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Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.)

Journal of Genetics and Genomics 2010年第2期37卷 147-157页

作者： Qiang fu Peijiang Zhang Lubin Tan Zuofeng Zhu Dan Ma yongcai fu Xinchun Zhan Hongwei Cai Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry National Center for Evaluation of Agricultural WiM Plants (Rice) Laboratory of Crop Heterosis and Utilization of Ministry of Education Beijing Key Laboratory of Crop Genetic Improvement Key Laboratory of Crop Genetic Improve- ment and Genome of Ministry of Agriculture Department of Plant Genetics and Breeding China Agricultural University Beijing 100193 China Institute of Rice Research Anhui Academy of Agricultural Sciences Hefei 230031 China

Using an accession of common wild rice （Oryza rufipogon Griff.） collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two gen- erations （BC4F2 and BC4F4）, a total of 26 QTLs were detected by employing single point analysis and interval mapping in both genera-tions. Of the 26 QTLs, the alleles of 10 （38.5%） QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.

关键词： common wild rice yield-related traits advanced backcross population QTL

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Molecular Evolution of the TACl Gene from Rice(Oryza sativa L.)

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Journal of Genetics and Genomics 2012年第10期39卷 551-560页

作者： Jiahuan Jiang Lubin Tan Zuofeng Zhu yongcai fu Fengxia Liu Hongwei Cai Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry National Centre for Evaluation of Agricultural Wild Plants(Rice)Department of Plant Genetics and BreedingChina Agricultural University Beijing 100193 China Rice Research Institute Fujian Academy of Agricultural ScienceFuzhou 350018China

Tiller angle is a key feature of the architecture of cultivated rice （Oryza sativa）, since it determines planting density and influences rice yield. Our previous work identified Tiller Angle Control 1 （TACI） as a major quantitative trait locus that controls rice filler angle. To further clarify the evolutionary characterization of the TAC1 gene, we compared a TACl-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of O. rufipogon and five accessions of O. nivara. Only one single nucleotide polymorphism （SNP）, a synonymous substitution, was detected in TAC1 coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions. These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution. Nucleotide diversities in the TAC1 gene regions of O. sativa and O. rufipogon of 0.00116 and 0.00112, respectively, further indicate that TAC1 has been highly conserved during the course of rice domestication. A functional nucleotide polymorphism （FNP） of TAC1 was only found in the japonica rice group. A neutrality test revealed strong selection, especially in the 3＇-flanking region of the TAC1 coding region containing the FNP in the japonica rice group. However, no selection occurred in the indica and wild-rice groups. A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose indepen- dently during the domestication of wild rice.

关键词： Diversity Evolution Rice Sequence TAC1

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Polyamine oxidase 3 is involved in salt tolerance at the germination stage in rice

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Journal of Genetics and Genomics 2022年第5期49卷 458-468页

作者： Guangyu Liu Wanxia Jiang Lei Tian yongcai fu Lubin Tan Zuofeng Zhu Chuanqing Sun Fengxia Liu State Key Laboratory of Plant Physiology and Biochemistry China Agricultural UniversityBeijing 100193China National Center for Evaluation of Agricultural Wild Plants(Rice) Beijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Soil salinity inhibits seed germination and reduces seedling survival rate,resulting in significant yield reductions in ***,we report the identification of a polyamine oxidase,OsPAO3,conferring salt tolerance at the germination stage in rice(Oryza sativa L.),through map-based cloning ***3 is up-regulated under salt stress at the germination stage and highly expressed in various *** of OsPAO3 increases activity of polyamine oxidases,enhancing the polyamine content in seed *** polyamine may lead to the enhance of the activity of ROS-scavenging enzymes to eliminate over-accumulated H;O;and to reduce Na;content in seed coleoptiles to maintain ion homeostasis and weaken Na;*** changes resulted in stronger salt tolerance at the germination stage in *** findings not only provide a unique gene for breeding new salt-tolerant rice cultivars but also help to elucidate the mechanism of salt tolerance in rice.

关键词： Polyamine oxidase OsPAO3 Salt tolerance Germination stage Rice

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GS6, A Member of the GRAS Gene Family,Negatively Regulates Grain Size in Rice

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Journal of Integrative Plant Biology 2013年第10期55卷 938-949页

作者： Lianjun Sun Xiaojiao Li yongcai fu Zuofeng Zhu Lubin Tan Fengxia Liu Xianyou Sun Xuewen Sun Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry National Center for Evaluation of Agricultural Wild Plants (Rice) MOE Key Laboratory of Crop Heterosis and Utilization Key Laboratory of Crop Genetic Improvement Department of Plant Genetics and Breeding China Agricultural University State Key Laboratory of Plant Physiology and Biochemistry National Center for Evaluation of Agricultural Wild Plants(Rice) MOE Key Laboratory of Crop Heterosis and Utilization Key Laboratory of Crop Genetic Improvement Department of Plant Genetics and Breeding China Agricultural University

Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today＇s cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 （GS6）, which plays an important role in reducing grain size in rice. A premature stop at the ＋348 position in the coding sequence （CDS） of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties （95%） harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a ＂ggc＂ repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.

关键词： Domestication GS6 , grain size haplotype Oryza sativa rice.

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Microarray-Assisted Fine-Mapping of Quantitative Trait Loci for Cold Tolerance in Rice

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Molecular Plant 2013年第3期6卷 757-767页

作者： Fengxia Liu Wenying Xu Qian Song Lubin Tan Jiayong Liu Zuofeng zhu yongcai fu Zhen Su Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry National Center for Evaluation of Agricultural Wild Plants (Rice) Coordinated Research Center for Crop Biology Key Laboratory of Crop Heterosis and Utilization of Ministry of Education Beijing Key Laboratory of Crop Genetic Improvement Department of Plant Genetics and Breeding China Agricultural University Beijing 100193 China State Key Laboratory of Plant Physiology and Biochemistry College of Biological Sciences China Agricultural University Beijing 100193 China

Many important agronomic traits, including cold stress resistance, are complex and controlled by quantitative trait loci （QTLs）. Isolation of these QTLs will greatly benefit the agricultural industry but it is a challenging task. This study explored an integrated strategy by combining microarray with QTL-mapping in order to identify cold-tolerant QTLs from a cold-tolerant variety ILl12 at early-seedling stage. All the early seedlings of IL112 survived normally for 9 d at 4-5℃, while Guichao2 （GC2）, an indica cultivar, died after 4 d under the same conditions. Using the F2-3 population derived from the progeny of GC2 and ILl12, we identified seven QTLs for cold tolerance. furthermore, we performed Affymetrix rice whole-genome array hybridization and obtained the expression profiles of ILl12 and GC2 under both low-temperature and normal conditions. Four genes were selected as cold QTL-related candidates, based on microarray data mining and QTL-mapping. One candidate gene, LOC_Os07g22494, was shown to be highly associated with cold tolerance in a number of rice varieties and in the F2-3 population, and its overexpression transgenic rice plants displayed strong tolerance to low temperature at early-seedling stage. The results indicated that overexpression of this gene （LOC_Os07g22494） could increase cold tolerance in rice seedlings. Therefore, this study provides a promising strategy for identifying candidate genes in defined QTL regions.

关键词： QTL fine-mapping cold tolerance rice.

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Additive and Over-dominant Effects Resulting from Epistatic Loci Are the Primary Genetic Basis of Heterosis in Rice

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Journal of Integrative Plant Biology 2009年第4期51卷 393-408页

作者： Xiaojin Luo yongcai fu Peijiang Zhang Shuang Wu Feng Tian Jiayong Liu Zuofeng Zhu Jinshui Yang Chuanqing Sun Department of Plant Genetics and Breeding and State Key Laboratory of Plant Physiology and Biochemistry China Agricultural University Beijing 100193 China National Centre for Evaluation of Agricultural Wild Plant (Rice) Beijing 100193 China Beijing Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture Beijing 100193 China State Key Laboratory of Genetic Engineenng Morgan-Tan Intemational Center for Life Sciences School of Life Sciences Fudan University Shanghai 200433 China Institute of Rice Research Anhui Academy of Agricultural Sciences Hefei 230031 China

A set of 148 F9 recombinant inbred lines （RILs） was developed from the cross of an indica cultivar 93-11 and japonica cultivar DTI13, showing strong F1 heterosis. Subsequently, two backcross F1 （BCFI） populations were constructed by backcrossing these 148 RILs to two parents, 93-11 and DT713. These three related populations （281BCF1 lines, 148 RILs） were phenotyped for six yield-related traits in two locations. Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations. A total of 42 main-effect quantitative trait loci （M-QTLs） and 109 epistatic effect QTL pairs （E-QTLs） were detected in the three related populations using the mixed model approach. By comparing the genetic effects of these QTLs detected in the RILs, BCF1 performance and mid-parental heterosis （HMp）, we found that, in both BCF1 populations, the QTLs detected could be classified into two predominant types： additive and over-dominant loci, which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs. further, we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations. All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.

关键词： additivity epistasis heterosis over-dominance quantitative trait locus.

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Identification and mapping of genes for improving yield from Chinese common wild rice (*** Griff.) using advanced backcross QTL analysis

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Chinese Science Bulletin 2002年第18期47卷 1533-1537页

作者： Dejun Li Chuanqing Sun yongcai fu Cheng Li Zuofeng Zhu Liang Chen Hongwei Cai Xiangkun Wang China Agr Univ Dept Genet & Plant Breeding Beijing 100094 Peoples R China

To identify useful genes from wild rice which have been lost or weakened in cultivated rice has become more and more important for modern breeding strategy. In this study, a BC4 population derived from 94W1, an accession of common wild rice (Oryza rufipogon Griff.) from Dongxiang in Jiangxi Province of China, as the donor, and a high-yielding Indica cultivar (O. sativa L.), 'Guichao 2', as the recipient, was used to identify quantitative trait loci (QTL) associated with yield and its components. Based on the analysis for the genotype of BC4F1 population with 87 SSR markers distributed throughout the genome and investigation of the plant height, yield and yield components of BC4F2, a total of 52 QTLs, were detected. Of 7 QTLs associated with grain yield per plant, 2 QTLs on chromosome 2 and chromosome 11 for grain yield, explaining 16% and 11% of the phenotypic variance respectively, were identified. The alleles from Dongxiang common wild rice in those two loci could increase the yield of 'Guichao 2' by

关键词： common wild rice yield yield components mapping AB-QTL.

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LHD1,an Allele of DTH8/Ghd8,Controls Late Heading Date in Common Wild Rice (Oryza rufipogon)

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Journal of Integrative Plant Biology 2012年第10期54卷 790-799页

作者： Xiaodong Dai Younian Ding Lubin Tan yongcai fu Fengxia Liu Zuofeng Zhu Xianyou Sun Xuewen Sun Ping Gu Hongwei Cai Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry National Evaluation Centre for Agricultural Wild Plants(Rice)Laboratory ofCrop Heterosis and Utilization of the Ministry of EducationBeijing Key Laboratory of Crop Genetic ImprovementDepartment of PlantGenetics and BreedingChina Agricultural UniversityBeijing 100193China

Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice （Oryza rufipogon Griff.） photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci （QTL） LHD1 （Late Heading Date 1）, an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehdl, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehdl, Hd3a and RFT1 under long-day conditions.

关键词： Rice LHD1 heading date CCAAT-box-binding transcription factor.

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Natural Variations at TIG1 Encoding a TCP Tran scription Factor Contribute to Plant Architecture Domestication in Rice

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Molecular Plant 2019年第8期12卷 1075-1089页

作者： Weifeng Zhang Lubin Tan Hongying Sun Xinhui Zhao Fengxia Liu Hongwei Cai yongcai fu Xianyou Sun Ping Gu Zuofeng Zhu Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry China Agricultural UniversityBeijing 100193China

The modification of plant architecture is a crucial target in rice domestication and modern genetic *** several genes regulating rice plant architecture have been characterized,the molecular mechanisms underlying rice plant architecture domestication remain largely *** we show that the inclined tiller growth in wild rice is controlled by a single dominant gene,TILLER INCLINED GROWTH 1 (T/Gf),which is located on chromosome 8 and encodes a TCP transcriptional ***1 is primarily expressed in the adaxial side of the tiller base,promotes cell elongation,and enlarges the tiller angle in wild *** in the TIG1 promoter of indica cultivars {tig1 allele) resulted in decreased expression of TIG1 in the adaxial side of tiller base and reduced cell length and tiller angle,leading to the transition from inclined tiller growth in wild rice to erect tiller growth during rice ***1 positively regulates the expression of EXP A3,EXPB5,and SAUR39 to promote cell elongation and increase the tiller *** sweep analysis revealed that the tig1 allele was selected in indica cultivars by human *** cloning and characterization of TIG1 supports a new scenario of plant architecture evolution in rice.

关键词： rice plant architecture tiller angle inclined growth domestication

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Rice transformation with a senescence-inhibition chimeric gene

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Chinese Science Bulletin 1998年第21期43卷 1810-1815页

作者： yongcai fu Yueyun Ding Xinfang Liu Chuanqin Sun Souyun Cao Dongjiang Wang Sijie He Xiangkun Wang Liangcai Li Wenzhong Tian Chinese Acad Sci Genet Inst Beijing 100101 Peoples R China China Agr Univ Beijing 100094 Peoples R China

A senescence-inhibition chimeric gene containing the specific promoter of SAG 12 and IPT gene was transferred into rice with the biolistic method. Results of PCR, Dot blotting and Southern blotting indicated that the chimeric gene had been integrated into rice genome. Analyses of GUS activity and cytokinin content in transgenic plants of rice and the observation of T 1 generation plant at grain formation stage indicated that the foreign gene was expressed.

关键词： rice specific promoter IPT gene senescence-inhibition biolistic transformation.

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