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(67...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.展开更多
LncPheDB(https://www.lncphedb.com/)is a systematic resource of genome-wide long non-coding RNAs(lncRNAs)-phenotypes associations for multiple species.It was established to display the genome-wide lncRNA annotations,ta...LncPheDB(https://www.lncphedb.com/)is a systematic resource of genome-wide long non-coding RNAs(lncRNAs)-phenotypes associations for multiple species.It was established to display the genome-wide lncRNA annotations,target genes prediction,variant-trait associations,gene-phenotype correlations,lncRNA-phenotype correlations,and the similar non-coding regions of the queried sequence in multiple species.LncPheDB sorted out a total of 203,391 lncRNA sequences,2000 phenotypes,and 120,271 variants of nine species(Zea mays L.,Gossypium barbadense L.,Triticum aestivum L.,Lycopersicon esculentum Mille,Oryza sativa L.,Hordeum vulgare L.,Sorghum bicolor L.,Glycine max L.,and Cucumis sativus L.).By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis,a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits.More importantly,to facilitate the study of the functions of lncRNAs,we analyzed the possible target genes of lncRNAs,constructed a blast tool for performing similar fragmentation studies in all species,linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks.In addition,LncPheDB also provides a user-friendly interface,a genome visualization platform,and multi-level and multi-modal convenient data search engine.We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data.展开更多
基金supported by the National Key Research and Development Program of China(2016YFD0100301 to Z.X.M.)the National Natural Science Foundation of China(31670211 and31970237 to Z.X.M.)+3 种基金Sanya Yazhou Bay Science and Technology City(SKJC-2020-02-001 to Z.X.M.)the Central Public-interest Scientific Institution Basal Research Fund(S2021ZD01 to Z.X.M.)the Major Incubation Project of Shenyang Normal University(ZD20210 to P.H.B.)the Hundred Talent Program of Shenyang Normal University(SSDBRJH2002012 to P.H.B.)。
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.
基金supported by the National Key Research and Development Program of China(2021YFD1200101 to Z.X.M.)the National Natural Science Foundation of China(31670211 and 31970237 to Z.X.M.)+1 种基金Sanya Yazhou Bay Science and Technology City(SKJC-2020–02-001 to Z.X.M.)the Central Public-interest Scientific Institution Basal Research Fund(S2021ZD01 to Z.X.M.).
文摘LncPheDB(https://www.lncphedb.com/)is a systematic resource of genome-wide long non-coding RNAs(lncRNAs)-phenotypes associations for multiple species.It was established to display the genome-wide lncRNA annotations,target genes prediction,variant-trait associations,gene-phenotype correlations,lncRNA-phenotype correlations,and the similar non-coding regions of the queried sequence in multiple species.LncPheDB sorted out a total of 203,391 lncRNA sequences,2000 phenotypes,and 120,271 variants of nine species(Zea mays L.,Gossypium barbadense L.,Triticum aestivum L.,Lycopersicon esculentum Mille,Oryza sativa L.,Hordeum vulgare L.,Sorghum bicolor L.,Glycine max L.,and Cucumis sativus L.).By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis,a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits.More importantly,to facilitate the study of the functions of lncRNAs,we analyzed the possible target genes of lncRNAs,constructed a blast tool for performing similar fragmentation studies in all species,linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks.In addition,LncPheDB also provides a user-friendly interface,a genome visualization platform,and multi-level and multi-modal convenient data search engine.We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data.
