disruption of a rice pentatricopeptide repeat protein causes a seedling-specific albino phenotype and its utilization to enhance seed purity in hybrid rice production. Plant Physiology 159: 227–238.
  22. 22. Hibara KI, Obara M, Hayashida E, Abe M, Ishimaru T, et al. (2009) The ADAXIALIZED LEAF1gene functions in leaf and embryonic pattern formation in rice. Developmental Biology 334: 345–354.
  23. 23. Chai CL, Fang J, Liu Y, Tong HN, Gong YQ, et al. (2011) ZEBRA2, encoding a carotenoid isomerase, is involved in photoprotection in rice. Plant Molecular Biology 75: 211–221.
  24. 24. Fang J, Chai CL, Qian Q, Li CL, Tang JY, et al. (2008) Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice. The Plant Journal 54: 177–189.
  25. 25. Liu S, Wei XJ, Shao GN, Tang SQ, Hu PS (2013) Map based cloning of a ‘Zebra’ leaf mutant gene zl2 in Rice. Chinese Journal of Rice Science (Chinese Version) 27: 231–239.
  26. 26. Han SH, Sakuraba Y, Koh HJ, Paek NC (2012) Leaf variegation in the rice zebra2 mutant is caused by photoperiodic accumulation of tetra-Cis-lycopene and singlet oxygen. Molecules and Cells 33: 87–97.
  27. 27. Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, et al. (2013) A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Scientific Reports 3.
  28. 28. Wang ZK, Huang YX, Miao ZD, Hu ZY, Song XZ, et al. (2013) Identification and characterization of BGL11(t), a novel gene regulating leaf-color mutation in rice (Oryza sativa L.). Genes Genomics35: 491–499.
  29. 29. Li JQ, Wang YH, Chai JT, Wang LH, Wang CM, et al. (2013) Green-revertible Chlorina 1(grc1) is required for the biosynthesis of chlorophyll and the early development of chloroplasts in rice. Journal of Plant Biology 56: 326–335.
  30. 30. Zhang XQ, Li XY, Zhu HT, Wang T, Jie XM (2010) Identification and candidate gene analysis of stage green-revertible albino mutant in rice (Oryza sativa L.). Chinese Science Bulletin(Chinese Version) 55: 2296–2301.
  31. 31. Dong H, Fei GL, Wu CY, Wu FQ, Sun YY, et al. (2013) A rice virescent-yellow leaf mutant reveals new insights into the role and assembly of plastid caseinolytic protease in higher plants. Plant Physiology 162: 1867–1880.
  32. 32. Zhou KN, Ren YL, Lv J, Wang YH, Liu F, et al. (2013) Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice. Planta 237: 279–292.
  33. 33. Bollivar DW, Suzuki JY, Beatty JT, Dobrowolski JM, Bauer CE (1994) Directed mutational analysis of bacteriochlorophyll a biosynthesis in rhodobacter capsulatus. Journal of Molecular Biology 237: 622–640.
  34. 34. Apchelimov AA, Soldatova OP, Ezhova TA, Grimm B, Shestakov SV (2007) The analysis of the ChlI 1 and ChlI 2 genes using acifluorfen-resistant mutant of Arabidopsis thaliana. Planta 225: 935–943.
  35. 35. Guo RB, Luo MD, Weinstein JD (1998) Magnesium-chelatase from developing pea leaves characterization of a soluble extract from chloroplasts and resolution into three required protein fractions. Plant Physiology 116: 605–615.
  36. 36. Willows RD, Hansson A, Birch D, Al-Karadaghi S, Hansson M (2004) EM single particle analysis of the ATP-dependent BchI complex of magnesium chelatase: an AAA+ hexamer. Journal of Structural Biology 146: 227–233.
  37. 37. Axelsson E, Lundqvist J, Sawicki A, Nilsson S, Schröder I, et al. (2006) Recessiveness and dominance in barley mutants deficient in Mg-chelatase subunit D, an AAA protein involved in chlorophyll biosynthesis. The Plant Cell 18: 3606–3616.
  38. 38. Masuda T, Fujita Y (2008) Regulation and evolution of chlorophyll metabolism. Photochemical and Photobiological Sciences 7: 1131–1149.
  39. 39. Zhang HT, Li JJ, Yoo JH, Yoo SC, Cho SuH, et al. (2006) Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development. Plant Molecular Biology 62: 325–337.
  40. 40. Sun XQ, Wang B, Xiao YH, Wan CM, Deng XJ, et al. (2011) Genetic analysis and fine mapping of gene ygl98 for yellow-green leaf of rice. Acta Agronomica Sinica(Chinese Version) 37: 991–997.
  41. 41. Jung KH, Hur JH, Ryu CH, Choi YJ, Chung YY, et al. (2003) Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. Plant and Cell Physiology 44: 463–472.
  42. 42. Song KB, Song ZG (2007) Discovery and preliminary research of the yellowish leaf mutant Annongbiao 810S in rice. Hybrid Rice(Chinese Version) 22: 71–73.
  43. 43. Wang CT, Kuang XD (2008) Application research on a yellowy-color mutant Biao810S. China Seed Industry(Chinese Version) 8: 24–25.
  44. 44. Chen XZ, Wang CT, Song KB (2009) Study on main agronomic characters of Annongbiao 810S. Acta Agriculturae Jiangxi(Chinese Version) 9: 008.
  45. 45. Rogers SO, Bendich AJ (1989) Extraction of DNA from plant tissues. Plant Molecular Biology Manual: Springer Netherlands. pp.73–83.
  46. 46. Perry KL, Francki RI (1992) Insect-mediated transmission of mixed and reassorted cucumovirus genomic RNAs. Journal of General Virology 73: 2105–2114.
  47. 47. Li YH, Qian Q, Zhou YH, Yan MX, Sun L, et al. (2003) BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. The Plant Cell 15: 2020–2031.
  48. 48. Tang YL, Huang JF, Wang RC (2004) Change law of hyperspectral data in related with chlorophyll and carotenoid inrice at different developmental stages. Rice Science 11: 274–282.
  49. 49. Wang JJ, Ou LJ, Kang GP, Liang MZ, Chen LB (2007) Photosynthetic characteristics of chlorophyll-deficint rice (Biao810S) at different leaf position. Journal of Natural Science of Hunan Normal University(Chinese Version) 30: 89–93.
  50. 50. Stenbaek A, Jensen PE (2010) Redox regulation of chlorophyll biosynthesis. Phytochemistry 71: 853–859.
  51. 51. Mochizuki N, Tanaka R, Tanaka A, Masuda T, Nagatani A (2008) The steady-state level of Mg-protoporphyrin IX is not a determinant of plastid-to-nucleus signaling in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 105: 15184–15189.
  52. 52. Osanai T, Imashimizu M, Seki A, Sato S, Tabata S, et al. (2009) ChlH, the H subunit of the Mg-chelatase, is an anti-sigma factor for SigE in Synechocystis sp. PCC 6803. Proceedings of theNational Academy of Sciences of the United States of America 106: 6860–6865.
  53. 53. Tsuzuki T, Takahashi K, Inoue S-i, Okigaki Y, Tomiyama M, et al. (2011) Mg-chelatase H subunit affects ABA signaling in stomatal guard cells, but is not an ABA receptor in Arabidopsis thaliana. Journal of Plant Research 124: 527–538.
  54. 54. Mochizuki N, Brusslan JA, Larkin R, Nagatani A, Chory J (2001) Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proceedings of the National Academy of Sciences of the United States of America 98: 2053–2058.
  55. 55. Rodermel S, Park S (2003) Pathways of intracellular communication: Tetrapyrroles and plastid-to-nucleus signaling. Bioessays 25: 631–636.
  56. 56. Nott A, Jung HS, Koussevitzky S, Chory J (2006) Plastid-to-nucleus retrograde signaling. Plant Biology 57: 739–759.