The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we repo...The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we report the cloning and characterization of OsNPF3.1,a gene that controls rice NUE.An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice.OsNPF3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain weight.The OsNPF3.1 protein is located in the plasma membrane.When OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica rice.OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.展开更多
Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identi...Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.展开更多
Rice has different colors of pericarp, such as red, white and black. Red rice pericarp is rich in proanthocyanins, which have antioxidant properties and are beneficial to human health. In the present study, we analyze...Rice has different colors of pericarp, such as red, white and black. Red rice pericarp is rich in proanthocyanins, which have antioxidant properties and are beneficial to human health. In the present study, we analyzed the red-pericarp gene Rc of 419 rice landraces in Guangxi by genome-wide association study （GWAS）, and validated that the Rc gene regulated the red periearp trait in flee. By analyzing the genomie DNA of 97 red-pericarp flee eultivars, we identified two new alleles in C139 and C323. Then, the exons of Rcc＇9 and Rcc were sequenced with Sanger method, and the results demonstrated that the natural mutations within Re ene resulted in the two alleles Rcc and Rcc.展开更多
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
基金supported by the National Natural Science Foundation of China(32060476 and 31860371)Guangxi Department of Science and Technology(AA22068087-4)+3 种基金Guangxi Natural Science Foundation of China(2015GXNSFAA139054,2018GXNSFAA138124,and 2020GXNSFAA259041)Guangxi Ministry of Science and Technology(AB21238009)Special Fund of Local Science and Technology Development for the Central Guidance(ZY21195034)Guangxi Academy of Agricultural Sciences(2021JM04,2021JM49,2021YT030,QN-25,and QN-35)。
文摘The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we report the cloning and characterization of OsNPF3.1,a gene that controls rice NUE.An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice.OsNPF3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain weight.The OsNPF3.1 protein is located in the plasma membrane.When OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica rice.OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.
基金supported by the National Natural Science Foundation of China(31760428,31860371,and 32060476)Guangxi Natural Science Foundation of China(2020GXNSFAA259041)+1 种基金Guangxi Science and Technology Project(Guike AB21238009)Guangxi Academy of Agricultural Sciences Foundation(2021JM04,JM49,YT030,QN-11,14,20,29,and 35).
文摘Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.
基金Supported by The National Key Research and Development Program of China(2016YFD0100101-03)Science Research and Technology Development Program of Guangxi(AB16380117)+1 种基金the Fund for Talent Team of Guangxi Academy of Agricultural Sciences(2015YT15)the Special Fund for Basic Science Research of Guangxi Academy of Agricultural Sciences(2015JZ16,2015JZ17,2017YM18)
文摘Rice has different colors of pericarp, such as red, white and black. Red rice pericarp is rich in proanthocyanins, which have antioxidant properties and are beneficial to human health. In the present study, we analyzed the red-pericarp gene Rc of 419 rice landraces in Guangxi by genome-wide association study （GWAS）, and validated that the Rc gene regulated the red periearp trait in flee. By analyzing the genomie DNA of 97 red-pericarp flee eultivars, we identified two new alleles in C139 and C323. Then, the exons of Rcc＇9 and Rcc were sequenced with Sanger method, and the results demonstrated that the natural mutations within Re ene resulted in the two alleles Rcc and Rcc.
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.
