Abstract
Background
Cytoplasmic effects on agronomic traits -involving cytoplasmic and nuclear genomes of either different species or different cultivars - are well documented in wheat but have seldom been demonstrated in rice (Oryza sativa L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three indica cultivars - Guichao 2, Jiangchengkugu, and Dianrui 449 - into the cytoplasms of six indica cultivars - Dijiaowujian, Shenglixian, Zhuzhan, Nantehao, Aizizhan, and Peta. These 18 nuclear substitution lines were evaluated during the winter season of 2005 in Sanya, Hainan, China, and during the summer season of 2006 in Kunming, Yunnan, China. The effects of 6 cytoplasm sources, 3 nucleus sources, 2 locations and their interactions were estimated for plant height, panicle length, panicle number per plant, spikelet number per panicle, grain weight, filled-grain ratio, and yield per plot.
Results
For five of the seven traits, analysis of variance showed that there were no significant cytoplasmic effects or interactions involving cytoplasmic effects. The effect of cytoplasm on 1000-grain weight was highly significant. Mean 1000-grain weight over the two locations in four of the six cytoplasms clustered close to the overall mean, whereas plants with Nantehao cytoplasm had a high, and those with Peta cytoplasm a low mean grain weight. There was a highly significant three-way interaction affecting filled-grain ratio. At Sanya, cytoplasms varied in very narrow ranges within nuclear backgrounds. Strong cytoplasmic effects were observed only at Kunming and in only two of the three nuclear backgrounds; in the Jianchenkugu nuclear background, there was no evidence of strong cytoplasmic effects at either location. In the Dianrui 449 and Guichao 2 nuclear background evaluated at Kunming, filled-grain ratios of the six cytoplasms showed striking rank shifts
Conclusions
We detected cytoplasmic variation for two agronomically important traits in indica rice. The cytoplasm source had a significant effect on grain weight across the two experimental locations. There was also a significant cytoplasmic effect on filled-grain ratio, but only in two of three nuclear background and at one of the two locations. The results extend our previous findings with japonica rice, suggesting that the selection of appropriate cytoplasmic germplasm is broadly important in rice breeding, and that cytoplasmic effects on some traits, such as filled-grain ratio, cannot be generalized; effects should be evaluated in the nuclear backgrounds of interest and at multiple locations.
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Background
Reductions in genetic diversity are of major concern to breeders, geneticists, and the agricultural community in general. In many crops, genetic improvement is usually associated with reduced genetic diversity in the gene pools used to develop the new cultivars, despite the fact that genetic uniformity is believed to increase the potential vulnerability of the crop to biotic and abiotic stresses [1].
The genetic base of cultivars of rice is narrow because of the long history of domestication and genetic improvement. Pedigree analysis indicates that the genetic diversity of indica irrigated rice in China depends on a genetic core derived from the varieties Aizizhan, Nantehao, Shenglixian, Peta, and Dijiaowujian [2]. Between three and six sources of genetic material per location have used by breeders of japonica rice cultivars in China [2, Statistical analysis Analysis of variance of the 6 × 3 factorial genetic design was used in order to determine in a single comprehensive analysis which among the seven traits were influenced by differences in the cytoplasmic genome and whether those effects depended on the nuclear background, the environment, or both. That preliminary information allowed us then to examine in more detail the differences and rankings of individual cytoplasms where significant differences occurred. Except for yield per plot, all data were from observations on 10 individuals selected randomly from each plot, and the plot mean was used in the analysis of variance. Fixed model analyses using type III sums of squares in SAS PROC GLM [38] were used to detect effects of nucleus, cytoplasm, and interaction between cytoplasm, nucleus, and location. For filled-grain ratio, arscin transformation of the ratio was performed before the analysis. If the three-way interactional effect among cytoplasm, nucleus, and location was significant for traits investigated, the least-squares means (LS-means) of fixed effects was employed to analyze the cytoplasmic effects within each location and nucleus. Duncan's multiple range test was used for multiple comparisons of the effect of cytoplasm and cytoplasm interaction with nucleus and location.
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Acknowledgements
This research was funded partially by grants from the Yunnan Department of Science and Technology (2005C0011Z) and the National Natural Science Foundation of China (30360054). China National Rice Research Institute (CNRRI) and International Rice Research Institute (IRRI) supplied the plant materials. The authors thank all the investigators who contributed to this study.
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Authors' contributions
DT participated in designing the experiment and in drafting the manuscript. PX made some of the nuclear substitution lines and carried out the experiment in Sanya, Hainan. JZ made some of the nuclear substitution lines and carried out the experiment in Kunming, Yunnan. XD carried out the experiment in Sanya, Hainan. JL, assistant to JZ, carried out the experiment in Kunming, Yunnan. WD, assistant to PX and XD, carried out the experiment in Sanya, Hainan. GY made some of the nuclear substitution lines. JY made some of the nuclear substitution lines. QL, assistant to JW, carried out the experiment in Kunming, Yunnan. FH made some of the nuclear substitution lines, participated in designing the experiment, analyzed the data, and participated in drafting the manuscript. All authors have read and approved the final manuscript.
Electronic supplementary material
12863_2009_907_MOESM1_ESM.XLS
Additional file 1:Agronomic-trait data on which Figure 1 and Additional Figures 1 through 6 are based. Means for seven traits expressed by backcross lines representing all combinations of three nuclear and six cytoplasmic genomes at two locations with four replications at each location. (XLS 52 KB)
12863_2009_907_MOESM2_ESM.PPT
Additional file 2:Mean plant height of 18 nuclear-cytoplasm combinations in indica rice. Means and standard errors for plant height recorded at two locations, Sanya and Kunming, China, from 18 backcross lines of indica rice representing all combinations of three nuclear and six cytoplasmic genomes. (PPT 192 KB)
12863_2009_907_MOESM3_ESM.PPT
Additional file 3:Mean panicle length of 18 nuclear-cytoplasm combinations in indica rice. Means and standard errors for panicle length recorded at two locations, Sanya and Kunming, China, from 18 backcross lines of indica rice representing all combinations of three nuclear and six cytoplasmic genomes. (PPT 212 KB)
12863_2009_907_MOESM4_ESM.PPT
Additional file 4:Mean number of panicles per plant of 18 nuclear-cytoplasm combinations in indica rice. Means and standard errors for number of panicles per plant recorded at two locations, Sanya and Kunming, China, from 18 backcross lines of indica rice representing all combinations of three nuclear and six cytoplasmic genomes. (PPT 218 KB)
12863_2009_907_MOESM5_ESM.PPT
Additional file 5:Mean number of spikelets per panicle of 18 nuclear-cytoplasm combinations in indica rice. Means and standard errors for number of spikelets per panicle recorded at two locations, Sanya and Kunming, China, from 18 backcross lines of indica rice representing all combinations of three nuclear and six cytoplasmic genomes. (PPT 206 KB)
12863_2009_907_MOESM6_ESM.PPT
Additional file 6:Mean 1000-grain weight of 18 nuclear-cytoplasm combinations in indica rice. Means and standard errors for 1000-grain weight recorded at two locations, Sanya and Kunming, China, from 18 backcross lines of indica rice representing all combinations of three nuclear and six cytoplasmic genomes. (PPT 216 KB)
12863_2009_907_MOESM7_ESM.PPT
Additional file 7:Mean yield per plot of 18 nuclear-cytoplasm combinations in indica rice. Means and standard errors for yield per plot recorded at two locations, Sanya and Kunming, China, from 18 backcross lines of indica rice representing all combinations of three nuclear and six cytoplasmic genomes. (PPT 204 KB)
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Tao, D., Xu, P., Zhou, J. et al. Cytoplasm affects grain weight and filled-grain ratio in indica rice. BMC Genet 12, 53 (2011). https://doi.org/10.1186/1471-2156-12-53
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DOI: https://doi.org/10.1186/1471-2156-12-53