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| 1 | Dissection of heterosis for yield and related traits using populations derived from introgression lines in rice显示文摘Despite the great success achieved by the exploitation of heterosis in rice,the genetic basis of heterosis is still not well understood.We adopted an advanced-backcross breeding strategy to dissect the genetic basis of heterosis for yield and eight related traits.Four testcross(TC) populations with 228 testcross F1 combinations were developed by crossing57 introgression lines with four types of widely used male sterile lines using a North Carolina II mating design.Analysis of variance indicated that the effects of testcross F1 combinations and their parents were significant or highly significant for most of the traits in both years,and all interaction effects with year were significant for most of the traits.Positive midparent heterosis(HMP) was observed for most traits in the four TC populations in the two years.The relative HMPlevels for most traits varied from highly negative to highly positive.Sixty-two dominant-effect QTL were identified for HMPof the nine traits in the four TC populations in the two years.Of these,22 QTL were also identified for the performance of testcross F1.Most dominant-effect QTL could individually explain more than 10% of the phenotypic variation.Four QTL clusters were observed including the region surrounding the RM9–RM297 region on chromosome 1,the RM110–RM279–RM8–RM5699–RM452 region on chromosome 2,the RM5463 locus on chromosome 6 and the RM1146–RM147 region on chromosome 10.The identified QTL for heterosis provide valuable information for dissecting the genetic basis of heterosis. | Chao Xiang Hongjun Zhang Hui Wang Shaobo Wei Binying Fu Jiafa Xia Zefu Li Yongming Gao Guoyou Ye | 2016 | The Crop Journal2016，4，6： | 3 |
| 2 | Progress on Molecular Mechanism of Aluminum Resistance in Rice显示文摘Aluminum(Al)toxicity in acid soils is a significant limitation to crop production worldwide,as 13%of the world's rice is produced in acid soil with high Al content.Rice is likely the most Al-resistant cereal and also the cereal,where Al resistance is the most genetically complex with external detoxification and internal tolerance.Many Al-resistance genes in rice have been cloned,including Al resistance transcription factor 1(ART1)and other transcription factors,organic acid transporter genes,and metal ion transporter gene.This review summarized the recent characterized genes affecting Al tolerance in rice and the interrelationships between Al and other plant nutrients. | Chen Jingguang Lai Qi Zeng Baiquan Guo Longbiao Ye Guoyou | 2020 | Rice science2020，27，6： | 3 |
| 3 | Understanding divergent domestication traits from the whole-genome sequencing of swamp-and river-buffalo populations显示文摘Domesticated buffaloes have been integral to rice-paddy agro-ecosystems formillennia,yet relatively little is known about the buffalo genomics.Here,we sequenced and assembled reference genomes for both swamp and river buffaloes and we re-sequenced 230 individuals(132 swamp buffaloes and 98 river buffaloes)sampled from across Asia and Europe.Beyond the many actionable insights that our study revealed about the domestication,basic physiology and breeding of buffalo,we made the striking discovery that the divergent domestication traits between swamp and river buffaloes can be explained with recent selections of genes on social behavior,digestion metabolism,strengths and milk production. | Xier Luo Yu Zhou Bing Zhang Yi Zhang Xiaobo Wang Tong Feng Zhipeng Li Kuiqing Cui Zhiqiang Wang Chan Luo Hui Li Yanfei Deng Fenghua Lu Jianlin Han Yongwang Miao Huaming Mao Xiaoyan Yi Cheng Ai Shigang Wu Alun Li Zhichao Wu Zijun Zhuo Do Da Giang Bikash Mitra Mohammad Farhad Vahidi Shahid Mansoor Sahar Ahmed Al-Bayatti Eka Meutia Sari Neena Amatya Gorkhali Sigit Prastowo Laiba Shafique Guoyou Ye Qian Qian Baoshan Chen Deshun Shi Jue Ruan Qingyou Liu | 2020 | National Science Review2020，7，3： | 3 |
| 4 | Rice Heavy Metal P-type ATPase OsHMA6 Is Likely a Copper Efflux Protein显示文摘P1B-type heavy metal ATPases(HMAs)are transmembrane metal-transporting proteins that play a key role in metal homeostasis.We here reported the characterization of rice OsHMA6,a member of the P1B-type ATPase family.Phylogenetic tree analysis showed that OsHMA6 belonged to the Cu/Ag subgroup of the HMA family and had a close evolutionary relationship with OsHMA9.Amino acid sequence alignment showed 82.78%consistency between OsHMA6 and OsHMA9.OsHMA6 expressed in all organs at different growth stages,including spikelet,and abundant in leaf blades,however,OsHMA9 most strongly expressed in roots,but very low in spikelet.Excessive Cu^2+can up-regulate the expression of OsHMA6 and OsHMA9 in rice seedlings.The heterologous expression in yeast showed that OsHMA6 can significantly rescue the growth of yeast strain CM52 when supplied with 3 or 6 mmol/L Cu^2+.Compared with the empty vector pYES2,the Cu concentration in OsHMA6-pYES2 decreased by 23.4%and 30.3%under 3 or 6 mmol/L Cu2+,respectively.Subcellular localization revealed that OsHMA6 was located in the plasma membrane.These results suggested that OsHMA6,similar to OsHMA9,is likely a copper efflux protein located in the plasma membrane. | ZOU Wenli LI Chang ZHU Yajun CHEN Jingguang HE Haohua YE Guoyou | 2020 | Rice science2020，27，2： | 2 |
| 5 | 结合QTL-seq和连锁分析发掘水稻中胚轴伸长相关QTL显示文摘中胚轴长度(mesocotyl length, ML)是影响旱直播水稻出苗和早期幼苗活力的重要性状。发掘中胚轴伸长相关位点,解析其遗传机制,选育长中胚轴品种是促进旱直播技术推广最为经济和有效的方式。本研究以长中胚轴品种‘Changai’和短中胚轴品种‘IR 145’为亲本构建的F_2遗传分离群体为材料,构建长池和短池并开展深度重测序(50×)。利用Δ(SNP-index)和G-value两种方法在3号染色体29.56~33.28 Mb处鉴定到1个中胚轴伸长相关位点qML3。在候选区域开发KASP标记,对184个F_2株系开展连锁分析,将候选区间缩小到28.89~31.03Mb。结合基因注释、连锁分析和基因表达分析结果,推测LOC_Os03g52450、LOC_Os03g56060、LOC_Os03g58290、LOC_Os03g58300、LOC_Os03g58320、LOC_Os03g56050和LOC_Os03g57640为候选基因。这些基因分别与植物激素的调控和细胞分裂相关机制有关。本研究发掘了一个水稻中胚轴伸长相关位点,对选育长中胚轴品种有一定帮助。 | 刘畅 孟云 刘金栋 王雅美 Guoyou Ye | 2021 | 作物学报2021，47，10： | 2 |
| 6 | Effect of introducing Bacillus thuringiensis gene on nitrogen metabolism in cotton显示文摘 | CHEN Dehua Ye Guoyou Yang Changqin | 2004 | Field Crops Research2004，87，4： | 1 |
| 7 | Chemoattractive effect on the effector cells of the supernatants from melanoma cells transfected with the interleukin-2 (IL-2), IL-4 or IL-6 gene显示文摘 | Xuetao Cao Guoyou Chen Long He Weiping Zhang Yizhi Yu TianXing Ye | 1998 | Journal of Cancer Research and Clinical Oncology1998，，2： | 1 |
| 8 | Pattern analysis on grain yield performance of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT显示文摘 | Yong Zhang Zhonghu He Aimin Zhang Maarten Ginkel Guoyou Ye | 2006 | Euphytica2006，，3： | 1 |
| 9 | Pattern analysis on grain yield performance of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT显示文摘 | Yong Zhang Zhonghu He Aimin Zhang Maarten Ginkel Guoyou Ye | 2006 | Euphytica2006，，3： | 1 |
| 10 | Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy 显示文摘 | Haydn Kuchel Guoyou Ye Rebecca Fox | 2005 | Molecular Breeding2005，16，： | 1 |
| 11 | Chaperone-mediated Autophagy Regulates Cell Growth by Targeting SMAD3 in Glioma显示文摘Previous studies suggest that the reduction of SMAD3(mothers against decapentaplegic homolog 3)has a great impact on tumor development,but its exact pathological function remains unclear.In this study,we found that the protein level of SMAD3 was greatly reduced in human-grade IV glioblastoma tissues,in which LAMP2A(lysosome-associated membrane protein type 2A)was significantly up-regulated.LAMP2A is a key ratelimiting protein of chaperone-mediated autophagy(CMA),a lysosome pathway of protein degradation that is activated in glioma.We carefully analyzed the amino-acid sequence of SMAD3 and found that it contained a pentapeptide motif biochemically related to KFERQ,which has been proposed to be a targeting sequence for CMA.In vitro,we confirmed that SMAD3 was degraded in either serum-free or KFERQ motif deleted condition,which was regulated by LAMP2A and interacted with HSC70(heat shock cognate 71 kDa protein).Using isolated lysosomes,amino-acid residues 75 and 128 of SMAD3 were found to be of importance for this process,which affected the CMA pathway in which SMAD3 was involved.Similarly,down-regulating SMAD3 or up-regulating LAMP2A in cultured glioma cells enhanced their proliferation and invasion.Taken together,these results suggest that excessive activation of CMA regulates glioma cell growth by promoting the degradation of SMAD3.Therefore,targeting the SMAD3-LAMP2Amediated CMA-lysosome pathway may be a promising approach in anti-cancer therapy. | Hanqun Liu Yuxuan Yong Xingjian Li Panghai Ye Kai Tao Guoyou Peng Mingshu Mo Wenyuan Guo Xiang Chen Yangfu Luo Yuwan Lin Jiewen Qiu Ziling Zhang Liuyan Ding Miaomiao Zhou Xinling Yang Lin Lu Qian Yang Pingyi Xu | 2022 | Neuroscience Bulletin2022，38，6： | 0 |
| 12 | Identification of Potential Zinc Deficiency Responsive Genes and Regulatory Pathways in Rice by Weighted Gene Co-expression Network Analysis显示文摘Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties.Here,a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis(WGCNA)and other in silico prediction tools to identify modules(denoting cluster of genes with related expression pattern)of co-expressed genes,modular genes which are conserved differentially expressed genes(DEGs)across independent RNA-Seq studies,and the molecular pathways of the conserved modular DEGs.WGCNA identified 16 modules of co-expressed genes.Twenty-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq studies.Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways and 15 Gene Ontology(GO)terms,including the substrate-specific transmembrane transporter and the small molecule metabolic process.Further,the well-studied transcription factors(OsWOX11 and OsbHLH120),protein kinase(OsCDPK20 and OsMPK17),and miRNAs(OSA-MIR397A and OSA-MIR397B)were predicted to target some of the identified conserved modular DEGs.Out of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive genes.Findings from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice. | Blaise Pascal MUVUNYI LU Xiang ZHAN Junhui HE Sang YE Guoyou | 2022 | Rice science2022，29，6： | 0 |
| 13 | Genomic prediction using composite training sets is an effective method for exploiting germplasm conserved in rice gene banks显示文摘Germplasm conserved in gene banks is underutilized,owing mainly to the cost of characterization.Genomic prediction can be applied to predict the genetic merit of germplasm.Germplasm utilization could be greatly accelerated if prediction accuracy were sufficiently high with a training population of practical size.Large-scale resequencing projects in rice have generated high quality genome-wide variation information for many diverse accessions,making it possible to investigate the potential of genomic prediction in rice germplasm management and exploitation.We phenotyped six traits in nearly 2000 indica(XI)and japonica(GJ)accessions from the Rice 3K project and investigated different scenarios for forming training populations.A composite core training set was considered in two levels which targets used for prediction of subpopulations within subspecies or prediction across subspecies.Composite training sets incorporating 400 or 200 accessions from either subpopulation of XI or GJ showed satisfactory prediction accuracy.A composite training set of 600 XI and GJ accessions showed sufficiently high prediction accuracy for both XI and GJ subspecies.Comparable or even higher prediction accuracy was observed for the composite training set than for the corresponding homogeneous training sets comprising accessions only of specific subpopulations of XI or GJ(within-subspecies level)or pure XI or GJ accessions(across-subspecies level)that were included in the composite training set.Validation using an independent population of 281 rice cultivars supported the predictive ability of the composite training set.Reliability,which reflects the robustness of a training set,was markedly higher for the composite training set than for the corresponding homogeneous training sets.A core training set formed from diverse accessions could accurately predict the genetic merit of rice germplasm. | Sang He Hongyan Liu Junhui Zhan Yun Meng Yamei Wang Feng Wang Guoyou Ye | 2022 | The Crop Journal2022，10，4： | 0 |
| 14 | Genome-wide selection and introgression of Chinese rice varieties during breeding显示文摘China is the largest rice-producing country,but the genomic landscape of rice diversity has not yet been clarified.In this study,we re-sequence 1070 rice varieties collected from China(400)and other regions in Asia(670).Among the six major rice groups(aus,indica-I,indica-II,aromatic,temperate japonica,and tropical japonica),almost all Chinese varieties belong to the indica-II or temperate japonica group.Most Chinese indica varieties belong to indica-II,which consists of two subgroups developed during different phases of rice breeding.The genomic segments underlying the differences between these subgroups span36.32 Mb.The Chinese japonica rice varieties fall into the temperate japonica group,consisting of two subgroups based on their geographical distribution.The genomic segments underlying the differences between these subgroups span 27.69 Mb.These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width.Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups.These findings provide new insights into rice diversity in China that will facilitate the molecular breeding. | Jinyue Ge Junrui Wang Hongbo Pang Fei Li Danjing Lou Weiya Fan Ziran Liu Jiaqi Li Danting Li Baoxuan Nong Zongqiong Zhang Yanyan Wang Jingfen Huang Meng Xing Yamin Nie Xiaorong Xiao Fan Zhang Wensheng Wang Jianlong Xu Sung Ryul Kim Ajay Kohli Guoyou Ye Weihua Qiao Qingwen Yang Xiaoming Zheng | 2022 | Journal of Genetics and Genomics2022，49，5： | 0 |
| 15 | Identification of QTLs for Cadmium Tolerance During Seedling Stage and Validation of qCDSL1 in Rice显示文摘Cadmium(Cd)is a non-essential toxic metal that is harmful to plants.To investigate the genetic mechanism of Cd tolerance in rice,quantitative trait loci(QTLs)associated with Cd tolerance at the seedling stage were analyzed using a recombinant inbred line(RIL)population derived from a cross between PA64s and 93-11.A total of 36 QTLs associated with shoot length,root length,shoot dry weight,root dry weight and total dry weight were detected in Hangzhou and Lingshui of China.Among them,15 QTLs were identified under the control condition and 15 QTLs were identified under the Cd stress condition,and 6 QTLs for Cd tolerant coefficient were detected on chromosomes 1,3,7 and 9.The qCDSL1.1 and qCDSL1.2 were identified in Hangzhou and Lingshui,respectively,and had overlapping intervals on chromosome 1.To further confirm the effects of qCDSL1.1 and qCDSL1.2,we developed a chromosome segment substitution line(CSSL),CSSLqCDSL1,in 93-11 background harboring qCDSL1.1/qCDSL1.2 from PA64s.Compared to 93-11,CSSLqCDSL1 had increased shoot length under the Cd stress condition.These results pave the way for further isolation of those genes controlling Cd tolerance in rice and marker-assistant selection of rice elite varieties with Cd tolerance. | Ding Shilin Liu Chaolei Shang Lianguang Yang Shenglong Zhang Anpeng Jiang Hongzhen Ruan Banpu Fang Guonan Tian Biao Ye Guoyou Guo Longbiao Qian Qian Gao Zhenyu | 2021 | Rice science2021，28，1： | 0 |
| 16 | CHCHD2 Thr61Ile mutation impairs F1F0-ATPase assembly in in vitro and in vivo models of Parkinson's disease显示文摘Mitochondrial dysfunction is a significant pathological alte ration that occurs in Parkinson's disease(PD),and the Thr61lle(T61I)mutation in coiled-coil helix coiled-coil helix domain containing 2(CHCHD2),a crucial mitochondrial protein,has been reported to cause Parkinson's disease.FIFO-ATPase participates in the synthesis of cellular adenosine triphosphate(ATP)and plays a central role in mitochondrial energy metabolism.However,the specific roles of wild-type(WT)CHCHD2 and T611-mutant CHCHD2 in regulating F1FO-ATPase activity in Parkinson's disease,as well as whether CHCHD2 or CHCHD2 T61I affects mitochondrial function through regulating F1FO-ATPase activity,remain unclea r.Therefore,in this study,we expressed WT CHCHD2 and T61l-mutant CHCHD2 in an MPP^(+)-induced SH-SY5Y cell model of PD.We found that CHCHD2 protected mitochondria from developing MPP^(+)-induced dysfunction.Under normal conditions,ove rexpression of WT CHCHD2 promoted F1FO-ATPase assembly,while T61I-mutant CHCHD2 appeared to have lost the ability to regulate F1FO-ATPase assembly.In addition,mass spectrometry and immunoprecipitation showed that there was an interaction between CHCHD2 and F1FO-ATPase.Three weeks after transfection with AAV-CHCHD2 T61I,we intraperitoneally injected 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine into mice to establish an animal model of chronic Parkinson's disease and found that exogenous expression of the mutant protein worsened the behavioral deficits and dopaminergic neurodegeneration seen in this model.These findings suggest that WT CHCHD2 can alleviate mitochondrial dysfunction in PD by maintaining F1F0-ATPase structure and function. | Xiang Chen Yuwan Lin Zhiling Zhang Yuting Tang Panghai Ye Wei Dai Wenlong Zhang Hanqun Liu Guoyou Peng Shuxuan Huang Jiewen Qiu Wenyuan Guo Xiaoqin Zhu Zhuohua Wu Yaoyun Kuang Pingyi Xu Miaomiao Zhou | 2024 | Neural Regeneration Research2024，19，1： | 0 |
| 17 | Genome-Wide Association Study for Milled Grain Appearance Traits Using Multi-Parent Advanced Generation Intercross Population in Rice显示文摘The identification of loci and markers associated with milled grain appearance traits is essential for breeding high-yielding and good-quality rice variety.To detect stable loci for these characteristics,grain length(GL),grain width(GW),grain length/width(GLW),chalkiness degree(CD),chalky-grain rate(CR)and translucency degree(TD)of 378 rice lines were evaluated in three seasons.These lines were derived from a multi-parent advanced generation intercross(MAGIC)population. | LI Xiaoxiang LIU Jindong GUO Liang WEI Xiucai WANG Yamei PAN Xiaowu DONG Zheng LIU Wenqiang LIU Licheng MIN Jun LIU Sanxiong YE Guoyou LI Yongchao | 2023 | Rice science2023，30，5： | 0 |
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