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    InDel and SNP Markers and Their Application in Map-Based Cloning of Rice Genes

    PAN Cun-hong ,WANG Zi-bin ,MA Yu-yin ,YIN Yue-jun ,ZHANG Ya-fang ,ZUO Shi-min ,CHEN Zong-xiang ,PAN Xue-biao
    Chinese Journal of Rice Science   
    Abstract12223)      PDF (1095KB)(7060)       Save
    The high-density markers are necessary for map-based cloning of rice genes,but the available marker could not reach the satisfying level.InDel(insertion-deletion length polymorphism) and SNP(single nucleotide polymorphism) are new molecular markers,which could basically meet the need of the fine mapping.InDel and SNP markers could be developed through bioinformatics approaches.InDel and SNP markers are valuable markers with the characteristics of low cost,high specificity and stability.The methods for designing InDel and SNP markers were introduced and the example of mapping of the rice rolled leaf gene was used to describe the design procedures in practice.In addition,some key factors for improving the design efficiency were discussed.
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    Expression of OsBC88, a Rice Cellulose Synthase Catalytic Subunit Gene
    Xiao-jing LI, Duo-duo XU, Yi-min XU, Kai-en ZHAI, Yao-long YANG, Jian-wei PAN, Yu-chun RAO
    Chinese Journal OF Rice Science    2015, 29 (2): 126-134.   DOI: 10.3969/j.issn.1001-7216.2015.02.003
    Abstract4541)   HTML1073807361)    PDF (5213KB)(6272)       Save

    Brittle culm mutant in gramineae plants is an ideal material for secondary cell wall research. Previous studies about bc88 mutant in rice show that BC88 encodes a cellulose synthase catalytic subunit, OsCesA9. The genetic transformation of rice by BC88 promoter fused with GUS vector showed that BC88 was expressed ubiquitously in root, stem, leaf, sheath, flower, with high expression in culm and root. The mutation in BC88 may affect normal development and function of root, thereby affect the shoot growth and lead to semi-dwarf phenotype. Transfer BC88 fused with GFP protein into rice and tobacco epidermal cells show that, OsCesA9 is located at plasma membrane where cellulose synthesized, coinciding with that OsCesA9 is one of the essential functional CESA units for cellulose synthesis of secondary cell wall. These results provided new information for analysis of BC88 biological function and it’s of great significance for the further understanding of BC88 in regulating the secondary cell wall synthesis or other related process.

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    Pollen Development and Its Stages in Rice (Oryza sativa L.)
    FENG Jiu-huan,LU Yong-gen,LIU Xiang-dong,XU Xue-bin
    Chinese Journal of Rice Science   
    Abstract15024)      PDF (349KB)(6050)       Save
    By using techniques of intact fresh anther observation, isolated male cell observation and semi thin section, an extensively cytological study was conducted on the pollen development of IR36, an indica cultivar. The results showed that the wholly developmental process could be tentatively divided into eight stages, i.e. microspore mother cell formation stage, microspore mother cell meiosis stage,early microspore stage, middle microspore stage, late microspore stage, early bicellular pollen stage,late bicellular pollen stage and mature pollen stage. The experiment proved that there was not contraction stage in naturally developmental process of the microspores. During the pollen developing, the tapetal cells underwent three types of morphological changes, which help to identify the stages of pollen development.
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    Genetics and Improvement of Resistance to Bacterial Blight in Hybrid Rice in China
    ZHANG Qi
    Chinese Journal of Rice Science   
    Abstract7049)      PDF (2483KB)(5800)       Save
    Since the 1980s, hybrid rice breeding for resistance to bacterial blight in China has been rapidly progressing. The gene Xa4 was mainly used in threeline indica hybrid and twoline hybrid rice grown in a large area. The disease has been seen “quiet” for 20 years in China, yet in recent years it has gradually emerged prevalently in fields planted with newly released rice varieties in the Yangtze River Valley. This situation for scientists inevitably raised several questions: what causes the resurgence? Is the resistance of variety still effective? And/or is resistance breeding still one of the main objectives of rice improvement? What approach do we take on resistance breeding so that the resistance will be more durable, and the resistance gene will be used more efficiently? A combined strategy composed of traditional method, molecular markerassisted selection, and transgenic technology should bring a new era to the bacterial blight resistance hybrid rice breeding program. The review also briefly discusses and deliberates on issues related to the broadening of bacterial blight resistance, and suitable utilization of resistance genes, alternation planting of available resistance genes, and introduces the virulent populations of the bacterial blight pathogen in China even in Asia.
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    Effect of Silicon Fertilizer Application on Yield and Grain Quality of japonica Rice from Northeast China
    SHANG Quan-yu,ZHANG Wen-zhong,HAN Ya-dong,RONG Rong,XU Hai,XU Zheng-jin,CHEN Wen-fu
    Chinese Journal of Rice Science    DOI: 10.3969/j.issn.1001-7216.2009.06.17
    Abstract7386)      PDF (354KB)(5717)       Save
    The effect of silicon fertilizer rate on rice yield and quality was studied by using Shennong 265 and Fengyou 2000 as materials in a pot experiment. The rice grain yield increased with the application of silicon,especially at a silicon fertilizer rate of 240 kg/hm2 for Shennong 265 and at 180 kg/hm2 for Fengyou 2000, respectively. For the yield components, the number of panicles per plant, 1000grain weight of the grains on the primary rachis branches, 1000grain weight of the grains on the secondary rachis branches, number of grains per panicles were increased with the application of silicon. The rice quality was significantly improved especially for brown rice rate, milled rice rate, head rice rate, chalky grain rate and chalkiness. Correlation analysis showed that the milled rice rate and head rice rate were significantly and positively correlated with silicon rate for the two varieties. In Shennong 265, the content of fatty acid was significantly and positively correlated with the silicon rate and taste value was significantly and negatively correlated with the silicon rate. There was no significant correlation between the content of amylose or protein and the silicon rate within a range of 0 to 240 kg/hm2. Considering the grain yield and quality together, 180 to 240 kg/hm2 silicon was suitable.
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    Discussion on Germplasm and Gene Utilization in Breeding of Super Rice
    CHENG Shihua,CAO Liyong,ZHUANG Jieyun,WU Weiming
    Chinese Journal of Rice Science   
    Abstract7315)      PDF (233KB)(5399)       Save
    Breeding of super rice is a new breeding method based on semidwarf breeding and utilization of heterosis in rice. It is the result of utilization of germplasms or genes and its interaction with environment. The paper reviews the current status of integrative utilization of germplasms and genes in the breeding of super rice in China. It deals with gene introgression of indica and japonica, pyramiding and using of yield QTLs in cultivated rice, exploitation and use of the genes related with highyielding, resistance to pests, plant and root architectures. Nowadays agronomical important genes and their closelylinked molecular markers are not enough to supply the strong basis for molecular breeding of super rice. The common cross breeding is still an effective method in breeding of super rice through interactive use of the rice germplasms. Therefore it is necessary to make great efforts to develop wideadaptable super rice or green super rice through exploitation of genes related with highyielding, high quality, resistance to pests and diseases, and tolerance to stresses. The modern molecular breeding methods in combination with common cross techniques should be adopted in the program of super rice breeding.
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    Microsatellite Marker-Based Analysis of Rice Varieties in National Regional Yield Trial of Southern China
    Cheng Ben-yi,Shi Yong-feng,Shen Wei-feng,Zhuang Jie-yun,Yang Shi-hua
    Chinese Journal of Rice Science   
    Abstract5937)      PDF (546KB)(5390)       Save
    A total of 199 rice varieties in the national regional yield trial of southern China in 2005 were assayed with a preferred set of 12 microsatellite markers(SSR). A DNA fingerprint database containing genotypic data of the 199 rice varieties at the 12 marker loci was constructed. It was found that the dominant alleles in conventional rice varieties were the same as in hybrid rice at most of the marker loci, but they differed greatly from indica to japonica rice. Conventional rice was of high homozygosity and most hybrid rice was of high heterozygosity. The variation in number of heterozygous loci was evident for hybrid rice with a normal distribution. On comparison among hybrid rice combinations derived from the same cytoplasmic male sterile(CMS) line, general consistency of the maternal allele of major CMS lines was observed at the SSR loci. Moreover, the distinctness assay of rice variety in the national regional yield trial of southern China, and the expansion of DNA fingerprint data base and the number of SSR markers for a feasible test were discussed.
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    Rice Cropping Regionalization in China
    Mei Fangquan,Wu Xianzhang,Yao Changxi,Li Luping,Wang Lei,Chen Qiuyun
    Chinese Journal of Rice Science   
    Abstract13816)      PDF (1089KB)(5378)       Save
    According to the ecological environments, social and economic backgrounds and rice cropping characteristics in different areas of China, the Chinese rice planting area is divided into 6 rice cropping regions(the first-grade regions) and 16 subregions (the second-grade regions). Their general information, natural and ecological environments, paddy field cropping systems, types of rice varieties and their distribution and major diseases and insect pests are respectively described. Orientations, approaches and measures for developing rice production are raised and meanwhile the suggestions are put forward on the layout of production, paddy field crops combination and selection and construction of commercial rice production bases.
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    Analysis on Correlation Between Heterosis and Genetic Distance Based on Simple Sequence Repeat Markers in japonica Rice
    ZHAO Qingyong ,ZHU Zhen ,ZHANG Yadong ,ZHAO Ling ,CHEN Tao ,ZHANG Qiaofeng ,WANG Cailin
    Chinese Journal of Rice Science   
    Abstract9584)      PDF (887KB)(5328)       Save
    Genetic diversity among 30 japonica rice was studied using the simple sequence repeat(SSR) markers, and relationship between genetic distance based on SSR markers and yield heterosis was analyzed using the materials consisted of 30 parents and 200 F1 hybrids with a 20×10 diallel crossing design. The results indicated that 64 pairs of SSR primers could produce 185 steady polymorphic bands among 30 parents averaging 2.9 bands for each pair of primers. The polymorphic index content (PIC) values varied from 0.064 to 0.844 with an average of 0.380. Cluster analysis by UPGMA classified 30 parents into seven groups based on genetic similarity, which was coincident with the heterotic groups determined by their pedigree analysis. The correlations between the genetic distance and yield heterosis and hybrid performance were significant except for the total number of spikelets per panicle, and the coefficients of correlations were ranged from -0.361 to 0.359. It is suggested that the molecular markers could be used as a useful tool for assigning heterotic group and measuring genetic diversity, but not for predicting heterosis because the coefficient of relationship between the genetic distance based on SSR markers and yield heterosis was too small.
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    Research Advances in Physiology of Super Rice  under HighYielding Cultivation
    FU Jing, YANG Jian-Chang*
    Chinese Journal of Rice Science    2011, 25 (4): 343-348.   DOI: 10.3969/j.issn.1001-7216.2011.04.001
    Abstract8584)      PDF (433KB)(5315)       Save
     China launched a program for breeding of  super rice or super hybrid rice    by  combining  intersubspecific heterosis with ideal  plant type   in 1996.  Today, about 80 super rice varieties have been released and some of them  have achieved   grain yields of 12-21 tons per hectare in field experiments. Compared with conventional cultivars, main reasons for high yield of super rice can be summarized as follows:  more spikelets per panicle and larger sink size (number of spikelets per square meter);  larger leaf area index, longer duration of green leaf area, higher photosynthetic rate and higher lodging resistance of culms;    more matter accumulation before the heading stage, more remobilization of prestored carbohydrates from stems and leaves to grains during the grain filling period; and   larger root system and greater root activity.  However, super rice also has two major problems in  production:  poor grainfilling of the laterflowering inferior spikelets (in contrast to earlierflowering superior spikelets), and   low and unstable seedsetting rate. The research advances in cultivation physiology  of super rice in respects of biological features, formation of yield components, population quality  and physiological mechanisms  were reviewed, and suggestion on further studies on super rice cultivation physiology  were put forward.
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    Rice Production Capacity in China
    FANG Fu-ping,CHENG Shi-hua*
    Chinese Journal of Rice Science    DOI: 10.3969/j.issn.1001-7216.2009.06.01
    Abstract6152)      PDF (1024KB)(5302)       Save
    Rice production development is the key to maintaining the food security in China. To know the rice production potential in China, the levels of realistic productivity, actual production capacity and potential production capacity were calculated. The actual rice production capacity and potential production capacity in China could reach 226.2 and 253.9 million tons, respectively, 34.28 and 62.00 million tons higher than the realistic productivity. Moreover, the causes for the stagnant increase in rice yield per unit area were discussed and the scientific and technical strategies for promoting rice productivity were put forward. To further improve the rice production capacity and steadily increase national rice production, some measures are suggested, i.e. strengthening the amelioration of medium and low yield fields to improve the quality of farmland, making efforts on super highyielding rice breeding and extension to form the variety structure dominated by widely adaptive super highyielding rice cultivars, optimizing cultivation techniques for super high yield to construct a lowcost and highefficiency production technology system with simplified techniques at its core, and strengthening agricultural technology extension to reduce the yield difference between realistic yield and potential yield. In short, it is needed to promote scientific and technical supporting ability to the productive capacity of rice.
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    Construction of Near Isogenic Lines for Pericarp Color and Evaluation on
    Their Near Isogenicity in Rice
    WANG Xiaoguang,JI Zhijuan,CAI Jing,MA Liangyong,LI Ximing,YANG Changdeng*
    Chinese Journal of Rice Science   
    Abstract7257)      PDF (1384KB)(5244)       Save
    The inheritance of purple pericarp was studied through genetic analysis using F2, BC1F1 and F3 from a cross between a purple pericarp rice variety Zixiangnuo and a white pericarp rice variety Chunjiangnuo 2. Seven pairs of near isogenic lines(NILs) for pericarp color of rice were further constructed. The genetic analysis indicated that the purple pericarp was controlled by two complementary genes (Pb and Pp). Analyses on agronomic traits showed that no significant differences on agronomic traits were found among NILs except grain weight. The polymorphic SSR markers for the two parents were detected only in target segments of the five pairs of NILs different in Pb, which revealed that the near isogenicities of them were fine. However, for the two pairs of NILs different in Pp, the polymorphic markers for the two parents were detected as well as in nontarget segments of chromosomes 11 and 12, respectively.
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    Current Situation and Suggestions  for Development of TwoLine Hybrid Rice in China
    SI Huamin, LIU Wenzhen, FU Yaping, SUN Zongxiu, HU Guocheng*
    Chinese Journal of Rice Science    2011, 25 (5): 544-552.   DOI: 10.3969/j.issn.10017216.2011.05.014
    Abstract11114)      PDF (891KB)(5177)       Save
    Great progress  has made in  Twoline hybrid rice breeding in China. Up to 2010, a total of 427 twoline hybrid combinations were registered in China. Among them, 62 were nationally registered and   titled  as “super rice” by the Ministry of Agriculture, China. From 1993 to 2009, there were 121 combinations with the  planting area over 6 700 hm2, and the total planting area reached 20.974 million hm2. With the  planting area of   825×105 hm2 in 2002,  Liangyoupeijiu  ranked   first among all hybrid combinations  in planting area. In the following 7 years, twoline hybrid combination ranked first  for 6 years, and second for one year. In recent years, twoline hybrid rice  has become an important type in rice production in China, accounting for about 20% of the total planting area of hybrid rice. The current situation of the development of twoline hybrid rice was introduced, the main problems were discussed and the suggestions were proposed.
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    Marker-Assisted Selection for Pyramiding Disease and Insect Resistance Genes in Rice
    PEI Qing-li ,#,WANG Chun-lian ,#,LIU Pi-qing ,WANG Jian ,ZHAO Kai-jun
    Chinese Journal of Rice Science    2011, 25 (2): 119-129.   DOI: 10.3969/j.issn.1001-7216.2011.02.001
    Abstract10927)      PDF (529KB)(5148)       Save
    Blast (Magnaporthe grisea), bacterial blight (Xanthomonas oryzae pv. oryzae), brown planthopper (Nilaparvata lugens ) and white-backed planthopper (Sogatella furcifera) are major diseases and pests of rice. Utilization of rice varieties carrying resistance genes is one of the most economical, effective, and environment- friendly measures for the management of diseases and pests. The molecular markers, chromosome localization and the donor varieties of the identified disease/insect resistance genes of rice were summarized, and recent progress on molecular mapping of the resistance genes and on pyramiding different disease/insect resistance genes in rice by marker-assisted selection was reviewed. In addition, the strategy for developing better disease/insect resistant varieties was discussed.
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    Effects of N, P, K Fertilizer Application on Grain Yield, Quality, Nutrient Uptake  and  Utilization of Rice
    WANG Weini1, LU Jianwei1, *, HE Yuqing2, LI Xiaokun1, LI Hui1
    Chinese Journal of Rice Science    2011, 25 (6): 645-653.   DOI: 10.3969/j.issn.10017216.2011.06.012
    Abstract9487)      PDF (949KB)(5088)       Save
    Based on the “3414” fertilizer experimental design,  the effects of N, P and K fertilizer application on grain yield, grain quality as well as nutrient uptake and utilization of rice  were researched     to  elucidate  the interactive effects among N, P and K in a field experiment   with four levels of nitrogen (N), phosphorus (P) and potassium (K) fertilizers. The results showed that the application of N, P and K significantly increased grain yield, and  the highest yield was found under the joint application of N, P and K fertilizer. The application of fertilizer also improved rice  quality  markedly. For example, head rice rate was increased and chalkiness degree, lengthwidth ratio of grain and amylose content of milled rice were decreased due to the application of N, P and K. And, the application of N and P increased protein content of brown rice and decreased green rice rate. The application of N, P and K fertilizer increased total nutrient (show as N, P2O5, K2O) accumulation and nutrient absorption per 100kg seeds, but reduced nutrient dry matter production efficiency and nutrient grain production efficiency. Meanwhile, fertilizer recovery efficiency, agronomic efficiency and physiological efficiency always declined with the increasing  N, P and K application rate. Grain yield was significantly influenced by the interaction between N and P, N and K, P and K, respectively, and the interactions were synergistic when fertilizers application rates were at lower or moderate levels, otherwise they were antagonistic. The most significant interactive effect on total N, P2O5 and K2O accumulation was between N and K, N and P, P and K, respectively. It is concluded that the influence of fertilizer on rice growth was various, which means that fertilizers application rate and ratio should be established with an integrated consideration of several factors including grain yield, grain quality and nutrient uptake, utilization efficiency.
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    Germination of Pollen and Growth Dynamic of Pollen Tube in Rice
    CHEN Shi-qiang ,WANG Zhong ,LIU Man-xi ,XIE Zhao-wei
    Chinese Journal of Rice Science   
    Abstract6620)      PDF (1350KB)(5053)       Save
    The germination of rice pollen grain in vitro and the growth of pollen tube in pistil were observed with a microscope.The stigma was removed at different time after pollination to investigate seed setting rate of floret.Results showed that rice pollen grain germinated 2 min after pollination and pollen tube would penetrate stigma into style in 5-10 min,30 min later the end of pollen tube reached the bottom of ovary,then some pollen tubes arrived at the embryo sac 40 min after pollination and meanwhile a small amount of callose formed in the pollen tubes,50 min later a great deal of callose was found,and the pollen grain began to shrink.The growing speed of pollen tube in rice stigma,style and ovary was 1500,5000,5400 μm/h,respectively.The seed setting rate was quite low when the stigma was removed at 10-15 min after pollination,and then it increased gradually from 20 min to 50 min,finally it was over 60% at 50 min after pollination and tended to be stable.
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    Progress in Research on Physiological and Ecological Response of Rice to Oxygen Nutrition and Its Environment Effects
    ZHAO Feng,WANG Dan ying,XU Chunmei ,ZHANG Weijian,ZHANG Xiufu
    Chinese Journal of Rice Science    DOI: 10.3969/j.issn.1001-7216.2009.04.01
    Abstract5792)      PDF (54KB)(4980)       Save
    s an important nutritional factor, oxygen performs great functions in physiological activities of rice. It is well known that in rice plants, atmospheric oxygen is transported from shoots to its roots through its continuous aerenchymatous system. Besides, rice roots also acquire oxygen from the rhizosphere environment across root epidermis. The leakage of O2 is enabled by a very permeable aerenchyma inside the roots which conducts O2 to the root tissue, and also enables the inside oxygen export to the external medium. The importance of oxygen is also reflected on the improvement of rhizosphere environment. By oxidizing Fe2+ and other phytotoxins, oxygen can detoxify the rhizosphere environment. In addition, the oxidation processes round the rhizosphere has significant effects on local pH and Eh, which exert an important influence on rice nutrient uptake. By decreasing oxygen concentration in the root medium, the transversal oxygen flux decrease and the longitudinal flux increase so as to compensate for the decrease of the former, but growing insufficiency in oxygen supply to the roots was observed in some older rice seedlings. This review summarized the progress in research on oxygen nutrient from the plant biological response and ecological effects of rhizosphere, which emphasized on the research of rice plant oxygen requirement, the effect of oxygen on rice morphology and anatomy, relative physiological and ecological mechanism, and the effect of oxygen on rice growing environment. The methods and techniques used to change the oxygen conditions in paddy field were also compared, and the further studies of rice oxygen nutrient were discussed.
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    Heterotic Group and Its Application in Hybrid Rice Breeding
    LU Zuo-mei,XU Bao-qin,
    Chinese Journal of Rice Science    DOI: 10.3969/j.issn.1001-7216.2010.01.01
    Abstract10116)      PDF (362KB)(4922)       Save
    Heterotic groups have played an important role in hybrid maize breeding for more than 100 years. The concept of heterotic groups and patterns, and their application in rice and maize were reviewed. Challenges for hybrid rice breeding in China were analyzed, and necessity and urgency for using heterotic groups in hybrid rice breeding were pointed out.
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    Construction of SSR Linkage Map and Analysis of QTL for Rolled Leaf of Restorer Line in japonica Rice (Oryza sativa)
    GUO Yuan,CHENG Baoshan ,HONG Delin
    Chinese Journal of Rice Science   
    Abstract6701)      PDF (1894KB)(4824)       Save
    SSR marker genotypes and phenotypes of flag leaf rolling index (LRI) were investigated in Xiushui 79 (P1, a japonica variety), C Bao(P2, a japonica restorer line) and 254 recombinant inbred lines derived from the cross between Xiushui 79 and C Bao in japonica rice (Oryza sativa L.). A genetic map of the cross was constructed. QTLs for LRI were detected and their interaction with environments was analyzed. Among 818 pairs of SSR primers detected, 90 primers amplified polymorphic products between P1 and P2. Twelve markers showed highly significant correlations with LRI in both two environments based on single marker regression analysis. A genetic map containing 74 information loci was constructed, which covers a total distance of 744.6 cM, averaging 10.1 cM between two loci. Three QTLs (qRL1, qRL7 and qRL81) were detected with two analysis softwares WinQTLcart 2.5 and QTLNetwork 2.0. qRL81 was a new locus, accounting for 155% and 12.8% of phenotypic variation in the two environments, respectively. Phenotypic variation explained by additive effect was 6.6%. No interaction was found between qRL81 genotype and environments.
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    SSR Analysis of Genetic Variation in Chinese Major Inbred Rice Varieties
    WEI Xinghua,YUAN Xiaoping,YU Hanyong,WANG Yiping,XU Qun,TANG Shengxiang
    Chinese Journal of Rice Science   
    Abstract6534)      PDF (4652KB)(4780)       Save
    A total of 40 SSR markers were used to assess the genetic variation in 329 Chinese major inbred rice varieties planted during the past 50 years. Of the 40 SSR loci, 39 were polymorphic while one locus (RM479) was monomorphic. All the 39 polymorphic loci revealed a total of 223 alleles. The mean number of alleles per locus (Na) was 5.7 with a range from 2 to 11. Total genetic diversity index of Nei (He) varied greatly among loci from 0.221 at RM174 to 0.873 at RM418, with an average value of 0.632. There existed visible difference in SSR allelic diversity between indica and japonica subspecies. Indica showed more variation than japonica both for Na (indica: 5.4; japonica: 4.4) and He (indica: 0.440; japonica: 0.397). The whole set of Chinese major rice varieties had smaller genetic identity (I = 0.366 ) than that of indica (I=0.558) and japonica rice (I=0.600). The narrow genetic base within subspecies was mainly due to the close relationship among primary parents in breeding programs. The differences among three season types were obvious in Nei′s genetic identity indexes, of which lateseason indica rice and earlyseason japonica rice had higher genetic variation. Cluster analysis indicated that the genetic distances between Chinese major rice varieties were season type and rice regiondependant, especially in japonica rice. Therefore, it is suggested that more alien elite genetic resources should be exploited in the rice breeding for broadening the genetic base of Chinese rice varieties.
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