Crop Science 43:1068-1071 (2003)
© 2003 Crop Science Society of America
CELL BIOLOGY & MOLECULAR GENETICS
Mapping of QTL for Embryo Size in Rice
Yanjun Dong*,
Eiji Tsuzuki,
Hiroshi Kamiunten,
Hiroyuki Terao and
Dongzhi Lin
Agricultural Faculty, Miyazaki University, Miyazaki City, 889-2192, Japan
* Corresponding author (a01120u{at}cc.miyazaki-u.ac.jp)
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ABSTRACT
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The development of molecular genetic maps has accelerated the identification and mapping of genomic regions controlling quantitative trait loci (QTL) in rice (Oryza sativa L.). Minimizing embryo size in rice would increase proportion of edible endosperm. This study was conducted to determine the genetic basis controlling embryo size of rice grains in a recombinant inbred (RI) population derived from cross of a japonica cultivar, Asominori, with an indica cultivar, IR24, by means of 289 restriction fragment length polymorphism (RFLP) markers. Two parameters, embryo length and embryo width, which represent embryo size in rice, were estimated for each RI line and their parental varieties. Continuous distributions and transgressive segregations of embryo length and embryo width in rice were observed in the RI population, suggesting that embryo size was quantitative in grains of conventional varieties. Three QTL for embryo length were detected on chromosomes 1, 2, and 3 and explained 17.9, 25.7, and 9.2%, respectively, of the total phenotypic variation. Three QTL for the embryo width were observed on chromosome 2, 8, and 10 and accounted for 13.5, 15.7, and 15.0% of total phenotypic variation, respectively. In addition, alleles with increasing and decreasing effects were detected from the both parents. The results and the tightly linked molecular markers that flank the QTL will be useful in breeding for embryo improvement in rice.
Abbreviations: CIM, composite interval mapping • cM, centimorgan • QTL, quantitative trait locus • RFLP, restriction fragment length polymorphism • RI, recombination inbred
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INTRODUCTION
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RICE IS A STAPLE FOOD for more than 50% of the world's population. The grain consists of endosperm and embryo. The endosperm is the major edible part for humankind. In contrast, the embryo, which is easily broken during processing, is usually used for an industrial material. At present, in rice-breeding programs, relatively little attention has been focused on embryo size. However, during the past two decades, breeding efforts to improve nutritional quality in rice has focused on enlarging the embryo for industrial purposes. Relative to other parts of the rice grain, the embryo has high concentrations of protein, oil, and vitamins (Juliano, 1985; Koh et al., 1994).
Satoh and Omura (1981) first found a giant-embryo mutant from a Japanese cultivar, Kinmaze, and mutant gene was located on chromosome 7 (Satoh and Iwata, 1990). In addition, Kim et al. (1991)( 1992) detected three giant-embryo mutants (gem, ge, ges), all at the same locus reported by Satoh and Iwata (1990). More recently, Koh et al. (1996) precisely mapped the ges locus controlling super-giant embryo to chromosome 7 using RFLP and microsatellite markers.
If the objectives of breeding programs are to increase embryo size, it is clearly important to study the giant-embryo mutants in rice. On the other hand, if the ultimate goal of a breeding program is to increase endosperm components, it is valuable to minimize the embryo size. Thus, an understanding the genetic basis underlying the inheritance of embryo size in rice has significant implications for quality improvement.
The recent advances in high-density marker linkage maps in rice have provided powerful tools for elucidating the genetic basis of quantitatively inherited traits (Causse et al., 1994; Harushima et al., 1998). As a result, numerous QTL (Yano and Sasaki, 1997) associated with yield and its components and other agronomic traits in rice have been identified and mapped by means of molecular markers. However, to our knowledge, genetic analysis of QTL associated with embryo size has not been conducted in normal grain rice. The aims of this study are to identify QTL for embryo size by means of RI lines from a japonica/indica cross and to determine the relationships between QTL for embryo size and QTL for grain size, which were found in previous studies (Redona and Mackill, 1998; Tan et al., 2000).
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MATERIALS AND METHODS
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Plant Materials
The RI lines in this study, kindly provided by professor A. Yoshimura of Agricultural faculty of Kyushu University, Japan, were developed by single seed descent from the progeny of a cross of japonica cultivar, Asominori, with indica cultivar, IR24. 165 F6 lines were randomly selected from 227 original F2 individual plants and used for mapping. The RFLP map covering 1275 centimorgans (cM) was constructed with 375 markers from the F6 and F7 generations of 71 RI lines (Tsunematsu et al., 1996). In the past, the RI population was used successfully for mapping QTL for important agronomic traits (Yoshimura et al., 1998; Yamazaki et al., 1999; Yamazaki et al., 2000; Sasahara et al., 1999). In this study, we used a subset of 289 RFLP markers, without overlapping, for all loci from the original genetic map (Tsunematsu et al., 1996) to map QTL affecting embryo size in rice, for which the average interval distance between pairs of markers was 4.4 cM.
Measurements of Length and Width of Embryo in Brown Rice Grains
The RI population along with its parents, Asominori and IR24, were grown at the Experimental Station of Miyazaki University, Japan, during summer–autumn 2001 with two replications in accordance with conventional methods. At maturity, rice grains from each line were harvested and dried naturally in the glasshouse. Then 50 grains from each line were randomly selected and hulled by hand with care and embryo length and width of was measured with a microscope under a magnification of 50x. All measurements for each line were replicated three times. Average values for each line were used for statistical analyses.
Detection of QTL
Two methods were used simultaneously to identify significant marker locus-trait associations: simple linear regression (single marker analysis) and composite interval mapping (CIM) analysis. The CIM analysis was applied to trait average and marker data to identify more precisely the QTL locations (Zeng, 1994). Single marker analysis and CIM analysis were performed by QTL Cartographer computer program software (Wang et al., 1999) version 1.13 g. The linkages between respective marker loci and putative QTL were determined by single marker analysis. When F values exceeded a value necessary for a probability value less than 0.005, the QTL were considered to be significant. CIM analyses were calculated by forward regression, the walk speed of 2 cM, and the window size of 10 cM. A locus with a LOD threshold value of more than 2.5 was to be declared a putative QTL.
In this study, only the QTL detected by both methods were listed. In addition, the additive effect and percentage of variation explained by an individual QTL were also estimated. The QTL were named according to the suggestions of McCouch et al. (1997).
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RESULTS
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Distribution of Length and Width in Embryo in Segregating RI Population
The average length and width for embryo of both parents (Asominori, IR24) and the frequency distributions of RI lines are presented in Fig. 1. The two parents, show differences in embryo size, especially for embryo length. Continuous phenotypic variation of both embryo length and width and transgressive segregation suggested that embryo length and width were quantitative traits.
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Fig. 1. Frequency distributions for length and width of embryo in rice grains using RI lines derived from a cross between Asominori and IR24.
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Mapping QTL for Embryo Size
Embryo Length
Three QTL controlling the embryo length were identified and mapped to chromosomes 1, 2, and 3 (Table 1 and Fig. 2) and tentatively named for qEML-1, qEML-2, and qEML-3, respectively. The qEML-2, located near C132 markers on chromosome 2, showed the largest effect on the trait with a LOD value of 4.3 and explained 25.7% of the total phenotype variation. Another QTL, qEML-1 (LOD = 3.7), was detected near XNpb393 on chromosome 1 and accounted for 17.9% of total variation. The remaining QTL, qEML-3, located near R1468B on chromosome 3, with a LOD value of 2.8, explained 9.2% of total phenotype variation. In addition, the IR24 alleles in both qEML-2 and qEML-3 contributed to the decrease in embryo length, whereas qEML-1 locus increased the embryo length.
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Table 1. QTL controlling embryo size in rice based on composite interval mapping (CIM) and single marker analysis methods (Wang et al., 1999) using RI lines derived from a cross between Asominori and IR24.
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Fig. 2. Chromosomal locations of QTL for embryo size in RI population derived from the cross between Asominori and IR24. Black and shaded bars indicate the genomic regions with P < 0.01 of QTL detected for embryo length and embryo width, respectively, based on single marker analysis. Black arrowheads indicate the location of peak LOD for QTL detected.
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Embryo Width
Three QTL (Table 1 and Fig. 2) affecting the embryo width were detected and mapped to chromosomes 2, 8, and 10, and tentatively designated as qEMW-2, qEMW-8, and qEMW-10, respectively. qEMW-8 had the largest effect (LOD = 5.1) and was located near XNpb41 on chromosome 8 and explained 15.7% of total phenotype variation. qEMW-2 had a LOD value of 2.6, was located near R712 on chromosome 2, and explained 13.5% of total variation; and qEMW-10 was located near C1361 marker on chromosome 10 and accounted for 15.0% of total phenotype variation. Further, the two alleles from the indica parent, IR24, in qEMW-8 and qEMW-10 decreased the embryo width, while qEMW-2 allele increased the embryo width.
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DISCUSSION
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In this study, we report the results of QTL mapping for embryo size with 289 RFLP markers in conventional cultivars using the RI lines derived from japonica Asominori and indica IR24. In the past, the set of RI lines used in our study was used to analyze QTL for days to heading (Yoshimura et al., 1998), whitebacked planthopper (Sogatella furcifera Horvath) (Yamazaki et al., 1999), ovicidal response to brown planthopper (Nilaparvata lugen Stal) (Yamazaki et al., 2000), and vascular bundle system and spike morphology (Sasahara et al., 1999). From those results, it was shown that these RI lines are very useful for identification of QTL in rice.
Three QTL (qEML-1, qEML-2, qEML-3), located on chromosomes 1, 2, and 3, for embryo length and three QTL (qEMW-2, qEMW-8, qEMW-10), located on chromosome 2, 8, 10, for embryo width were detected. In addition, alleles with increasing and decreasing effects for embryo size were detected from the both parents. The indica parent, IR24, had decreasing alleles for embryo size at qEML-2, qEML-3, and qEMW-2, but increasing alleles at qEML-1, qEMW-8, and qEMW-10, while Asominori alleles had the opposite effects. These results could explain the transgression and continuous distributions for embryo size in the RI population. It is noted that all six QTL detected in the study were independent of the three alleles (gem, ge, ges) that control the giant-embryo trait in rice, located on chromosome 7 in previous studies (Kim et al., 1991; Satoh and Iwata, 1990; Koh et al., 1996).
However, in an attempt to increase the utilization of rice grains by minimizing embryo dimensions in normal grains, it is a prerequisite that there be neither tight linkages nor pleiotropic effects between QTL for embryo size and grain size. In the past, Tan et al. (2000) reported three QTL for grain length, located on chromosomes 3, 6, and 7 and three QTL for grain width on chromosomes 1, 5, and 8, respectively. Redona and Mackill (1998) also identified seven QTL for grain length, located on chromosomes 2, 3 (two regions), 4 (two regions), 7, 10, and four QTL for grain width, located on chromosomes 2, 3, 7, 8, using an F2 population derived from tropical japonica/indica cross. In comparing the genomic positions of the QTL identified by Tan et al. (2000) and Redona and Mackill (1998) for grain size with the six QTL detected in our studies for embryo size, qEMW-8 on chromosome 8 is tightly linked to or allelic to the one for grain width reported by Tan et al. (2000) and Redona and Mackill (1998); furthermore, qEML-3 on chromosome 3 might be closely linked to a QTL for grain length (Redona and Mackill, 1998), which was obviously different from the one QTL reported by Tan et al. (2000). The other four QTL (qEML-1, qEML-2, qEMW-2, and qEMW-10) for embryo size discovered in this research were different from grain-size QTL located in other genomic regions. Hence, these four QTL could be used for rice embryo improvement since they do not affect whole grain size.
In summary, the results from this study can be useful for increasing the utilization of edible endosperms of rice grains by decreasing embryo size in conventional cultivars. The closely linked molecular markers that flank four QTL (qEML-1, qEML-2, qEMW-2, qEMW-10) that are independent of grain-size QTL detected in our studies should be very useful for marker-assisted breeding to improve embryo size in rice when transferring the quantitative genes in breeding programs.
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ACKNOWLEDGMENTS
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We are greatly indebted to Professor A. Yoshimura (plant breeding laboratory, Agricultural faculty of Kyushu University, Japan) for kindly providing materials, molecular data and valuable advice and Professor Phillip E. McClean for his valuable comments in preparation of this paper. This study was jointly supported by a grant from the Heiwa Nakajima Foundation of Japan and a grant from the Iijima Memorial Foundation for the Promotion of Food Science and Technology of Japan. We thank the Japan Society for the Promotion of Science for postdoctoral fellowship (No. P03112) to Dr. Yanjun Dong, which enables him to pursue this study.
Received for publication July 10, 2002.
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TOP
ABSTRACT
INTRODUCTION
