Journal of Experimental Botany, Vol. 52, No. 362, pp. 1827-1833,
September 1, 2001
© 2001 Oxford University Press
Original Papers |
Are contents of Rubisco, soluble protein and nitrogen in flag leaves of rice controlled by the same genetics?
1 National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
2 Rice Genome Research Program, National Institute of Agrobiological Sciences/Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
Received 2 February 2001; Accepted 11 June 2001
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Abstract |
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Genetic relations among the contents of Rubisco, soluble protein and total leaf nitrogen (N) in leaves of rice (Oryza sativa L.) were studied by quantitative trait loci (QTL) analysis with a population of backcross inbred lines (BILs) of japonica Nipponbarexindica Kasalath. The ratio of Rubisco to total leaf N in leaves is the main target in improving photosynthetic N-use efficiency in plants. QTLs controlling Rubisco content were not detected near QTLs for total leaf N content. These results indicate that contents of Rubisco and total leaf N are controlled by different genetics. QTLs that controlled the ratio of Rubisco to total leaf N (CORNs) were detected. These results suggest that some mechanism(s) may be involved in determining this ratio, while the contents of Rubisco and total leaf N are controlled in other ways. In elite BILs, the ratios of Rubisco to total leaf N were higher than those of both parents. These results suggest a good possibility of improving N-use efficiency by CORNs in cultivated rice. A QTL controlling Rubisco content was mapped near a QTL for soluble protein content on chromosome 8 at 5 d after heading and on chromosome 9 at 25 d. In each chromosome region, the peaks of both QTLs overlapped accurately, giving a high possibility of pleiotropic effects by the same genes. Different QTLs controlling soluble protein or Rubisco were detected from those detected at 5 d or 25 d after heading. This suggests that these traits are genetically controlled depending on the growth stages of leaves.
Key words: Nitrogen, Oryza sativa (rice), quantitative trait loci (QTL), Rubisco.
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Introduction |
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TopAbstractIntroductionMaterials and methodsResultsDiscussionReferences |
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Rubisco, the key enzyme in C3 photosynthesis, is the most abundant protein in leaves (Evans, 1989
). The kinetics of Rubisco and the ratio of Rubisco to total leaf nitrogen (N) are the two main factors determining N-use efficiency, indicating the rate of CO2 assimilation per unit amount of N per unit leaf area (for review see Mae, 1997). Rubisco from higher plants consists of eight large subunits (rbcL) encoded in the chloroplast genome and eight small subunits (rbcS) encoded in the nuclear genome (Spreitzer, 1999). It is difficult to change the kinetic character of Rubisco (Mae, 1997). Therefore, the ratio of Rubisco to total leaf N is the main target for the improvement of N-use efficiency (Mae, 1997). The relationship between Rubisco and N content is studied with respect to changes in environmental factors. Regardless of irradiance, temperature or high CO2 conditioning during growth, the ratio of Rubisco to total N in a rice leaf appears to be determined only by the amount of N. In other words, Rubisco content is thought to be due to total leaf N content (Mae, 1997; Makino et al., 1994, 1997; Nakano et al., 1997).
Recent progress in the generation of a well-saturated molecular genetic map and markers for rice has made it possible to map individual genes associated with complex traits called quantitative trait loci (QTL) (Yano and Sasaki, 1997; Ishimaru et al., 2001a, b). Identifying the location of QTLs for traits clarifies the linkage relationships and whether a gene with pleiotropic effects controls plural traits or not. There are several reports of the map locations of QTLs and major genes affecting the same trait (Beavis et al., 1994; Edwards et al., 1992; Veldboom and Lee, 1994). These reports support Robertson's hypothesis that QTLs allelic with major genes affect the same trait (Robertson, 1985). A comparison of locations between structural genes and QTLs can be available for the determination of the most likely candidate among various genes that comprehensively control a trait. Edwards et al. called this the candidate gene strategy (Edwards et al., 1992). By this method, Sh1 was thought to be the most important candidate gene controlling sucrose content in maize leaves (Prioul et al., 1997). QTL analysis can now evaluate the existence of unknown genes. Xiao et al. identified new genes at QTLs affecting the yield from wild rice, Oryza rufipogon (Xiao et al., 1996a).
As Koornneef et al. and the authors of this paper have already mentioned (Koornneef et al., 1997; Ishimaru et al., 2001b), genetic analysis by the QTL approach is a powerful tool for plant physiologists. However, as far as is known, there is no report about the genetic relationships among the contents of Rubisco, soluble protein and total leaf N. In this study, an attempt has been made to elucidate these genetic relationships in rice leaves by QTL analysis, and the relationships between QTLs and candidate genes have been studied.
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Materials and methods |
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Plant materials
A rice japonica variety, Nipponbare, was crossed with an indica variety, Kasalath. A resultant F1 plant was crossed with Nipponbare to produce seeds of backcross inbred lines (BILsF1). Ninety-eight BILsF7 (BILs) were developed from the resultant BILsF1 plants by the single-seed descent method. Genotypes of 245 RFLP markers were determined (Harushima et al., 1998
; Lin et al., 1998). The 98 BILsF7 and their two parental lines were sown on 6 May 1997. For evaluation of their traits, their seedlings were transplanted on 5 June and were grown under natural conditions in Tsukuba, Japan (latitude 38° N), in a random design to reduce the effects of environmental factors. Forty seedlings per line were grown under natural conditions in a randomized complete design with two replicates. At 5 d or 25 d after heading, flag leaves were harvested at around noon (about 7 h after sunrise) on a sunny day. Leaves were frozen immediately in liquid nitrogen and stored at -80 °C before use. The frozen leaves were divided into several parts and used for several measurements.
Biochemical assays
The contents of soluble protein and Rubisco in leaves at 5 d and 25 d after heading were analysed. The amounts of soluble protein and Rubisco were determined according to the methods of Makino et al. (Makino et al., 1985) with some modifications. Frozen leaves were ground in liquid nitrogen to a fine powder and suspended in a buffer containing 100 mM NaH2PO4/Na2HPO4 (pH 7.0), 1 mM phenylmethylsulphonylfluoride, 1% (w/v) insoluble polyvinyl polypyrrolidone, and 1% (v/v) ß-mercaptoethanol, and then centrifuged for 5 min at 9800 g. The soluble protein concentration in the supernatant was determined using BSA as a standard (Bradford, 1976). Soluble proteins (2 µg) were subjected to SDS-PAGE on 12.5% (w/v) gels containing 0.1% (w/v) SDS; the gels were stained with Coomassie brilliant blue. The intensity of the band corresponding to the large subunit of Rubisco was measured with an image analyser (Umax Technologies, Inc., CA, USA). A calibration curve with a high correlation (r>0.99) was obtained for Rubisco purified from rice leaves.
Content of total leaf N
Samples were oven-dried at 80 °C for 3 d. Total leaf N contents were determined with a CN-Corder (Yanaco Co., Tokyo, Japan).
QTL and statistical analysis
Chromosomal locations of putative QTLs were determined by a single-point analysis with the general linear model procedure of QGENE (Nelson, 1997) according to the method of Ishimaru et al. (Ishimaru et al., 2001b). A probability level of 0.01 was used as the threshold for detecting significant differences in mean values of the two genotypic classes, homozygous for Nipponbare and Kasalath alleles (Ishimaru et al., 2001b). To represent a QTL on the map, the chromosome region corresponding to a log of the likelihood odds ratio (LOD) greater than the maximum LOD minus 1 was selected, called an LOD–1 interval (Hirel et al., 2001). The location of the nitrate reductase (NR) gene came from a rice linkage map (Kurata et al., 1994), and that of rbcS from the database of the Rice Genome Project (http://www.dna.affrc.go.jp:82/). The means of 10 replications per line were used in the data analysis for each trait. Means and descriptive statistics were generated with SAS (SAS Institute, 1988). The QTL controlling Rubisco content at 5 d after heading has been reported (Ishimaru et al., 2001b).
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Results |
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TopAbstractIntroductionMaterials and methodsResultsDiscussionReferences |
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Variation in the contents of soluble protein, Rubisco, and total leaf N in flag leaves
BILs showed continuous variations in contents of soluble protein, Rubisco and total leaf N, and in the ratio of Rubisco to leaf N; all traits were inherited quantitatively (Fig. 1
). Transgressive segregants were observed in all traits. The contents of soluble protein and Rubisco in leaves of Nipponbare were higher than those of Kasalath at 5 d and 25 d after heading (Fig. 1A, B). The contents of soluble protein and Rubisco decreased markedly at 25 d compared with those at 5 d (Fig. 1A–D). The contents of total leaf N were similar in both Nipponbare and Kasalath, at about 70 mmol m-2, whereas those in BILs ranged from 50–130 mmol m-2 (Fig. 1E). The ratios of Rubisco to total leaf N were almost the same in Nipponbare and Kasalath; 17% of BILs outperformed their parents (Fig. 1F). In BILs there was a high correlation among the contents of soluble protein and Rubisco at 5 d (r=0.554; P<0.01), and a low correlation at 25 d (r=0.248; P<0.05) after heading (Table 1). Leaf N contents were positively correlated with the contents of soluble protein (r=0.456; P<0.01) and Rubisco (r=0.367; P<0.05).
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QTLs for traits
QTL controlling total leaf N content was not mapped near other QTLs for Rubisco content or soluble protein content (Fig. 2). Three CORNs (QTLs controlling the ratio of Rubisco to leaf N) were detected. Nipponbare alleles gave positive effects at CORN1 or CORN5; Kasalath alleles did so at CORN12. QTLs controlling soluble protein were detected differently depending on the growth stage of leaves (5 d or 25 d after heading) (Fig. 2). The QTL for Rubisco at 5 d was mapped to the same region of chromosome 8 as a QTL associated with soluble protein content at 5 d (Fig. 2). The peak of LOD of Rubisco at 5 d coincided with that of soluble protein content (Fig. 3A). The effect of the allele contributed by Kasalath was positive for both phenotypes. At 25 d after heading, the QTL controlling Rubisco was closely linked to the QTL controlling soluble protein on chromosome 9, and the Nipponbare allele positively affected both (Fig. 2). The peaks of their QTLs overlapped accurately (Fig. 3B).
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Comparison between QTLs and candidate genes
The QTL for soluble protein content at 25 d was positioned between markers C1370 and C86 on chromosome 1 (Fig. 2
). The peak of LOD of this QTL was close to that of C813 and corresponded to a position of 4.4 cm from NR. rbcS did not detect the region of the QTL controlling Rubisco content at 25 d that was mapped on chromosome 12 (Fig. 2). The maximum LOD of CORN12 lay between C443 and G2140 on chromosome 12. There was a difference of 5.6 cm between the peak of LOD of CORN12 and the location of rbcS.
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Discussion |
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TopAbstractIntroductionMaterials and methodsResultsDiscussionReferences |
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The ratio of Rubisco to total leaf N content is not influenced by environmental changes (Mae, 1997
; Makino et al., 1994, 1997; Nakano et al., 1997). However, QTLs controlling the Rubisco content of flag leaves were not mapped near those controlling total leaf N content. These results suggest that Rubisco and total leaf N content are controlled by different genetics (Fig. 2). The detection of CORNs suggests that there may be some mechanisms that determine the ratio of Rubisco to total leaf N content. A few reports showed that when N content was limiting to growth, the content of Rubisco declined in proportion to the content of total leaf N under long-term CO2 enrichment (Sage et al., 1989; Rowland-Bamford et al., 1991; Rogers et al., 1996). In these results, 17% of BILs outperformed their parents (Nipponbare and Kasalath) in this ratio (Fig. 1F). These results suggest that the ratio of Rubisco to total leaf N can be controlled by genetic methods. For example, CORN12, with positive effects by the Kasalath allele, may improve the N-use efficiency of cultivar Nipponbare, even though Nipponbare and Kasalath had almost the same ratio. The combination of high-yielding rice cultivars and the high use of N fertilizer since 1960 have been credited for the increased yields of the Green Revolution, but the high input of N-fertilizer has reduced the fertility of the soil (Mann, 1999). As mentioned in the Introduction, the ratio of Rubisco to total leaf N content is the main target for improving N-use efficiency in rice (Mae, 1997). Therefore, controlling N-use efficiency with CORNs could be valuable for maintaining high yields with reduced inputs of N fertilizer.
BILs showed continuous variations in all traits (Fig. 1); these variations could be caused by transgressive segregants. Xiao et al. found transgressive segregants in BILs where there was no significant difference between parents (Xiao et al., 1996b). Prioul et al. reported that transgressive segregants seemed to result from alleles affecting a trait that may be dispersed between parents (Prioul et al., 1997).
The overlap between QTLs controlling Rubisco and soluble protein contents was detected on chromosome 8 at 5 d after heading or on chromosome 9 at 25 d (Figs 2, 3). There are two possible explanations for the occurrence of QTLs associated with different traits at the same locus. One is that the QTLs are closely linked genetically but unrelated phenotypically. The second is that multiple traits are controlled by a single locus, and a gene may have two functions, or the expression of one trait may, in part, cause the expression of another trait. The peaks of the LODs of the QTLs for Rubisco and soluble protein contents overlapped exactly in each region of the chromosome (Fig. 3). This suggests a strong possibility of pleiotropic effects by the same genes on these chromosome regions. In contrast, a few QTLs for soluble protein content that did not overlap QTLs for Rubisco content were detected (Fig. 2). These results suggest that the Rubisco and soluble protein contents may be partly controlled by the same genetic regulation, and that these QTLs may be related to the contents of other soluble proteins besides Rubisco.
Because a trait is controlled by different expression dynamics of QTLs during development, QTL analysis by plural observations gives better information in genetics than analysis by only 1 observation (Wu et al., 1999). The coincidence of QTLs between Rubisco and soluble protein contents differed between 5 d and 25 d after heading, and some QTLs for these traits were detected at either 5 d or 25 d (Fig. 2; Table 2). These results suggest that these traits might be genetically controlled depending on the growth stage of leaves. In rice plants, N is reallocated from leaves to new sinks (panicles) during senescence (Mae, 1997). Thus, QTLs controlling Rubisco and soluble protein contents at 25 d after heading (the senescence period) could be related to this reallocation.
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Nitrate taken up from the soil by higher plants is reduced to ammonium by two enzymes, NR and nitrite reductase. Reduction of nitrate to nitrite catalysed by NR is a rate-limiting step in the nitrate assimilation pathway in higher plants (Miflin and Lea, 1977
). The amount of Rubisco is reduced in rbcS antisense C3 and C4 plants (Furbank et al., 1996; Makino et al., 1997). At the level of translation, rbcS may directly control the expression of rbcL (Rodermel et al., 1996). NR and rbcS were mapped near QTLs controlling soluble protein content at 25 d after heading and CORN12, respectively (Fig. 2). However, neither NR nor rbcS coincided with the peak of the LOD score for their QTLs. These results suggest that the contents of soluble protein, Rubisco or total leaf N may not be directly related to the structural genes, NR and rbcS, in this environment and with the materials used in this study.
The degradation of Rubisco in rice leaves occurs independently of the synthesis of Rubisco (Makino et al., 1984), and the total leaf N content is determined by the contents of nitrate and ammonium but not protein. CORNs might relate to the degradation of Rubisco or to the contents of nitrate and ammonium, or both. Near isogenic lines have been developed with a specific chromosome region in Nipponbare replaced by that of Kasalath (Yano and Sasaki, 1997). Such lines with Kasalath CORN replacing the Nipponbare alleles can be used for investigating how the ratio of Rubisco to total leaf N is determined.
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Acknowledgments |
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We thank the staff of the Farm Management Division (National Institute of Agrobiological Sciences, Japan) for their care of the plants used in these experiments, and Mr H Sakai (National Institute of Agro-Environmental Sciences) for the operation of the CN-Corder. This work was supported in part by a Grant-in-Aid (Bio Cosmos Program) from the Ministry of Agriculture, Forestry and Fisheries, Japan.
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Notes |
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3 To whom correspondence should be addressed. Fax: +81 298 38 8347. E-mail: kenshi{at}nias.affrc.go.jp
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