Research Article

Identification and Genetic Characterization of a New d10 Mutated Indica Rice Germplasm  

Liangrong Jiang1 , Bin Xu1 , Rongyu Huang1 , Fangyu Chen1 , Kangmei Dong1 , Yumin Huang1 , Houcong Wang1 , Yi Tao1 , Jingsheng Zheng1 , Xuanjun Fang2,3
1. School of Life Sciences, Xiamen University, Xiamen 361005, China
2. Institute of Life Sciences, Jiyang College of Zhejiang A&F University, Zhuji, 311800, China
3. Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, China
Author    Correspondence author
Plant Gene and Trait, 2015, Vol. 6, No. 6   doi: 10.5376/pgt.2015.06.0006
Received: 27 Nov., 2015    Accepted: 02 Dec., 2015    Published: 05 Dec., 2015
© 2015 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Jiang L.R.., Xu B., Huang R.Y., Chen F.Y., Dong K.M., Huang Y.M., Wang H.C., Tao Y., Zheng J.S., Fang X.J., 2015, Identification and Genetic Characterization of a New d10 Mutated Indica Rice Germplasm, Plant Gene and Trait, Vol.6, No.6 1-12 (doi: 10.5376/pgt.2015.06.0006)


Plant architecture is a determining factor for yield of cereal crop rice. Multi-tiller and dwarf mutants are useful germplasms for the study of rice plant architecture. In this research, we investigated a new multi-tiller and dwarf mutant, Jiahecong’ai (JHCA), and compared its genetic characteristics with 6 other rice varieties or lines. Two F2 populations were developed by crossing JHCA with Gaoliangdao 1 (GLD1) and Guangchang 13 (GC13), which were used for further studies. Our results showed that the extreme dwarf and multitiller phenotype of JHCA was controlled by a recessive locus named xmd(t). The xmd(t) locus was fine mapped to an interval between XMd-SSR4 and XMd-SSR25 marker on chromosome 2, which spans 190 kb in length including 28 annotated genes. Allelic sequence analysis revealed that the xmd(t) of JHCA has a 40-bp deletion in D10 gene, which encodes a carotenoid cleavage dioxygenase 8 (OsCCD8) involved in strigolactone (SL) biosynthesis pathway. Further genetic analysis suggested that JHCA should be a good rice germplasm for studying plant architecture in rice as well as metabolism interactions between gibberellin and strigolactone based on the reinforcement of dwarfing effect by d10 and sd1.

Rice (Oryza sativa L.); multi-tiller; dwarf culm; d10 gene; plant architecture

Tiller and dwarf culm are two important traits for building plant architecture in rice. Rice mutants exhibiting phenotypes in tillering and plant height have become important resources in the studying molecular mechanisms underlying rice architecture determination. Up to date, mutant genes in many of these mutants have been mapped and cloned. According to the number of tillers, these mutants can be classified into two categories: ones that have less tillers or even no tiller, the others that have more tillers or even infinite tillers. 
The mutants with less tillers include rcn series (reduced culm number), moc1 (mono culm), lgd1, tad1 and ltn (Nakagawa, 2002; Jiang et al., 2006; Li et al., 2003; Thangasamy et al., 2012; Xu et al., 2012; Fujita et al., 2010). The mutants with increasing number of tillers include the d series (dwarfing ), fc1, htd1, htd2, hw-1(t), tdr1, ht1 and dwt1 etc. (Ishikawa et al., 2005; Arite et al., 2007; Arite et al., 2009; Lin et al., 2009; Zhou et al., 2013; Jiang, et al., 2013; Zhao et al., 2014; Takeda et al., 2005; Minakuchi et al., 2010; Zou et al., 2005; Zou et al., 2006; Liu et al., 2009; Gao et al., 2009; Guo et al., 2012; Yamamoto et al., 2005; Li et al., 2010; Wang et al., 2013). Interestingly, most of those mutants also exhibit dwarfism, except for the ht1 and dwt1 mutant. Most of d series (dwarfing ) such as D3, D10, D14, D27, D53, have been cloned (Ishikawa et al., 2005; Zhao et al., 2014; Arite et al., 2007; Arite et al., 2009; Zhou et al., 2013; Lin et al., 2009; Jiang et al., 2013). D10 encodes a carotenoid cleavage dioxygenase 8 (OsCCD8), which participates in the biosynthesis of strigolactones (SL), a new plant hormone, or their biosynthetic precursors (Zou et al., 2006). Strigolactones inhibit plant shoot branching (Zou et al., 2006; Arite et al., 2007; Umehara et al., 2008; Gomez-Roldan et al., 2008; Lin et al., 2009). 
Our group had previously identified a mutant, Jiahecong’ai (JHCA), exhibiting slim stem, multi-tiller and dwarfism phenotypes. The mutant trait was speculated to be controlled by a recessive locus (Chen et al., 2012). Our previous studies showed that GR24, a synthetic SL analog, can rescue the mutant trait of elongated mesocotyl in JHCA in darkness and some diffrerentially expressed proteins and phosphorylated proteins in response to GR24 at seeding stage were identified as well (Chen et al., 2014). JHCA has good panicle traits, such as high seed setting percentage, slender grain and low chalkiness rate. It is thus a good donor germplasm for breeding new indica rice varieties. In the present study, we crossed JHCA with other rice varieties and developed two F2 populations, clarified the genetic background of the mutant and mapped the mutant locus based on BSA approach as well as identified a candidate gene using allelic sequencing strategy.
1.1 Characteristics of Jiahecong’ai (JHCA)
Phenotypes of JHCA were investigated in tiller number (TN), plant height (PH), panicle length (PL) and internode length (IL) in this study. The result showed that JHCA was dwarf (PH around 45.3 cm), multi-tiller and had slim stems (Figure 1A and S1A), whereas XJC1 and XJC2 were semidwarf (PH around 94.3 cm and 85.4 cm, respectively) (Figure 1B and S1A). Similarly, the semidwarf varieties, AJNT and GLA4, were 93.5 cm and 90.5 cm in height, respectively. GLD1 and GC13 were high culm varieties with PH around 167.8 cm and 144.5 cm, respectively (Figure 1C, 1D and S1C). PL and all ILs of JHCA’s main stem were shorter than those of AJNT and GLA4, and PL and IL1 had greater contributions to the PH of JHCA (Table S1 and S2; Figure 2A and S1B). Simarily, each internode length of XJC1’s and XJC2’s main stem is shorter than that of the corresponding internode of GLD1 and GC13 and IL5 and IL6 had greater contributions to their PHs(Table S1 and S2; Figure 1A and 2A). In summary, these results indicate the shorter PL and ILs resulte in the JHCA’s dwarf and XJC’s semi-dwarf hpenotypes.


Figure 1 Morphology of tested materials.

A: JHCA; B: XJC1; C: the left is JHCA and the right is GLD1; D: the left is JHCA and the right is GC13



Figure 2 Panicle length and internode length and their contributions to the plant height in tested materials.

A: PL and IL of tested materials; B: The contributions of PL and IL to the PH.


1.2 Fine Mapping of a novel dwarfing locus
Among 505 pairs of SSR primers used, 8 pairs exhibited polymorphisms between the mutant DNA pool and wildtype DNA pool in GLD1/JHCA F2 population (Table S3, Figure S2A). Genotypes of 190 mutant lines (Figure S1D) were analyzed using these 8 pairs of primers. Linkage analysis was then carried out. The target locus was mapped to an interval between RM128 and RM302 on the long arm of chromosome 1, which was named as the Xiamen dwarf locus, xmd(t) (Figure 3 CHROM.1a). In the mean time, five pairs of primers exhibited the polymorphisms between the two DNA pools from GC13/JHCA F2 population (Figure S1E) and xmd(t) was mapped to an interval between RM128 and RM212 on the long arm of chromosome 1 (Table S3; Figure 3 CHROM.1b), which confirmed the mapping result using the GLD1/JHCA F2 population.


Figure 3 Loci of xmd(t) on Rice Chromosome in Two F2 Populations.

CHROM.1a: the map for the F2 population of GLD1/JHCA; CHROM.1b: the map for the F2 population of GC13/JHCA.


Fine mapping of xmd (t) was carried by genotyping 4588 mutant lines from GLD1/JHCA F2 population (Figure S1E) and 1500 mutant lines from GC13/JHCA F2 population. 7 pairs of SSR primers located within the intervel of RM128-RM302 (RM1183,RM3411,RM1268,RM11669,RM11678,RM3709 and RM6648) were used for fime mapping xmd(t) (Table S5; Figure S2B and S2C). Results from genotyping and linkage analysis revealed that xmd(t) locates in the region between marker RM1183 and RM3411 that is 296 kb long (Figure 4).



Figure 4 Fine mapping of xmd(t) in rice.

Chrom.1’ means rice chromosome 1; ▲ shows the target gene, xmd(t).


31 pairs of SSR primers in the interval of RM1183-RM3411 were designed according to the sequences of Niponbare and 9311 in that region. Four of these primers showed polymorphism between the GLD1 and JHCA (Table S4). Linkage analysis indicated that there was only one recombinant plant with gene exchange between the SSR markers, XMd-SSR4 or XMd-SSR25 and xmd (t) respectively, and XMd -SSR16 and xmd (t) were co-separated. As a result, xmd (t) was fine mapped in a 190-kb region between XMd-SSR4 and XMd-SSR25 (Figure 4).
According to information from the Gramene website (, there are 28 annotated genes in this region, one of which is D10 (Os01g0746400). Phenotypes of JHCA are similar to those of d10 (Chen et al., 2014). We thus spectulate that xmd (t) is a d10 mutant (Chen et al., 2014).
1.3 Sequence Analysis of candidate gene of xmd(t)
Three markers, XMd10-1, XMd10-2 and XMd10-3, were designed to amplify D10 in JHCA, GC13 and AJNT (Table 1). DNA sequencing showed that there is a 40-bp deletion in the second extron of D10 in JHCA (Figure 5), which led to a shift of the open reading frame of the downstream sequences. 


 Table 1 The primers designed for amplifying xmd(t)



Figure 5 Deletion mutation in D10 gene of JHCA.

Every ‘.’ means an one-bp deletion.


The result also revealed that the D10 sequences of GC13 and AJNT are both the same as that of 9311, an indica variety whose whole genome has been sequenced Besides the 40-bp deletion ,the rest of the D10 sequence of JHCA was the same as that of NIP, a japonica variety whose whole genome has been sequenced (Figure S3). There are 8 single base substitutions and one 15-bp insertion comparing 9311 to NIP (Table 2; Figure S3). Three of these substitutions (No.24, 2102 and 3109) occurred in extons, but only the substitution at No.3109 site leads to the change of amino acid from Lys to Asn. The 15-bp insertion occurred in intron one, which should not affect the protein sequence(Figure S3). 



 Table 2 The sequence difference of D10 between NIP and 9311


1.4 The additive effect between xmd(t) and sd1
Our previous studies showed that the multi-tiller and dwarfism trait of JHCA was caused by a recessive mutant gene and sd1 (Chen et al., 2012). Based on the tiller number and plant height, two separable phenotypes were found in the F2 populations of AJNT/JHCA or GLA4/JHCA, while four were found in the F2 population of GC13/JHCA (Chen et al., 2012). In this research, a high stalk line with Sd1Sd1 genotype was used to make cross with JHCA, and four separated types were also found in the F2 population. The four types of traits are multi-tiller and dwarfism (T1), multi-tiller and semi-dwarfism (T2), normal tiller and semi-dwarfism (T3) and normal tiller and high culm (T4) (Figure 6 and S1D), and there were 35, 12, 15 and 129 individuals for each type, respectively (Table 3). Obviously, the segregation ratio don’t follow to the ratio of 9:3:3:1 of the independent separation law of two genes. While the ratio between the multi-tiller plants (T1 and T2) and normal tiller plant (T3 and T4) was consistant with the separation law of one gene, 3:1 (Table 4). Referring to the result of fine mapping of xmd(t), we found the physical distance between xmd(t) and SD1 was 7.16 Mb, which suggested these two genes should be linked tightly. T1, T2, T3 and T4, carried xmd (t) xmd (t )sd1sd1, xmd(t) xmd(t) Sd1Sd1, XMD(t) XMD(t) sd1sd1 and XMD(t) XMD(t) Sd1Sd1 respectively, and their plant height was 41.9±4.4 cm,61.5±5.6 cm,118.3±8.7 cm and 146.2±10.5 cm respectively (Table 3). T1 was shorter than T2 and T3, just as JHCA was shorter than XJC1, XJC2 and other semidwarf rice varieties (Table S1), which demonstated that xmd(t) and sd1 together might enhance the dwarfing effects.


 Table 3 The phenotype of 4 separeted types in F2 of GLD1/JHCA and and its parents



 Table 4 Separeted ratio of TN and PH traits in F2 of GLD1/JHCA



Figure 6 The separation plant types in F2 population of GLD1/JHCA.

P1: JHCA; P2:GLD1; T1: the multi-tiller and dwarf type of plants (like JHCA) in GLD1/JHCA F2 population; T2: the multi-tiller and semidwarf type of plants in the population; T3: the normal tiller and semidwarf type of plants in the population; T4: the normal tiller and high culm type of plants (like GLD1) in the population.


2.1 Sequence Character and Origin of xmd(t)
There was a nucleotide base transition happened from T to C,  which converted the 112 th amino acid from Leu to Pro in d10-1 and a base transversion from C to A, which generated a termination codon in the 5th exon in d10-2 (Arite et al., 2007). Comparing to the wild type varieties, the candidate gene of xmd (t) in JHCA appears a 40-bp deletion in the second extron of D10, which leads to the alteration of the amino acid sequence and the absence of the protein. What’s more, the phenotype and hereditary character of target trait in JHCA are very similar to that in d10 (Chen et al., 2012; Chen et al., 2014). Therefore, we speculate xmd(t) should be a mutant gene of D10.
9311, and the xmd (t) sequence of JHCA was consistent with that of NIP (Nipponbare) except the 40-bp deletion. which suggested that xmd (t) in JHCA be likely to derive from japonica rice. JHCA is one of the progenies derieved from the cross between two rice varieties, Jiahezhaozhan and Tefengzhan. Jiahezhaozhan is an elite indica variety we bred baseing on a technology to generate rice mutants from mature pollen by γ ray irradiation. Tefengzhan is an indica line that breeded by Guangdong Academy of Agricultural Sciences, which has some genetic materials from japonica germplasms.
The source of JHCA implied that contains some japonica genome. As a donor parent applying in rice breeding program, JHCA will bring the new indica rice varieties with some japonica genotypes, which possible increase the heterosis of new varieties. 
2.2 SL-GA Crosstalk in Plant Height?
The physical genetic distance between D10 and SD1 was about 7.16 Mb, which suggeste the two genes link tightly together. In this study, we found the average PH of the plants with the genotypes xmd (t) xmd (t) d1sd1, xmd (t) xmd (t) Sd1Sd1 and XMD (t) XMD (t) sd1sd1 are 41.9±4.4 cm,61.5±5.6 cm,and 118.3±8.7 cm respectively (Table 3), which exhibited the dwarfing effects from d10 and sd1 would be accumulated. The both loci are additive. 
Sd1, known as the ‘green revolution gene’, encodes a gibberellin 20-oxidase, which is the key enzyme in the GA biosynthesis pathway (Monna et al., 2002). sd1 shows semidwarf phenotype that results from the relative low concentration of GA in vivo (Monna et al., 2002; Spielmeyer et al., 2002). GA is able to promote stem growth in a wide range of species (Taiz and Zeiger, 2010). However, D10 encodes an OsCCD8, an enzyme in the SL biosynthesis pathway. SLs are recently known as a new plant hormone class or their biosynthetic precursors,related with plant shoot branching. The rice multi-tiller and dwarf mutants, d3, d10 (xmd(t)), d27, htd1(d17) and hw-1(t),are supposed to involve in the strigolactone biosynthesis(Ishikaw et al., 2005; Arite et al., 2007; Lin et al., 2009; Zou et al., 2005; Zou et al., 2006; Guo et al., 2012). It was obvious that two genes, xmd (t) and sd1, involve in two different biosynthesis pathways, while the dwarfing effects can not be complementary but cumulative.
Many studies showed that SLs,besides regulating shoot branching,participated in shoot and root development and seed germination (Zhang et al., 2013). In addition,SLs also negatively regulated hypocotyl elongation in Arabidopsis and mesocotyl elongation in rice under the  dark condition (Hu et al., 2010; Jia et al., 2014), and stimulated cambial activity in the secondary growth of stems in Arabidopsis (Agustia et al., 2011). So far, some studies also suggested that SLs might interact with other plant hormones, such as ABA, auxin, ethylene, cytokinin and GA, etc. (Zhang et al., 2013). For instance, SLs alleviated thermoinhibition in Arabidopsis seed germination synergistically with GA and ABA (Toh et al., 2012). Therefore,whether we could speculate that the synergistic effect between SLs and GA leads to the extreme dwarfism of JHCA? This should be a very interesting question. JHCA,XJC1 and XJC1 would be good research materials for uncovering this secret in the future. 
2.3 Proteomics Research Evidence the Present Results
Our research group carried out map-based cloning of the target gene, and the proteinics research related with the mutant. The research results in protein have been published (Chen et al., 2012). Based on the study of the two populations, GLA4/JHCA and GC13/JHCA, using proteimics and Real-time PCR, we identified a protein, a putative carboxyvinyl-carboxyphosphonate phosphorylmutase (CPPM), cosegregating with the normal-tillering phenotype. In the present research, GLA4/JHCA, GC13/JHCA and GLD1/JHCA (Figure S1E) F2 populations were used to do genetic analysis and fine mapping. As a result, the target gene was mapped in a 190kb-length interval, and D10 is presumed to be the candidate gene, which was a valuable reference for the proteomics research. Accordingly, the proteomics research also confirmed the analysis in present study. Our result of gene cloning was mentioned and declared in Chen’s paper(Chen et al., 2012), but the data was not pulbised yet.
3.1 Rice materials used in this study
Five rice germplasms and two offsprings were used in this study. Jiahecong’ai (JHCA, indica rice), was developed by Prof. Huang’ group at Xiamen University in 2000. Aijiaonante (AJNT) and Guangluai 4 (GLA4), are well known cultivars with sd1 gene. Gailiangdao 1 (GLD1) and Guangchang 13 (GC13), were classified as high stalk rices that carry a wild type Sd1 gene. Both of them are taller than AJNT and GLA4. Xingjiacong 1 (XJC1) and Xingjiacong2 (XJC2) were derived from the F6 crossing generation of JHCA/GC13 and JHCA/GLD1, respectively, and both carry the xmd(t) and Sd1 genes.
Two F2 populations, JHCA/GC13 and JHCA/GLD1, were generated by crossing JHCA with GC13 and GLD1, respectively.
3.2 Rice materials planted in the field
All rice materials were planted in the field of the Morden Agriculture Research and Training Experimental Farm of Xiamen University. Rice seedlings were transplanted individually with a row/column space of 23 cm × 23 cm and maintained by good agronomic practice, including watering, fertilizer using and disease and insect controlling etc. 
3.3 Phenotyping analysis in internode length, panicle length and tiller number
The morphological features were measured on mainly tiller number (TN), panicle length (PL) and each internode length (ILn) (n is the Arabic numerals counting from top to bottom except panicle). The plants used for phenotyping were randomly collected at maturation stage. 
3.4 DNA extracttion
Genomic DNAs were extracted from young leaves using a protocol developed by Wang and Fang (Wang and Fang, 2003). DNAs were dissolved in 200 μL of 1× TE buffer and stored at –20°C, and a final DNA concentration of 25 ng/μL was used as a working stock. 
3.5 Bulked Segregant Analysis (BSA)
For BSA, DNAs from either 15 F2 homozygous dwarf and multi- tillering individuals or 15 F2 wildtype plants were bulked. Each bulk was diluted to a final concentration of 30 ng/μL. 30 ng of DNA was used in a 10 μL PCR reaction for screening polymorphic simple sequence repeat (SSR)  markers. The PCR program was as following: denaturation at 94 ℃ for 5 min, 35 cycles of 20 sec at 94 ℃, 20 sec at 55 ℃ and 40 sec at 72 ℃, followed by 10 min at 72 ℃. PCR products were separated on 6% nondenaturing polyacrylamide gel. The DNA bands were observed after 0.1% silver nitrate staining.
3.6 Designs of SSR markers and specific markers
The information of 505 SSR markers was downloaded from GRAMENE website ( In addition, 31 additional SSR markers were designed using Primer Premier 6.0 (PREMIER Biosoft International, 2009) based on the flanking sequences of the target locus in the Nipponbare (NIP) and indica rice 9311. All SSR markers were synthesized by Life Technology Corporation (Shanghai). 
Three markers, XMd10-1,XMd10-2 and XMd10-3, were designed and synthesized to specifically amplify D10 gene.
3.7 Fine mapping the dwarf gene
Polymorphic SSR markers were designed to detect 190 mutant lines from GLD1/JHCA F2 population and 190 mutant lines from GC13/JHCA F2 population. Linkage analysis was performed using MapMaker /EXP 3.0 software (Lincoln et al., 1993). MapChart 2.2 software (Voorrips, 2002) was used to draw the linkage map. 
According to preliminary mapping results, new primers were chose or designed in the target interval to further map the dwarf gene.
This research was jointly supported by the Natural Science Foundation of Fujian Province of China (No.2011J01249), the grants from the National Natural Science Foundation of China (No.31100866) and the Agriculture Science Technology Achievement Transformation Fund (No.2012GB2C410517).
JHCA, Jiahecong’ai; GLD1, Gaoliangdao 1; GC13, Guangchang13; AJNT, Aijiaonante; GLA4, Guangluai 4; XJC, Xingjiacong; NIP, Nipponbare; PH, plant height; TN, tiller number; PL, panicle length; IL1-LI6,  internode length, that the number refers to the orders of the IL counted down from the top (panicle); SSR, simple sequence repeat; BSA, bulk sergeant analysis; SL, strigolactone; GA, gibberellin; WT, wild type; PCR, polymerase chain reaction; OsCCD7, rice carotenoid cleavage dioxygenase 7; OsCCD8, rice carotenoid cleavage dioxygenase 8.
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