Reproductive transition of grasses is characterized by switching the pattern of lateral branches,featuring the suppression of outgrowth of the subtending leaves(bracts)and rapid formation of higher-order branches in t...Reproductive transition of grasses is characterized by switching the pattern of lateral branches,featuring the suppression of outgrowth of the subtending leaves(bracts)and rapid formation of higher-order branches in the inflorescence(panicle).However,the molecular mechanisms underlying such changes remain largely unknown.Here,we show that bract suppression is required for the reproductive branching in rice.We identified a pathway involving the intrinsic time ruler microRNAI56/529,their targets SQUAMOSA PROMOTER BINDING PROTEIN LIKE(SPL)genes,NECK LEAF1(NL1),and PLASTOCHRON1(PLA1),which regulates the bract outgrowth and thus affects the pattern switch between vegetative and reproductive branching.Suppression of the bract results in global reprogramming of transcriptome and chromatin accessibility following the reproductive transition,while these processes are largely dysregu-lated in the mutants of these genes.These discoveries contribute to our understanding of the dynamic plant architecture and provide novel insights for improving crop yields.展开更多
Three-dimensional(3D)phenotyping is important for studying plant structure and function.Light detection and ranging(LiDAR)has gained prominence in 3D plant phenotyping due to its ability to collect 3D point clouds.How...Three-dimensional(3D)phenotyping is important for studying plant structure and function.Light detection and ranging(LiDAR)has gained prominence in 3D plant phenotyping due to its ability to collect 3D point clouds.However,organ-level branch detection remains challenging due to small targets,sparse points,and low signal-to-noise ratios.In addition,extracting biologically relevant angle traits is difficult.In this study,we developed a stratified,clustered,and growing-based algorithm(SCAG)for soybean branch detection and branch angle calculation from LiDAR data,which is heuristic,open-source,and expandable.SCAG achieved high branch detection accuracy(F-score=0.77)and branch angle calculation accuracy(r=0.84)when evaluated on 152 diverse soybean varieties.Meanwhile,the SCAG outperformed 2 other classic algorithms,the support vector machine(F-score=0.53)and density-based methods(F-score=0.55).Moreover,after applying the SCAG to 405 soybean varieties over 2 consecutive years,we quantified various 3D traits,including canopy width,height,stem length,and average angle.After data filtering,we identified novel heritable and repeatable traits for evaluating soybean density tolerance potential,such as the ratio of average angle to height and the ratio of average angle to stem length,which showed greater potential than the well-known ratio of canopy width to height trait.Our work demonstrates remarkable advances in 3D phenotyping and plant architecture screening.The algorithm can be applied to other crops,such as maize and tomato.Our dataset,scripts,and software are public,which can further benefit the plant science community by enhancing plant architecture characterization and ideal variety selection.展开更多
Branch angle is an important plant architecture trait and is considerably important for the ideal plant architecture of high density cultivation of rapeseed. In this study,12 representative rapeseed lines were first m...Branch angle is an important plant architecture trait and is considerably important for the ideal plant architecture of high density cultivation of rapeseed. In this study,12 representative rapeseed lines were first measured for whole-plant branch angles using image processing technology. Top branch angle (TBA) and basal branch angle (BBA) were significantly different in each line in which TBA was greater than BBA. Then, 156 rapeseed germplasm lines were evaluated for TBA and BBA in main cultivated regions of the Yangtze River Basin (Zunyi; Wuhan; Lu'an). In these three environments, the TBA and BBA of the rapeseed germplasm sources varied, in which ranges of 33.44°-73.17°and 18.73°-59.11°, 29.66°-61.91°and 22.32°-60.16°, and 28.47°-76.32°and 22.98°-72.68°, respectively. ANOVA showed that TBA and BBA were susceptible to environmental and had broadsense heritability (H2) values of 89.09%and 87.40%, respectively. Interactions of genotype by environment were also significant. There was diversity in branch angle among rapeseed genotypes. GGE biplot analysis showed that compact accession lines (Nilla, Purler and AV-SAPPHI) were the most desirable compact genotypes in all environments. Stability analysis showed that the genotype with the most minimum branch angle was stable for compact plant architecture.展开更多
基金the National Key Research and Development Program of China(2016YFD0100903)the National Natural Science Foundation of China(31600983 and 31821005)+1 种基金the China Postdoctoral Science Foundation(2017T100564 and 2016M590699)the Earmarked Fund for the China Agricultural Research System(CARS-01-05).
文摘Reproductive transition of grasses is characterized by switching the pattern of lateral branches,featuring the suppression of outgrowth of the subtending leaves(bracts)and rapid formation of higher-order branches in the inflorescence(panicle).However,the molecular mechanisms underlying such changes remain largely unknown.Here,we show that bract suppression is required for the reproductive branching in rice.We identified a pathway involving the intrinsic time ruler microRNAI56/529,their targets SQUAMOSA PROMOTER BINDING PROTEIN LIKE(SPL)genes,NECK LEAF1(NL1),and PLASTOCHRON1(PLA1),which regulates the bract outgrowth and thus affects the pattern switch between vegetative and reproductive branching.Suppression of the bract results in global reprogramming of transcriptome and chromatin accessibility following the reproductive transition,while these processes are largely dysregu-lated in the mutants of these genes.These discoveries contribute to our understanding of the dynamic plant architecture and provide novel insights for improving crop yields.
基金supported in part by the Science and Technology Innovation 2030-Major Project(2023ZD04034)the Fundamental Research Funds for the Central Universities(KYCYXT2022017 and KYQN2023021)+6 种基金Hainan Yazhou Bay Seed Laboratory(B21HJ1005)Jiangsu Province Key Research and Development Program(BE2023369)the Natural Science Foundation of Jiangsu Province(BK20231469)the National Natural Science Foundation of China(32201656)J.Z.was supported by the Sanya Yazhou Bay Science and Technology City(SCKJ-JYRC-2022-20)J.Wu was supported by the HKU Seed Funding for Strategic Interdisciplinary Research Schemethe Innovation and Technology Fund(funding support to State Key Laboratories in Hong Kong of Agrobiotechnology)of the HKSA R,China.
文摘Three-dimensional(3D)phenotyping is important for studying plant structure and function.Light detection and ranging(LiDAR)has gained prominence in 3D plant phenotyping due to its ability to collect 3D point clouds.However,organ-level branch detection remains challenging due to small targets,sparse points,and low signal-to-noise ratios.In addition,extracting biologically relevant angle traits is difficult.In this study,we developed a stratified,clustered,and growing-based algorithm(SCAG)for soybean branch detection and branch angle calculation from LiDAR data,which is heuristic,open-source,and expandable.SCAG achieved high branch detection accuracy(F-score=0.77)and branch angle calculation accuracy(r=0.84)when evaluated on 152 diverse soybean varieties.Meanwhile,the SCAG outperformed 2 other classic algorithms,the support vector machine(F-score=0.53)and density-based methods(F-score=0.55).Moreover,after applying the SCAG to 405 soybean varieties over 2 consecutive years,we quantified various 3D traits,including canopy width,height,stem length,and average angle.After data filtering,we identified novel heritable and repeatable traits for evaluating soybean density tolerance potential,such as the ratio of average angle to height and the ratio of average angle to stem length,which showed greater potential than the well-known ratio of canopy width to height trait.Our work demonstrates remarkable advances in 3D phenotyping and plant architecture screening.The algorithm can be applied to other crops,such as maize and tomato.Our dataset,scripts,and software are public,which can further benefit the plant science community by enhancing plant architecture characterization and ideal variety selection.
基金supported by National Natural Science Foundation of China(No.31471535, 31771842)the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(Group No.118)+1 种基金the Earmarked Fund for China Agriculture Research System (CARS-13)Hubei Agricultural Science and Technology Innovation Center
文摘Branch angle is an important plant architecture trait and is considerably important for the ideal plant architecture of high density cultivation of rapeseed. In this study,12 representative rapeseed lines were first measured for whole-plant branch angles using image processing technology. Top branch angle (TBA) and basal branch angle (BBA) were significantly different in each line in which TBA was greater than BBA. Then, 156 rapeseed germplasm lines were evaluated for TBA and BBA in main cultivated regions of the Yangtze River Basin (Zunyi; Wuhan; Lu'an). In these three environments, the TBA and BBA of the rapeseed germplasm sources varied, in which ranges of 33.44°-73.17°and 18.73°-59.11°, 29.66°-61.91°and 22.32°-60.16°, and 28.47°-76.32°and 22.98°-72.68°, respectively. ANOVA showed that TBA and BBA were susceptible to environmental and had broadsense heritability (H2) values of 89.09%and 87.40%, respectively. Interactions of genotype by environment were also significant. There was diversity in branch angle among rapeseed genotypes. GGE biplot analysis showed that compact accession lines (Nilla, Purler and AV-SAPPHI) were the most desirable compact genotypes in all environments. Stability analysis showed that the genotype with the most minimum branch angle was stable for compact plant architecture.
