| Development of a Highly Informative Microsatellite （SSR） Marker Framework for Rice （Oryza sativa L.） Genotyping |
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| 作者姓名： | JIANG Shu-kun HUANG Cheng ZHANG Xi-juan WANG Jia-yu CHEN Wen-fu XU Zheng-jin |
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| 作者单位： | [1]Key Laboratory of Crop Physiology, Ecology, Genetics and Breeding, Ministry of Agriculture/Key Laboratory of Northern Japonica Rice Breeding of Liaoning Province, Shenyang Agricultural University, Shenyang 110086, P.R. China [2]Dandong Academy of Agricultural Sciences, Dandong 118109, PR. China |
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| 基金项目： | This study was supported by the National Natural Science Foundation of China （30871468） and the National Basic Research Program of China （973 Program, 2009CB126007）. |
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| 摘 要： | To select highly informative microsatellite markers （SSRs） and establish a useful genetic SSR framework for rice genotyping, 15 rice （Oryza sativa L.） cultivars including six indica varieties and nine japonica varieties were used to analyze the polymorphism information content （PIC） value of 489 SSR markers. A total of 1 296 alleles were detected by 405 polymorphic markers with an average of 3.2 per locus. The PIC value of each chromosome was ranged from 0.4039 （chromosome 2） to 0.5840 （chromosome 11）. Among the two rice subspecies, indica （0.3685-0.4952） gave a higher PIC value than japonica （0.1326-0.3164） and displayed a higher genetic diversity. Genetic diversity of indica was high on chromosome 12 （0.4952） and low on chromosome 8 （0.3685）, while that for japonica was high on chromosome 11 （0.3164） and low on chromosome 2 （0.1326）. A SSR framework including 141 highly informative markers for genotyping was selected from 199 SSR markers （PIC〉0.50）. Ninety-three SSR markers distributed on 12 chromosomes were found to be related to indica-japonica differentiation. Of these 93 pairs of SSR primers, 17 pairs were considered as core primers （all the japonica varieties have the same specific alleles, while the indica varieties have another specific alleles）, 48 pairs as the second classic primers （all the japonica or indica varieties have the same specific alleles, while the indica or japanica varieties have two or more other specific alleles ） and 28 pairs as the third classic primers （all the japonica and indica varieties have two or more alleles, but the specific alleles are different between japonica and indica）. Thirty-two SSR markers were selected to be highly informative and useful for genetic diversity analysis of japonica varieties. This work provides a lot of useful information of SSR markers for rice breeding programs, especially for genotyping, diversity analysis and genetic mapping.
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| 关 键 词： | 微卫星标记 基因分型 SSRS Oryza 水稻 框架 遗传多样性分析 1号染色体 |
| 收稿时间： | 21 January 2010 |
Development of a Highly Informative Microsatellite (SSR) Marker Framework for Rice (Oryza sativa L.) Genotyping |
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| JIANG Shu-kun,HUANG Cheng,ZHANG Xi-juan,WANG Jia-yu,CHEN Wen-fu,XU Zheng-jin.Development of a Highly Informative Microsatellite (SSR) Marker Framework for Rice (Oryza sativa L.) Genotyping[J].Agricultural Sciences in China,2010,9(12):1697-1704. |
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| Authors: | JIANG Shu-kun HUANG Cheng ZHANG Xi-juan WANG Jia-yu CHEN Wen-fu XU Zheng-jin |
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| Institution: | 1. Key Laboratory of Crop Physiology,Ecology,Genetics and Breeding,Ministry of Agriculture/Key Laboratory of Northern Japonica Rice Breeding of Liaoning Province,Shenyang Agricultural University,Shenyang 110086,P.R.China
2. Key Laboratory of Crop Physiology,Ecology,Genetics and Breeding,Ministry of Agriculture/Key Laboratory of Northern Japonica Rice Breeding of Liaoning Province,Shenyang Agricultural University,Shenyang 110086,P.R.China;Dandong Academy of Agricultural Sciences,Dandong 118109,P.R.China |
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| Abstract: | To select highly informative microsatellite markers (SSRs) and establish a useful genetic SSR framework for rice genotyping,15 rice (Oryza sativa L.) cultivars including six indica varieties and nine japonica varieties were used to analyze the polymorphism information content (PIC) value of 489 SSR markers. A total of 1 296 alleles were detected by 405 polymorphic markers with an average of 3.2 per locus. The PIC value of each chromosome was ranged from 0.4039 (chromosome 2) to 0.5840 (chromosome 11). Among the two rice subspecies, indica (0.3685-0.4952) gave a higher PIC value than japonica (0.1326-0.3164) and displayed a higher genetic diversity. Genetic diversity of indica was high on chromosome 12 (0.4952)and low on chromosome 8 (0.3685), while that for japonica was high on chromosome 11 (0.3164) and low on chromosome 2 (0.1326). ASSR framework including 141 highly informative markers for genotyping was selected from 199 SSR markers (PIC ＞ 0.50). Ninety-three SSR markers distributed on 12 chromosomes were found to be related to indica-japonica differentiation. Of these 93 pairs of SSR primers, 17 pairs were considered as core primers (all the japonica varieties have the same specific alleles, while the indica varieties have another specific alleles), 48 pairs as the second classic primers (all the japonica or indica varieties have the same specific alleles, while the indica or japanica varieties have two or more other specific alleles ) and 28 pairs as the third classic primers (all the japonica and indica varieties have two or more alleles, but the specific alleles are different between japonica and indica). Thirty-two SSR markers were selected to be highly informative and useful for genetic diversity analysis of japonica varieties. This work provides a lot of useful information of SSR markers for rice breeding programs, especially for genotyping, diversity analysis and genetic mapping. |
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| Keywords: | SSR marker core primers rice variety differentiation diversity analysis genetic mapping |
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