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Fan J, Ma X, Zou J, Li S, Liu Y, Guo D, Jiang W, Li X, Liu F, Tan L. LATA1, a RING E3 ligase, modulates the tiller angle by affecting auxin asymmetric distribution and content in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39052425 DOI: 10.1111/tpj.16948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/18/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
The tiller angle is an important agronomic trait that determines plant architecture and grain yield in rice (Oryza sativa L.). However, the molecular regulation mechanism of the rice tiller angle remains unclear. Here, we identified a rice tiller angle gene, LARGE TILLER ANGLE 1 (LATA1), using the MutMap approach. LATA1 encodes a C3H2C3-type RING zinc finger E3 ligase and the conserved region of the RING zinc finger is essential for its E3 activity. LATA1 was highly expressed in the root and tiller base and LATA1-GFP fusion protein was specifically localized to the nucleus. The mutation of LATA1 significantly reduced indole-3-acetic acid content and attenuated lateral auxin transport, thereby resulting in defective shoot gravitropism and spreading plant architecture in rice. Further investigations found that LATA1 may indirectly affect gravity perception by modulating the sedimentation rate of gravity-sensing amyloplasts upon gravistimulation. Our findings provide new insights into the molecular mechanism underlying the rice tiller angle and new genetic resource for the improvement of plant architecture in rice.
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Affiliation(s)
- Jinjian Fan
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xin Ma
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jun Zou
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Shuangzhe Li
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuntao Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Daokuan Guo
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Wanxia Jiang
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xianyi Li
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Fengxia Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Lubin Tan
- Frontiers Science Center for Molecular Design Breeding (MOE), Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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2
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Li Z, Ye J, Yuan Q, Zhang M, Wang X, Wang J, Wang T, Qian H, Wei X, Yang Y, Shang L, Feng Y. BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38940609 DOI: 10.1111/jipb.13726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/09/2024] [Indexed: 06/29/2024]
Abstract
Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.
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Affiliation(s)
- Zhen Li
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Junhua Ye
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Mengchen Zhang
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Xingyu Wang
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jing Wang
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tianyi Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hongge Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xinghua Wei
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Yaolong Yang
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yue Feng
- China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
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3
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Wang W, Huang L, Song Y, Gui S, Cao J, Zhang H, Du M, Chen J, Wang Z, Zhou J, Meng X, Zeng D, Li J, Wang Y. LAZY4 acts additively with the starch-statolith-dependent gravity-sensing pathway to regulate shoot gravitropism and tiller angle in rice. PLANT COMMUNICATIONS 2024:100943. [PMID: 38897199 DOI: 10.1016/j.xplc.2024.100943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024]
Abstract
Rice tiller angle is a key agronomic trait that has significant effects on the establishment of a high-yield rice population. However, the molecular mechanism underlying the control of rice tiller angle remains to be clarified. Here, we characterized the novel tiller-angle gene LAZY4 (LA4) in rice through map-based cloning. LA4 encodes a C3H2C3-type RING zinc-finger E3 ligase localized in the nucleus, and an in vitro ubiquitination assay revealed that the conserved RING finger domain is essential for its E3 ligase activity. We found that expression of LA4 can be induced by gravistimulation and that loss of LA4 function leads to defective shoot gravitropism caused by impaired asymmetric auxin redistribution upon gravistimulation. Genetic analysis demonstrated that LA4 acts in a distinct pathway from the starch biosynthesis regulators LA2 and LA3, which function in the starch-statolith-dependent pathway. Further genetic analysis showed that LA4 regulates shoot gravitropism and tiller angle by acting upstream of LA1 to mediate lateral auxin transport upon gravistimulation. Our studies reveal that LA4 regulates shoot gravitropism and tiller angle upstream of LA1 through a novel pathway independent of the LA2-LA3-mediated gravity-sensing mechanism, providing new insights into the rice tiller-angle regulatory network.
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Affiliation(s)
- Wenguang Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Linzhou Huang
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Yuqi Song
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Songtao Gui
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Jiajia Cao
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Han Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Mengchen Du
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Jiaze Chen
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Zihao Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China
| | - Jie Zhou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dali Zeng
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Jiayang Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China; Yazhouwan National Laboratory, Sanya 572024, China
| | - Yonghong Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai' an 271018, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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4
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Liu L, Zhao L, Liu Y, Zhu Y, Chen S, Yang L, Li X, Chen W, Xu Z, Xu P, Wang H, Yu D. Transcription factor OsWRKY72 controls rice leaf angle by regulating LAZY1-mediated shoot gravitropism. PLANT PHYSIOLOGY 2024; 195:1586-1600. [PMID: 38478430 DOI: 10.1093/plphys/kiae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/13/2024] [Indexed: 06/02/2024]
Abstract
Leaf angle is a major trait of ideal architecture, which is considered to influence rice (Oryza sativa) cultivation and grain yield. Although a few mutants with altered rice leaf inclination angles have been reported, the underlying molecular mechanism remains unclear. In this study, we showed that a WRKY transcription factor gene, OsWRKY72, was highly expressed in the leaf sheath and lamina joint. Phenotypic analyses showed that oswrky72 mutants had smaller leaf angles than the wild type, while OsWRKY72 overexpression lines exhibited an increased leaf angle. This observation suggests that OsWRKY72 functions as a positive regulator, promoting the enlargement of the leaf angle. Our bioinformatics analysis identified LAZY1 as the downstream gene of OsWRKY72. Electrophoretic mobility shift assays and dual-luciferase analysis revealed that OsWRKY72 directly inhibited LAZY1 by binding to its promoter. Moreover, knocking out OsWRKY72 enhanced shoot gravitropism, which contrasted with the phenotype of lazy1 plants. These results imply that OsWRKY72 regulates the leaf angle through gravitropism by reducing the expression of LAZY1. In addition, OsWRKY72 could directly regulate the expression of other leaf angle-related genes such as FLOWERING LOCUS T-LIKE 12 (OsFTL12) and WALL-ASSOCIATED KINASE 11 (OsWAK11). Our study indicates that OsWRKY72 contributes positively to the expansion of the leaf angle by interfering with shoot gravitropism in rice.
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Affiliation(s)
- Lei Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lirong Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunwei Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Yi Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
| | - Shidie Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
| | - Lu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Xia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
| | - Wanqin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Zhiyu Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Houping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
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5
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Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife 2024; 12:RP91523. [PMID: 38441122 PMCID: PMC10942638 DOI: 10.7554/elife.91523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.
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Affiliation(s)
- Ivan Kulich
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Julia Schmid
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | | | - Linlin Qi
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Jiří Friml
- Institute of Science and Technology AustriaKlosterneuburgAustria
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6
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Newman TE, Jacques S, Grime C, Mobegi FM, Kamphuis FL, Khentry Y, Lee R, Kamphuis LG. Genetic dissection of domestication traits in interspecific chickpea populations. THE PLANT GENOME 2024; 17:e20408. [PMID: 37961823 DOI: 10.1002/tpg2.20408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
Chickpea (Cicer arietinum) is a pulse crop that provides an integral source of nutrition for human consumption. The close wild relatives Cicer reticulatum and Cicer echinospermum harbor untapped genetic diversity that can be exploited by chickpea breeders to improve domestic varieties. Knowledge of genomic loci that control important chickpea domestication traits will expedite the development of improved chickpea varieties derived from interspecific crosses. Therefore, we set out to identify genomic loci underlying key chickpea domestication traits by both association and quantitative trait locus (QTL) mapping using interspecific F2 populations. Diverse phenotypes were recorded for various agronomic traits. A total of 11 high-confidence markers were detected on chromosomes 1, 3, and 7 by both association and QTL mapping; these were associated with growth habit, flowering time, and seed traits. Furthermore, we identified candidate genes linked to these markers, which advanced our understanding of the genetic basis of domestication traits and validated known genes such as the FLOWERING LOCUS gene cluster that regulates flowering time. Collectively, this study has elucidated the genetic basis of chickpea domestication traits, which can facilitate the development of superior chickpea varieties.
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Affiliation(s)
- Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Christy Grime
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fredrick M Mobegi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fiona L Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Robert Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia
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7
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Lei S, Chen L, Liang F, Zhang Y, Zhang C, Xiao H, Tang R, Yang B, Wang L, Jiang H. Identification of a major QTL and candidate genes analysis for branch angle in rapeseed ( Brassica napus L.) using QTL-seq and RNA-seq. FRONTIERS IN PLANT SCIENCE 2024; 15:1340892. [PMID: 38450405 PMCID: PMC10914954 DOI: 10.3389/fpls.2024.1340892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024]
Abstract
Introduction Branching angle is an essential trait in determining the planting density of rapeseed (Brassica napus L.) and hence the yield per unit area. However, the mechanism of branching angle formation in rapeseed is not well understood. Methods In this study, two rapeseed germplasm with extreme branching angles were used to construct an F2 segregating population; then bulked segregant analysis sequencing (BSA-seq) and quantitative trait loci (QTL) mapping were utilized to localize branching anglerelated loci and combined with transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qPCR) for candidate gene mining. Results and discussion A branching angle-associated quantitative trait loci (QTL) was mapped on chromosome C3 (C3: 1.54-2.65 Mb) by combining BSA-seq as well as traditional QTL mapping. A total of 54 genes had SNP/Indel variants within the QTL interval were identified. Further, RNA-seq of the two parents revealed that 12 of the 54 genes were differentially expressed between the two parents. Finally, we further validated the differentially expressed genes using qPCR and found that six of them presented consistent differential expression in all small branching angle samples and large branching angles, and thus were considered as candidate genes related to branching angles in rapeseed. Our results introduce new candidate genes for the regulation of branching angle formation in rapeseed, and provide an important reference for the subsequent exploration of its formation mechanism.
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Affiliation(s)
- Shaolin Lei
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Li Chen
- Guizhou Rapeseed Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Fenghao Liang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yuling Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chao Zhang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Huagui Xiao
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Rong Tang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Bin Yang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Lulu Wang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Huanhuan Jiang
- Guizhou Oil Crops Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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8
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Sun L, Xu H, Song J, Yang X, Wang X, Liu H, Pang M, Hu Y, Yang Q, Ning X, Liang S, Zhang S, Luan W. OsNAC103, a NAC Transcription Factor, Positively Regulates Leaf Senescence and Plant Architecture in Rice. RICE (NEW YORK, N.Y.) 2024; 17:15. [PMID: 38358523 PMCID: PMC10869678 DOI: 10.1186/s12284-024-00690-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/03/2024] [Indexed: 02/16/2024]
Abstract
Leaf senescence, the last stage of leaf development, is essential for crop yield by promoting nutrition relocation from senescence leaves to new leaves and seeds. NAC (NAM/ATAF1/ATAF2/CUC2) proteins, one of the plant-specific transcription factors, widely distribute in plants and play important roles in plant growth and development. Here, we identified a new NAC member OsNAC103 and found that it plays critical roles in leaf senescence and plant architecture in rice. OsNAC103 mRNA levels were dramatically induced by leaf senescence as well as different phytohormones such as ABA, MeJA and ACC and abiotic stresses including dark, drought and high salinity. OsNAC103 acts as a transcription factor with nuclear localization signals at the N terminal and a transcriptional activation signal at the C terminal. Overexpression of OsNAC103 promoted leaf senescence while osnac103 mutants delayed leaf senescence under natural condition and dark-induced condition, meanwhile, senescence-associated genes (SAGs) were up-regulated in OsNAC103 overexpression (OsNAC103-OE) lines, indicating that OsNAC103 positively regulates leaf senescence in rice. Moreover, OsNAC103-OE lines exhibited loose plant architecture with larger tiller angles while tiller angles of osnac103 mutants decreased during the vegetative and reproductive growth stages due to the response of shoot gravitropism, suggesting that OsNAC103 can regulate the plant architecture in rice. Taken together, our results reveal that OsNAC103 plays crucial roles in the regulation of leaf senescence and plant architecture in rice.
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Affiliation(s)
- Lina Sun
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Hanqin Xu
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Juan Song
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Xiaoying Yang
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - XinYi Wang
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Haiyan Liu
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Mengzhen Pang
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Youchuan Hu
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Qi Yang
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Xiaotong Ning
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Shanshan Liang
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Siju Zhang
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China
| | - Weijiang Luan
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, 300387, China.
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9
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Kerr SC, Shehnaz S, Paudel L, Manivannan MS, Shaw LM, Johnson A, Velasquez JTJ, Tanurdžić M, Cazzonelli CI, Varkonyi-Gasic E, Prentis PJ. Advancing tree genomics to future proof next generation orchard production. FRONTIERS IN PLANT SCIENCE 2024; 14:1321555. [PMID: 38312357 PMCID: PMC10834703 DOI: 10.3389/fpls.2023.1321555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024]
Abstract
The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.
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Affiliation(s)
- Stephanie C Kerr
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Saiyara Shehnaz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lucky Paudel
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mekaladevi S Manivannan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - Amanda Johnson
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Jose Teodoro J Velasquez
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Miloš Tanurdžić
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Peter J Prentis
- School of Biology and Environmental Science, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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10
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Waite JM, Dardick C. IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle. BMC Biol 2024; 22:8. [PMID: 38233837 PMCID: PMC10795295 DOI: 10.1186/s12915-024-01813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Plants adjust their growth orientations primarily in response to light and gravity signals. Considering that the gravity vector is fixed and the angle of light incidence is constantly changing, plants must somehow integrate these signals to establish organ orientation, commonly referred to as gravitropic set-point angle (GSA). The IGT gene family contains known regulators of GSA, including the gene clades LAZY, DEEPER ROOTING (DRO), and TILLER ANGLE CONTROL (TAC). RESULTS Here, we investigated the influence of light on different aspects of GSA phenotypes in LAZY and DRO mutants, as well as the influence of known light signaling pathways on IGT gene expression. Phenotypic analysis revealed that LAZY and DRO genes are collectively required for changes in the angle of shoot branch tip and root growth in response to light. Single lazy1 mutant branch tips turn upward in the absence of light and in low light, similar to wild-type, and mimic triple and quadruple IGT mutants in constant light and high-light conditions, while triple and quadruple IGT/LAZY mutants show little to no response to changing light regimes. Further, the expression of IGT/LAZY genes is differentially influenced by daylength, circadian clock, and light signaling. CONCLUSIONS Collectively, the data show that differential expression of LAZY and DRO genes are required to enable plants to alter organ angles in response to light-mediated signals.
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Affiliation(s)
- Jessica Marie Waite
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, USA.
- Present Address: USDA Tree Fruit Research Laboratory, 1104 N Western Avenue, Wenatchee, WA, USA.
| | - Christopher Dardick
- United States Department of Agriculture (USDA) Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, USA
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11
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Niu M, Tian K, Chen Q, Yang C, Zhang M, Sun S, Wang X. A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits. FRONTIERS IN PLANT SCIENCE 2024; 14:1302359. [PMID: 38259929 PMCID: PMC10801003 DOI: 10.3389/fpls.2023.1302359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Ideal plant architecture is essential for enhancing crop yields. Ideal soybean (Glycine max) architecture encompasses an appropriate plant height, increased node number, moderate seed weight, and compact architecture with smaller branch angles for growth under high-density planting. However, the functional genes regulating plant architecture are far not fully understood in soybean. In this study, we investigated the genetic basis of 12 agronomic traits in a panel of 496 soybean accessions with a wide geographical distribution in China. Analysis of phenotypic changes in 148 historical elite soybean varieties indicated that seed-related traits have mainly been improved over the past 60 years, with targeting plant architecture traits having the potential to further improve yields in future soybean breeding programs. In a genome-wide association study (GWAS) of 12 traits, we detected 169 significantly associated loci, of which 61 overlapped with previously reported loci and 108 new loci. By integrating the GWAS loci for different traits, we constructed a genetic association network and identified 90 loci that were associated with a single trait and 79 loci with pleiotropic effects. Of these 79 loci, 7 hub-nodes were strongly linked to at least three related agronomic traits. qHub_5, containing the previously characterized Determinate 1 (Dt1) locus, was associated not only with plant height and node number (as determined previously), but also with internode length and pod range. Furthermore, we identified qHub_7, which controls three branch angle-related traits; the candidate genes in this locus may be beneficial for breeding soybean with compact architecture. These findings provide insights into the genetic relationships among 12 important agronomic traits in soybean. In addition, these studies uncover valuable loci for further functional gene studies and will facilitate molecular design breeding of soybean architecture.
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Affiliation(s)
- Mengrou Niu
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
| | - Kewei Tian
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
| | - Qiang Chen
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Mengchen Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Shiyong Sun
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
| | - Xuelu Wang
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
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12
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Gupta P, Elser J, Hooks E, D’Eustachio P, Jaiswal P, Naithani S. Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Nucleic Acids Res 2024; 52:D1538-D1547. [PMID: 37986220 PMCID: PMC10767815 DOI: 10.1093/nar/gkad1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023] Open
Abstract
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional species, spanning single-cell photoautotrophs, non-vascular plants, and higher plants, thus encompassing a wide-ranging taxonomic diversity. Currently, Plant Reactome houses a collection of 339 reference pathways, covering metabolic and transport pathways, hormone signaling, genetic regulations of developmental processes, and intricate transcriptional networks that orchestrate a plant's response to abiotic and biotic stimuli. Beyond being a mere repository, Plant Reactome serves as a dynamic data discovery platform. Users can analyze and visualize omics data, such as gene expression, gene-gene interaction, proteome, and metabolome data, all within the rich context of plant pathways. Plant Reactome is dedicated to fostering data interoperability, upholding global data standards, and embracing the tenets of the Findable, Accessible, Interoperable and Re-usable (FAIR) data policy.
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Affiliation(s)
- Parul Gupta
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Elizabeth Hooks
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sushma Naithani
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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13
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Tokuyama Y, Omachi M, Kushida S, Hikichi K, Okada S, Onishi K, Ishii T, Kishima Y, Koide Y. Different contributions of PROG1 and TAC1 to the angular kinematics of the main culm and tillers of wild rice (Oryza rufipogon). PLANTA 2023; 259:19. [PMID: 38085356 DOI: 10.1007/s00425-023-04300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.
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Affiliation(s)
- Yoshiki Tokuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Miku Omachi
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Shiori Kushida
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Kiwamu Hikichi
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Shuhei Okada
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Kazumitsu Onishi
- Research Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro-Shi, Hokkaido, 080-8555, Japan
| | - Takashige Ishii
- Graduate School of Agricultural Science, Kobe University, Kobe-Shi, Hyogo, 657-8501, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan.
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14
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Zhang N, Gui S, Wang Y. LAZing around: The intricate dance of amyloplast sedimentation and gravity sensing in plants. MOLECULAR PLANT 2023; 16:1887-1889. [PMID: 37919895 DOI: 10.1016/j.molp.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/04/2023]
Affiliation(s)
- Ning Zhang
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signaling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Songtao Gui
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yonghong Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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15
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Chen J, Liu Y, Liu M, Guo W, Wang Y, He Q, Chen W, Liao Y, Zhang W, Gao Y, Dong K, Ren R, Yang T, Zhang L, Qi M, Li Z, Zhao M, Wang H, Wang J, Qiao Z, Li H, Jiang Y, Liu G, Song X, Deng Y, Li H, Yan F, Dong Y, Li Q, Li T, Yang W, Cui J, Wang H, Zhou Y, Zhang X, Jia G, Lu P, Zhi H, Tang S, Diao X. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nat Genet 2023; 55:2243-2254. [PMID: 38036791 PMCID: PMC10703678 DOI: 10.1038/s41588-023-01571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet.
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Affiliation(s)
- Jinfeng Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Minxuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiyao Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Liyuan Zhang
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Mingyu Qi
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Zhiguang Li
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Min Zhao
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Junjie Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoqiang Song
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Yarui Deng
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Hai Li
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Feng Yan
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yang Dong
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Qingquan Li
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Tao Li
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenyao Yang
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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16
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Chu W, Zhu X, Jiang T, Wang S, Ni W. Genome-wide identification of peanut IGT family genes and their potential roles in the development of plant architecture. Sci Rep 2023; 13:20400. [PMID: 37990054 PMCID: PMC10663514 DOI: 10.1038/s41598-023-47722-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
IGT family genes play essential roles in shaping plant architecture. However, limited amount of information is available about IGT family genes in peanuts (Arachis hypogaea). In the current study, 13 AhIGT genes were identified and classified into three groups based on their phylogenetic relationship. Gene structure, conserved domain analyses indicated all AhIGTs were observed to share a similar exon-intron distribution pattern. AhIGTs within the same subfamily maintained a consistent motif composition. Chromosomal localization and synteny analyses showed that AhIGTs were unevenly localized on 9 chromosomes and that segmental duplication and purifying selection may have played important roles in the evolution of AhIGT genes. The analysis of conserved motifs, GO annotation, and transcript profile suggested that AhLAZY1-3 may play roles in gravity sensing and shaping peanut plant architecture. Transcript profile analysis suggested that AhTAC1 could potentially be involved gynophore ('peg') penetration into the soil. The cis-element analysis revealed that the light-responsive elements accounted for most of all cis-acting elements. Furthermore, qRT-PCR analysis showed that the expression of several AhIGT genes, like AhTAC1-2/4, was light-dependent, indicating that these genes may regulate plant architecture in response to light signals. This study may facilitate functional studies of the IGT genes in peanut.
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Affiliation(s)
- Wen Chu
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaofeng Zhu
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Tao Jiang
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Song Wang
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wanli Ni
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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17
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Wang W, Gui S, Wang Y. Uncover the mystery of pleiotropic effects of PROG1 during rice domestication. MOLECULAR PLANT 2023; 16:1722-1723. [PMID: 37766431 DOI: 10.1016/j.molp.2023.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023]
Affiliation(s)
- Wenguang Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Songtao Gui
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Yonghong Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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18
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Chen J, Yu R, Li N, Deng Z, Zhang X, Zhao Y, Qu C, Yuan Y, Pan Z, Zhou Y, Li K, Wang J, Chen Z, Wang X, Wang X, He SN, Dong J, Deng XW, Chen H. Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants. Cell 2023; 186:4788-4802.e15. [PMID: 37741279 PMCID: PMC10615846 DOI: 10.1016/j.cell.2023.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/04/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Gravity controls directional growth of plants, and the classical starch-statolith hypothesis proposed more than a century ago postulates that amyloplast sedimentation in specialized cells initiates gravity sensing, but the molecular mechanism remains uncharacterized. The LAZY proteins are known as key regulators of gravitropism, and lazy mutants show striking gravitropic defects. Here, we report that gravistimulation by reorientation triggers mitogen-activated protein kinase (MAPK) signaling-mediated phosphorylation of Arabidopsis LAZY proteins basally polarized in root columella cells. Phosphorylation of LAZY increases its interaction with several translocons at the outer envelope membrane of chloroplasts (TOC) proteins on the surface of amyloplasts, facilitating enrichment of LAZY proteins on amyloplasts. Amyloplast sedimentation subsequently guides LAZY to relocate to the new lower side of the plasma membrane in columella cells, where LAZY induces asymmetrical auxin distribution and root differential growth. Together, this study provides a molecular interpretation for the starch-statolith hypothesis: the organelle-movement-triggered molecular polarity formation.
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Affiliation(s)
- Jiayue Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Renbo Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Vegetable Research Center, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Na Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Zhaoguo Deng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xinxin Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yaran Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chengfu Qu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yanfang Yuan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhexian Pan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yangyang Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kunlun Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiajun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhiren Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaoyi Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolian Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shu-Nan He
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haodong Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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Wang X, Zhang Z, Peng W, Huang J, Yan X, Yao W, Ouyang J, Li S. Inositolphosphorylceramide synthases, OsIPCSs, regulate plant height in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111798. [PMID: 37467787 DOI: 10.1016/j.plantsci.2023.111798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Inositolphosphorylceramide synthase (IPCS) catalyses ceramides and phosphatidylinositol (PI) into inositolphosphorylceramide (IPC), which is involved in the regulation of plant growth and development. A total of three OsIPCS family genes have been identified in rice. However, most of their functions remain unknown. Here, the functions of OsIPCSs were analyzed by CRISPR/Cas9 technology, lipidomics analysis, and transcriptomics analysis. Single-gene mutation of OsIPCSs resulted in dwarf phenotype. Among them, the phenotype of osipcs3 mutant was more severe. Multi-gene mutation of OsIPCS genes led to more severe phenotypes, indicating the additive effects of OsIPCSs. We further determined that a significant decrease in epidermal cell elongation of internode in the mutants. There was a significant decrease in the content of IPC detected in the osipcs2/3 and osipcs1/2/3 mutants. The contents of glycosyl inositol phosphoryl ceramide (GIPC) were also decreased by 20% and 10% in osipcs2/3 and osipcs1/2/3, respectively. The results of RNA-seq showed that numerous DEGs found to be associated with cellular component organization, anatomical structure morphogenesis, and cell growth in the osipcs2, osipcs2/3, and osipcs1/2/3. Taken together, OsIPCSs may be involved in the regulation of plant height through affecting cell growth and sphingolipid metabolism in rice.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China; Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Zongfei Zhang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Wei Peng
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Jinqiu Huang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China.
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20
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Dougherty L, Borejsza-Wysocka E, Miaule A, Wang P, Zheng D, Jansen M, Brown S, Piñeros M, Dardick C, Xu K. A single amino acid substitution in MdLAZY1A dominantly impairs shoot gravitropism in Malus. PLANT PHYSIOLOGY 2023; 193:1142-1160. [PMID: 37394917 DOI: 10.1093/plphys/kiad373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023]
Abstract
Plant architecture is 1 of the most important factors that determines crop yield potential and productivity. In apple (Malus domestica), genetic improvement of tree architecture has been challenging due to a long juvenile phase and growth as complex trees composed of a distinct scion and a rootstock. To better understand the genetic control of apple tree architecture, the dominant weeping growth phenotype was investigated. We report the identification of MdLAZY1A (MD13G1122400) as the genetic determinant underpinning the Weeping (W) locus that largely controls weeping growth in Malus. MdLAZY1A is 1 of the 4 paralogs in apple that are most closely related to AtLAZY1 involved in gravitropism in Arabidopsis (Arabidopsis thaliana). The weeping allele (MdLAZY1A-W) contains a single nucleotide mutation c.584T>C that leads to a leucine to proline (L195P) substitution within a predicted transmembrane domain that colocalizes with Region III, 1 of the 5 conserved regions in LAZY1-like proteins. Subcellular localization revealed that MdLAZY1A localizes to the plasma membrane and nucleus in plant cells. Overexpressing the weeping allele in apple cultivar Royal Gala (RG) with standard growth habit impaired its gravitropic response and altered the growth to weeping-like. Suppressing the standard allele (MdLAZY1A-S) by RNA interference (RNAi) in RG similarly changed the branch growth direction to downward. Overall, the L195P mutation in MdLAZY1A is genetically causal for weeping growth, underscoring not only the crucial roles of residue L195 and Region III in MdLAZY1A-mediated gravitropic response but also a potential DNA base editing target for tree architecture improvement in Malus and other crops.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Ewa Borejsza-Wysocka
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Alexandre Miaule
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
| | - Ping Wang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Desen Zheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Michael Jansen
- United States Department of Agriculture-Agricultural Research Service, Systematic Entomology Laboratory, Electron and Confocal Microscopy Unit, Beltsville, MD 20705, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
| | - Miguel Piñeros
- School of Integrative Plant Sciences, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY 14853, USA
| | - Christopher Dardick
- United States Department of Agriculture-Agricultural Research Service, Appalachian Fruit Research Station, Kearneysville, WV 25430, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, NY 14456, USA
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21
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Wang Z, Guo Z, Zou T, Zhang Z, Zhang J, He P, Song R, Liu Z, Zhu H, Zhang G, Fu X. Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara. RICE (NEW YORK, N.Y.) 2023; 16:38. [PMID: 37668809 PMCID: PMC10480103 DOI: 10.1186/s12284-023-00655-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. RESULTS In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them. CONCLUSION The results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication.
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Affiliation(s)
- Zhangqiang Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zisheng Guo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Tuo Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhe Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ping He
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ruifeng Song
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ziqiang Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Xuelin Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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22
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Wang J, Huang J, Bao J, Li X, Zhu L, Jin J. Rice domestication-associated transcription factor PROSTRATE GROWTH 1 controls plant and panicle architecture by regulating the expression of LAZY 1 and OsGIGANTEA, respectively. MOLECULAR PLANT 2023; 16:1413-1426. [PMID: 37621089 DOI: 10.1016/j.molp.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023]
Abstract
Plant architecture and panicle architecture are two critical agronomic traits that greatly affect the yield of rice (Oryza sativa). PROSTRATE GROWTH 1 (PROG1) encodes a key C2H2-type zinc-finger transcription factor and has pleiotropic effects on the regulation of both plant and panicle architecture, thereby influencing the grain yield. However, the molecular mechanisms through which PROG1 controls plant and panicle architecture remain unclear. In this study, we showed that PROG1 directly binds the LAZY 1 (LA1) promoter and acts as a repressor to inhibit LA1 expression. Conversely, LA1 acts as a repressor of PROG1 by directly binding to the PROG1 promoter. These two genes play antagonistic roles in shaping plant architecture by regulating both tiller angle and tiller number. Interestingly, our data showed that PROG1 controls panicle architecture through direct binding to the intragenic regulatory regions of OsGIGANTEA (OsGI) and subsequent activation of its expression. Collectively, we have identified two crucial targets of PROG1, LA1 and OsGI, shedding light on the molecular mechanisms underlying plant and panicle architecture control by PROG1. Our study provides valuable insights into the regulation of key domestication-related traits in rice and identifies potential targets for future high-yield rice breeding.
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Affiliation(s)
- Jun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinlin Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xizhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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23
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Wang H, Ouyang J, Jian W, Li M, Zhong J, Yan X, Gao J, Wang X, Li S. Rice miR5504 regulates plant height by affecting cell proliferation and expansion. PHYSIOLOGIA PLANTARUM 2023; 175:e14023. [PMID: 37882316 DOI: 10.1111/ppl.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
miRNAs play critical roles in the regulation of plant growth and development by cleaving mRNA or repressing transcription. In our previous study, miR5504 with unknown functions was captured by small RNA sequencing. Here, the function and characters of miR5504 were extensively analyzed using CRISPR/Cas9, overexpression strategy, Northern blot, cytological analysis, and transcriptomics analysis. We found that the dwarf phenotype of mir5504 mutants (mir5504-1 and mir5504-2) appeared on 35-day seedlings and became more apparent at the mature stage. The cytological results showed a substantial decrease in the vascular bundle number, cell number and cell length in the mir5504 mutant compared with NIP. In addition, we found that miR5504 regulated plant height by targeting LOC_Os08g16914. The results of RNA-seq revealed that numerous biological processes were mainly enriched, including DNA-binding transcription factor activity, transferase activity, regulation of transcription, metabolic process, and protein binding. Meanwhile, KEEG analysis showed that numerous proteins were associated with cellular processes and metabolism pathways. Taken together, miR5504 may be involved in the regulation of plant height by affecting cell expansion and division of internode in rice.
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Affiliation(s)
- Huihui Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Wenjia Jian
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiancong Zhong
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
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24
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Nishimura T, Mori S, Shikata H, Nakamura M, Hashiguchi Y, Abe Y, Hagihara T, Yoshikawa HY, Toyota M, Higaki T, Morita MT. Cell polarity linked to gravity sensing is generated by LZY translocation from statoliths to the plasma membrane. Science 2023; 381:1006-1010. [PMID: 37561884 DOI: 10.1126/science.adh9978] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
Organisms have evolved under gravitational force, and many sense the direction of gravity by means of statoliths in specialized cells. In flowering plants, starch-accumulating plastids, known as amyloplasts, act as statoliths to facilitate downstream gravitropism. The gravity-sensing mechanism has long been considered a mechanosensing process by which amyloplasts transmit forces to intracellular structures, but the molecular mechanism underlying this has not been elucidated. We show here that LAZY1-LIKE (LZY) family proteins involved in statocyte gravity signaling associate with amyloplasts and the proximal plasma membrane. This results in polar localization according to the direction of gravity. We propose a gravity-sensing mechanism by which LZY translocation to the plasma membrane signals the direction of gravity by transmitting information on the position of amyloplasts.
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Affiliation(s)
- Takeshi Nishimura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Course for Basic Biology, The Graduate Institute for Advanced Studies, SOKENDAI, Hayama 240-0115, Japan
| | - Shogo Mori
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Hiromasa Shikata
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Course for Basic Biology, The Graduate Institute for Advanced Studies, SOKENDAI, Hayama 240-0115, Japan
| | - Moritaka Nakamura
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Yasuko Hashiguchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshinori Abe
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
| | - Takuma Hagihara
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
| | | | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, Saitama 338-8570, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Takumi Higaki
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Miyo Terao Morita
- Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Course for Basic Biology, The Graduate Institute for Advanced Studies, SOKENDAI, Hayama 240-0115, Japan
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25
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Jiang X, Hong WJ, Lee SK, Jung KH. Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2959. [PMID: 37631170 PMCID: PMC10458737 DOI: 10.3390/plants12162959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023]
Abstract
The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.
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Affiliation(s)
- Xu Jiang
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (X.J.); (S.-K.L.)
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea;
| | - Su-Kyoung Lee
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (X.J.); (S.-K.L.)
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea; (X.J.); (S.-K.L.)
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26
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Clark CB, Ma J. The genetic basis of shoot architecture in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:55. [PMID: 37351274 PMCID: PMC10281916 DOI: 10.1007/s11032-023-01391-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2023] [Indexed: 06/24/2023]
Abstract
Shoot architecture refers to the three-dimensional body plan of the above ground organs of the plant. The patterning of this body plan results from the tight genetic control of the size and maintenance of meristems, the initiation of axillary growth, and the timing of developmental phase transition. Variation in shoot architecture can result in dramatic differences in plant productivity and/or grain yield due to their effects on light interception, photosynthetic efficiency, response to agronomic inputs, and environmental adaptation. The fine-tuning of shoot architecture has consequently been of great interest to plant breeders, driving the need for deeper understanding of the genes and molecular mechanisms governing these traits. In soybean, the world's most important oil and protein crop, major components of shoot architecture include stem growth habit, plant height, branch angle, branch number, leaf petiole angle, and the size and shape of leaves. Key genes underlying some of these traits have been identified to integrate hormonal, developmental, and environmental signals modulating the growth and orientation of shoot organs. Here we summarize the current knowledge and recent advances in the understanding of the genetic control of these important architectural traits in soybean.
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Affiliation(s)
- Chancelor B. Clark
- Department of Agronomy, Purdue University, 915 W Mitch Daniels Blvd, West Lafayette, 47907 IN USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, 915 W Mitch Daniels Blvd, West Lafayette, 47907 IN USA
- Center for Plant Biology, Purdue University, West Lafayette, IN USA
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27
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Wang H, Tu R, Ruan Z, Chen C, Peng Z, Zhou X, Sun L, Hong Y, Chen D, Liu Q, Wu W, Zhan X, Shen X, Zhou Z, Cao L, Zhang Y, Cheng S. Photoperiod and gravistimulation-associated Tiller Angle Control 1 modulates dynamic changes in rice plant architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:160. [PMID: 37347301 DOI: 10.1007/s00122-023-04404-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/11/2023] [Indexed: 06/23/2023]
Abstract
KEY MESSAGE TAC1 is involved in photoperiodic and gravitropic responses to modulate rice dynamic plant architecture likely by affecting endogenous auxin distribution, which could explain TAC1 widespread distribution in indica rice. Plants experience a changing environment throughout their growth, which requires dynamic adjustments of plant architecture in response to these environmental cues. Our previous study demonstrated that Tiller Angle Control 1 (TAC1) modulates dynamic changes in plant architecture in rice; however, the underlying regulatory mechanisms remain largely unknown. In this study, we show that TAC1 regulates plant architecture in an expression dose-dependent manner, is highly expressed in stems, and exhibits dynamic expression in tiller bases during the growth period. Photoperiodic treatments revealed that TAC1 expression shows circadian rhythm and is more abundant during the dark period than during the light period and under short-day conditions than under long-day conditions. Therefore, it contributes to dynamic plant architecture under long-day conditions and loose plant architecture under short-day conditions. Gravity treatments showed that TAC1 is induced by gravistimulation and negatively regulates shoot gravitropism, likely by affecting auxin distribution. Notably, the tested indica rice containing TAC1 displayed dynamic plant architecture under natural long-day conditions, likely explaining the widespread distribution of TAC1 in indica rice. Our results provide new insights into TAC1-mediated regulatory mechanisms for dynamic changes in rice plant architecture.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Ranran Tu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zheyan Ruan
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Chi Chen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Zequn Peng
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xingpeng Zhou
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Lianping Sun
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Yongbo Hong
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Daibo Chen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Qunen Liu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Weixun Wu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xiaodeng Zhan
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Xihong Shen
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Zhengping Zhou
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China
| | - Liyong Cao
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.
| | - Shihua Cheng
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory for Zhejiang Super Rice Research, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 311401, China.
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Zhong Q, Jia Q, Yin W, Wang Y, Rao Y, Mao Y. Advances in cloning functional genes for rice yield traits and molecular design breeding in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1206165. [PMID: 37404533 PMCID: PMC10317195 DOI: 10.3389/fpls.2023.1206165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/31/2023] [Indexed: 07/06/2023]
Abstract
Rice, a major food crop in China, contributes significantly to international food stability. Advances in rice genome sequencing, bioinformatics, and transgenic techniques have catalyzed Chinese researchers' discovery of novel genes that control rice yield. These breakthroughs in research also encompass the analysis of genetic regulatory networks and the establishment of a new framework for molecular design breeding, leading to numerous transformative findings in this field. In this review, some breakthroughs in rice yield traits and a series of achievements in molecular design breeding in China in recent years are presented; the identification and cloning of functional genes related to yield traits and the development of molecular markers of rice functional genes are summarized, with the intention of playing a reference role in the following molecular design breeding work and how to further improve rice yield.
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Affiliation(s)
- Qianqian Zhong
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Qiwei Jia
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Wenjing Yin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yijian Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China
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Li J, Wang Z, Song C, Nie Y, Li H, Kong M, Cong H, Wang S, Yin N, Hu L, Bermudez RS, He W. Identification of LsLAZY1 gene in Leymus secalinus and validation of its function in Arabidopsis thaliana. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:783-790. [PMID: 37520815 PMCID: PMC10382429 DOI: 10.1007/s12298-023-01326-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023]
Abstract
Root systems anchor plants to the substrate in addition to transporting water and nutrients, playing a fundamental role in plant survival. The LAZY1 gene mediates gravity signal transduction and participates in root and shoot development and auxin flow in many plants. In this study, a regulator, LsLAZY1, was identified from Leymus secalinus based on previous transcriptome data. The conserved domain and evolutionary relationship were further analyzed comprehensively. The role of LsLAZY1 in root development was investigated by genetic transformation and associated gravity response and phototropism assay. Subcellular localization showed that LsLAZY1 was localized in the nucleus. LsLAZY1 overexpression in Arabidopsis thaliana (Col-0) increased the length of the primary roots (PRs) and the number of lateral roots (LRs) compared to Col-0. Furthermore, 35S:LsLAZY1 transgenic seedlings affected auxin transport and showed a stronger gravitational and phototropic responses. It also promoted auxin accumulation at the root tips. These results indicated that LsLAZY1 affects root development and auxin transport. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01326-4.
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Affiliation(s)
- Jialin Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Zenghui Wang
- Shandong Institute of Pomology, Tai’an, 271000 Shandong China
| | - Chunying Song
- Xilin Gol League Agricultural and Animal Product Quality and Safety Monitoring Center, Xilinhot City, 026000 China
| | - Yanshun Nie
- Fengtang Ecological Agriculture Technology Research and Development Co. LTD, Tai’an, 271000 Shandong China
| | - Hongmei Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Mengmeng Kong
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Hanhan Cong
- School of Information Science and Engineering, University of Jinan, Jinan, 250022 China
| | - Siqi Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Ning Yin
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Linyue Hu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Ramon Santos Bermudez
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022 China
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Cai Y, Huang L, Song Y, Yuan Y, Xu S, Wang X, Liang Y, Zhou J, Liu G, Li J, Wang W, Wang Y. LAZY3 interacts with LAZY2 to regulate tiller angle by modulating shoot gravity perception in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1217-1228. [PMID: 36789453 DOI: 10.1111/pbi.14031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 05/27/2023]
Abstract
Starch biosynthesis in gravity-sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity-sensing tissues is still unclear. We characterized a novel tiller angle gene LAZY3 (LA3) in rice through map-based cloning. Biochemical, molecular and genetic studies further demonstrated the essential roles of LA3 in gravity perception of rice shoot and tiller angle control. The shoot gravitropism and lateral auxin transport were defective in la3 mutant upon gravistimulation. We showed that LA3 encodes a chloroplast-localized tryptophan-rich protein associated with starch granules via Tryptophan-rich region (TRR) domain. Moreover, LA3 could interact with the starch biosynthesis regulator LA2, determining starch granule formation in shoot gravity-sensing tissues. LA3 and LA2 negatively regulate tiller angle in the same pathway acting upstream of LA1 to mediate asymmetric distribution of auxin. Our study defined LA3 as an indispensable factor of starch biosynthesis in rice gravity-sensing tissues that greatly broadens current understanding in the molecular mechanisms underlying the starch granule formation in gravity-sensing tissues, and provides new insights into the regulatory mechanism of shoot gravitropism and rice tiller angle.
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Affiliation(s)
- Yueyue Cai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Linzhou Huang
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Yuqi Song
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Yundong Yuan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Shuo Xu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueping Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Liang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Jie Zhou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Guifu Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiayang Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenguang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Yonghong Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
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Yu X, Li Y, Cui X, Wang X, Li J, Guo R, Yan F, Zhang S, Zhao R, Song D, Si T, Zou X, Wang Y, Zhang X. Simultaneously mapping loci related to two plant architecture traits by phenotypic recombination BSA/BSR in peanut (Arachis hypogaea L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:144. [PMID: 37249697 DOI: 10.1007/s00122-023-04385-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
KEY MESSAGE We developed a new method phenotypic recombination BSA/BSR (PR-BSA/BSR), which could simultaneously identify the candidate genomic regions associated with two traits in a segregating population. Bulked segregant analysis sequencing (BSA-seq) has been widely used for identifying the genomic regions affecting a certain trait. In this study, we developed a modified BSA/bulked segregant RNA-sequencing (BSR-seq) method, which we named phenotypic recombination BSA/BSR (PR-BSA/BSR), to simultaneously identify candidate genomic regions associated with two traits in a segregating population. Lateral branch angle (LBA) and flower-branch pattern (FBP) are two important traits associated with the peanut plant architecture because they affect the planting density and light use efficiency. We generated an F6 population (with two segregating traits) derived from a cross between the inbred lines Pingdu9616 (erect and sequential; ES-type) and Florunner (spreading and alternating; SA-type). The selection of bulks with extreme phenotypes was a key step in this study. Specifically, 30 individuals with recombinant phenotypes [i.e., spreading and sequential (SS-type) and erect and alternating (EA-type)] were selected to generate two bulks. The transcriptomes of individuals were sequenced and then the loci related to LBA and FBP were simultaneously detected via a ΔSNP-index strategy, which involved the direction of positive and negative peaks in the ∆SNP-index plot. The LBA-related locus was mapped to a 6.82 Mb region (101,743,223-108,564,267 bp) on chromosome 15, whereas the FBP-related locus was mapped to a 2.16 Mb region (117,682,534-119,846,824 bp) on chromosome 12. Furthermore, the marker-based classical QTL mapping method was used to analyze the PF-F6 population, which confirmed our PR-BSA/BSR results. Therefore, the PR-BSA/BSR method produces accurate and reliable data.
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Affiliation(s)
- Xiaona Yu
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Yaoyao Li
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xinyuan Cui
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xianheng Wang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Jihua Li
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Rui Guo
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Fanzhuang Yan
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Shaojing Zhang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Ruihua Zhao
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Danlei Song
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Tong Si
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xiaoxia Zou
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Yuefu Wang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China
| | - Xiaojun Zhang
- Dry Farming Technology Key Laboratory of Shandong Province/College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
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Naithani S, Mohanty B, Elser J, D’Eustachio P, Jaiswal P. Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice ( Oryza sativa). PLANTS (BASEL, SWITZERLAND) 2023; 12:2146. [PMID: 37299125 PMCID: PMC10255735 DOI: 10.3390/plants12112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| | - Bijayalaxmi Mohanty
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore;
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
| | - Peter D’Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (J.E.); (P.J.)
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Cheng F, Song M, Zhang M, Zha G, Yin J, Cheng C, Chen J, Lou Q. A mutation in CsABCB19 encoding an ATP-binding cassette auxin transporter leads to erect and compact leaf architecture in cucumber (Cucumis sativus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111625. [PMID: 36758728 DOI: 10.1016/j.plantsci.2023.111625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Leaf architecture, including leaf position and leaf morphology, is a critical component of plant architecture that directly determines plant appearance, photosynthetic utilization, and ultimate productivity. The mechanisms regulating leaf petiole angle and leaf flatness in cucumber remain unclear. In this study, we identified an erect and compact leaf architecture mutant (ecla) from an EMS (ethyl methanesulfonate) -mutagenized cucumber population, which exhibited erect petioles and crinkled leaves. Histological examination revealed significant phenotypic variation in ecla was associated with asymmetric cell expansion. MutMap sequencing combined with genetic mapping revealed that CsaV3_5G037960 is the causative gene for the ecla mutant phenotype. Through protein sequence alignment and Arabidopsis genetic complementation, we identified this gene as a functional direct homolog encoding the ATP-binding cassette transporter AtABCB19, hence named CsABCB19. A nonsynonymous mutation in the eleventh exon of CsABCB19 leads to premature termination of translation. The expression level of CsABCB19 in the ecla mutant was significantly reduced in all tissues compared to the wild type (WT). Transcriptome analysis revealed that auxin and polarity-related genes were significantly differentially expressed in mutant petioles and leaves, compared with those in WT. Auxin assay and exogenous treatment further demonstrated that CsABCB19 regulates leaf architecture by mediating auxin accumulation and transport. Our research is the first report describing the role of the ABCB19 transporter protein in auxin transport controlling cucumber leaf development. Furthermore, this study provides recent insights into the genetic mechanisms conferring morphological diversity and regulation of petiole angle and leaf flattening. DATA AVAILABILITY: The RNA-seq data in this study have been deposited in the NCBI SRA under BioProject accession number PRJNA874548.
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Affiliation(s)
- Feng Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mengfei Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mengru Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Gaohui Zha
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Juan Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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Li L, Chen X. Auxin regulation on crop: from mechanisms to opportunities in soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:16. [PMID: 37313296 PMCID: PMC10248601 DOI: 10.1007/s11032-023-01361-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/10/2023] [Indexed: 06/15/2023]
Abstract
Breeding crop varieties with high yield and ideal plant architecture is a desirable goal of agricultural science. The success of "Green Revolution" in cereal crops provides opportunities to incorporate phytohormones in crop breeding. Auxin is a critical phytohormone to determine nearly all the aspects of plant development. Despite the current knowledge regarding auxin biosynthesis, auxin transport and auxin signaling have been well characterized in model Arabidopsis (Arabidopsis thaliana) plants, how auxin regulates crop architecture is far from being understood, and the introduction of auxin biology in crop breeding stays in the theoretical stage. Here, we give an overview on molecular mechanisms of auxin biology in Arabidopsis, and mainly summarize auxin contributions for crop plant development. Furthermore, we propose potential opportunities to integrate auxin biology in soybean (Glycine max) breeding.
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Affiliation(s)
- Linfang Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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Yang Y, Wang W, Hu Q, Raman H, Liu J. Genome-wide association and RNA-seq analyses identify loci for pod orientation in rapeseed ( Brassica napus). FRONTIERS IN PLANT SCIENCE 2023; 13:1097534. [PMID: 36714779 PMCID: PMC9880488 DOI: 10.3389/fpls.2022.1097534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Spatial distribution and orientation of pods on the main raceme (stem) and branches could affect rapeseed yield. However, genomic regions underlying the pod orientation were not described in Brassica species. Here, we determined the extent of genetic variation in pod orientation, described as the angles of pedicel on raceme (APR) and angles of the pod on pedicel (APP) among 136 rapeseed accessions grown across three environments of the upper, middle and lower Yangtze River in China. The APR ranged from 59° to 109°, while the APP varied from 142° to 178°. Statistical analysis showed that phenotypic variation was due to genotypic (G) and environmental (E) effects. Using the genome-wide association analysis (GWAS) approach, two QTLs for APR (qBnAPR.A02 and qBnAPR.C02) and two for APP (qBnAPP.A05 and qBnAPP.C05), having minor to moderate allelic effects (4.30% to 19.47%) were identified. RNA-seq analysis revealed 606 differentially expressed genes (DEGs) in two rapeseed accessions representing the extreme phenotypes for pod orientation and different alleles at the QTLs of APR. Three DEGs (BnLAZY4.A02, BnSAUR32.A02, and BnSAUR32.C02) were identified as the most likely candidates responsible for variation in pod orientation (APR). This study elucidates the genomic regions and putative candidate genes underlying pod orientation in B. napus.
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Affiliation(s)
- Yuting Yang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Shenzhen Graduate School, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Wenxiang Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Harsh Raman
- New South Wales (NSW) Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Jia Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
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Che X, Splitt BL, Eckholm MT, Miller ND, Spalding EP. BRXL4-LAZY1 interaction at the plasma membrane controls Arabidopsis branch angle and gravitropism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:211-224. [PMID: 36478485 PMCID: PMC10107345 DOI: 10.1111/tpj.16055] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Gravitropism guides growth to shape plant architecture above and below ground. Mutations in LAZY1 impair stem gravitropism and cause less upright inflorescence branches (wider angles). The LAZY1 protein resides at the plasma membrane and in the nucleus. The plasma membrane pool is necessary and sufficient for setting branch angles. To investigate the molecular mechanism of LAZY1 function, we screened for LAZY1-interacting proteins in yeast. We identified BRXL4, a shoot-specific protein related to BREVIS RADIX. The BRXL4-LAZY1 interaction occurred at the plasma membrane in plant cells, and not detectably in the nucleus. Mutations in the C-terminus of LAZY1, but not other conserved regions, prevented the interaction. Opposite to lazy1, brxl4 mutants displayed faster gravitropism and more upright branches. Overexpressing BRXL4 produced strong lazy1 phenotypes. The apparent negative regulation of LAZY1 function is consistent with BRXL4 reducing LAZY1 expression or the amount of LAZY1 at the plasma membrane. Measurements indicated that both are true. LAZY1 mRNA was three-fold more abundant in brxl4 mutants and almost undetectable in BRXL4 overexpressors. Plasma membrane LAZY1 was higher and nuclear LAZY1 lower in brxl4 mutants compared with the wild type. To explain these results, we suggest that BRXL4 reduces the amount of LAZY1 at the plasma membrane where it functions in gravity signaling and promotes LAZY1 accumulation in the nucleus where it reduces LAZY1 expression, possibly by suppressing its own transcription. This explanation of how BRXL4 negatively regulates LAZY1 suggests ways to modify shoot system architecture for practical purposes.
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Affiliation(s)
- Ximing Che
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Bessie L. Splitt
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Magnus T. Eckholm
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Nathan D. Miller
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Edgar P. Spalding
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
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Zhao L, Zheng Y, Wang Y, Wang S, Wang T, Wang C, Chen Y, Zhang K, Zhang N, Dong Z, Chen F. A HST1-like gene controls tiller angle through regulating endogenous auxin in common wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:122-135. [PMID: 36128872 PMCID: PMC9829390 DOI: 10.1111/pbi.13930] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 05/29/2023]
Abstract
Tiller angle is one of the most important agronomic traits and one key factor for wheat ideal plant architecture, which can both increase photosynthetic efficiency and greatly enhance grain yield. Here, a deacetylase HST1-like (TaHST1L) gene controlling wheat tiller angle was identified by the combination of a genome-wide association study (GWAS) and bulked segregant analysis (BSA). Ethyl methane sulfonate (EMS)-mutagenized tetraploid wheat lines with the premature stop codon of TaHST1L exhibited significantly smaller tiller angles than the wild type. TaHST1L-overexpressing (OE) plants exhibited significantly larger tiller angles and increased tiller numbers in both winter and spring wheat, while TaHST1L-silenced RNAi plants displayed significantly smaller tiller angles and decreased tiller numbers. Moreover, TaHST1L strongly interacted with TaIAA17 and inhibited its expression at the protein level, and thus possibly improved the content of endogenous auxin in the basal tissue of tillers. The transcriptomics and metabolomics results indicated that TaHST1L might change plant architecture by mediating auxin signal transduction and regulating endogenous auxin levels. In addition, a 242-bp insertion/deletion (InDel) in the TaHST1L-A1 promoter altered transcriptional activity and TaHST1L-A1b allele with the 242-bp insertion widened the tiller angle of TaHST1L-OE transgenic rice plants. Wheat varieties with TaHST1L-A1b allele possessed the increased tiller angle and grain yield. Further analysis in wheat and its progenitors indicated that the 242-bp InDel possibly originated from wild emmer and was strongly domesticated in the current varieties. Therefore, TaHST1L involved in the auxin signalling pathway showed the big potential to improve wheat yield by controlling plant architecture.
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Affiliation(s)
- Lei Zhao
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Yueting Zheng
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Ying Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Shasha Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Tongzhu Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Canguan Wang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Yue Chen
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Kunpu Zhang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Ning Zhang
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Zhongdong Dong
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science / CIMMYT‐China Wheat and Maize Joint Research Center /Agronomy CollegeHenan Agricultural UniversityZhengzhouChina
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Qi Y, Wang L, Li W, Xie Y, Zhao W, Dang Z, Li W, Zhao L, Zhang J. Phenotypic analysis of Longya-10 × pale flax hybrid progeny and identification of candidate genes regulating prostrate/erect growth in flax plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1044415. [PMID: 36561460 PMCID: PMC9763623 DOI: 10.3389/fpls.2022.1044415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Flax is a dual-purpose crop that is important for oil and fiber production. The growth habit is one of the crucial targets of selection during flax domestication. Wild hybridization between cultivated flax and wild flax can produce superior germplasms for flax breeding and facilitate the study of the genetic mechanism underlying agronomically important traits. In this study, we used pale flax, Linum grandiflorum, and L. perenne to pollinate Longya-10. Only pale flax interspecific hybrids were obtained, and the trait analysis of the F1 and F2 generations showed that the traits analyzed in this study exhibited disparate genetic characteristics. In the F1 generation, only one trait, i.e., the number of capsules per plant (140) showed significant heterosis, while the characteristics of other traits were closely associated with those of the parents or a decline in hybrid phenotypes. The traits of the F2 generation were widely separated, and the variation coefficient ranged from 9.96% to 146.15%. The quantitative trait locus underlying growth habit was preliminarily found to be situated on chromosome 2 through Bulked-segregant analysis sequencing. Then linkage mapping analysis was performed to fine-map GH2.1 to a 23.5-kb interval containing 4 genes. Among them, L.us.o.m.scaffold22.109 and L.us.o.m.scaffold22.112 contained nonsynonymous SNPs with Δindex=1. Combined with the qRT-PCR results, the two genes might be possible candidate genes for GH2.1. This study will contribute to the development of important germplasms for flax breeding, which would facilitate the elucidation of the genetic mechanisms regulating the growth habit and development of an ideal architecture for the flax plant.
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Pan J, Zhou X, Ahmad N, Zhang K, Tang R, Zhao H, Jiang J, Tian M, Li C, Li A, Zhang X, He L, Ma J, Li X, Tian R, Ma C, Pandey MK, Varshney RK, Wang X, Zhao C. BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4457-4468. [PMID: 36181525 DOI: 10.1007/s00122-022-04231-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping. Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one "F-box protein" and two "2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)" encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program.
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Affiliation(s)
- Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Naveed Ahmad
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Kun Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People's Republic of China
| | - Ronghua Tang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Huiling Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Jing Jiang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Mengdi Tian
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, People's Republic of China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Aiqin Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Xianying Zhang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jing Ma
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaojie Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Kawamoto N, Morita MT. Gravity sensing and responses in the coordination of the shoot gravitropic setpoint angle. THE NEW PHYTOLOGIST 2022; 236:1637-1654. [PMID: 36089891 PMCID: PMC9828789 DOI: 10.1111/nph.18474] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Gravity is one of the fundamental environmental cues that affect plant development. Indeed, the plant architecture in the shoots and roots is modulated by gravity. Stems grow vertically upward, whereas lateral organs, such as the lateral branches in shoots, tend to grow at a specific angle according to a gravity vector known as the gravitropic setpoint angle (GSA). During this process, gravity is sensed in specialised gravity-sensing cells named statocytes, which convert gravity information into biochemical signals, leading to asymmetric auxin distribution and driving asymmetric cell division/expansion in the organs to achieve gravitropism. As a hypothetical offset mechanism against gravitropism to determine the GSA, the anti-gravitropic offset (AGO) has been proposed. According to this concept, the GSA is a balance of two antagonistic growth components, that is gravitropism and the AGO. Although the nature of the AGO has not been clarified, studies have suggested that gravitropism and the AGO share a common gravity-sensing mechanism in statocytes. This review discusses the molecular mechanisms underlying gravitropism as well as the hypothetical AGO in the control of the GSA.
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Affiliation(s)
- Nozomi Kawamoto
- Division of Plant Environmental ResponsesNational Institute for Basic BiologyMyodaijiOkazaki444‐8556Japan
| | - Miyo Terao Morita
- Division of Plant Environmental ResponsesNational Institute for Basic BiologyMyodaijiOkazaki444‐8556Japan
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Zhang H, Wafula EK, Eilers J, Harkess A, Ralph PE, Timilsena PR, dePamphilis CW, Waite JM, Honaas LA. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes. FRONTIERS IN PLANT SCIENCE 2022; 13:975942. [PMID: 36452099 PMCID: PMC9702816 DOI: 10.3389/fpls.2022.975942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/21/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.
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Affiliation(s)
- Huiting Zhang
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Eric K. Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jon Eilers
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Alex E. Harkess
- College of Agriculture, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Paula E. Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Claude W. dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jessica M. Waite
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Loren A. Honaas
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
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Duan H, Li J, Sun Y, Xiong X, Sun L, Li W, Gao J, Li N, Zhang J, Cui J, Fu Z, Zhang X, Tang J. Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis. Front Genet 2022; 13:1004211. [PMID: 36437932 PMCID: PMC9691904 DOI: 10.3389/fgene.2022.1004211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10–6), and individual QTL explained 4.80%–24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wenlong Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Junli Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiangkuan Cui
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Xuehai Zhang, ; Jihua Tang,
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
- *Correspondence: Xuehai Zhang, ; Jihua Tang,
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Kumari G, Shanmugavadivel PS, Lavanya GR, Tiwari P, Singh D, Gore PG, Tripathi K, Madhavan Nair R, Gupta S, Pratap A. Association mapping for important agronomic traits in wild and cultivated Vigna species using cross-species and cross-genera simple sequence repeat markers. Front Genet 2022; 13:1000440. [PMID: 36406138 PMCID: PMC9669911 DOI: 10.3389/fgene.2022.1000440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/06/2022] [Indexed: 10/10/2023] Open
Abstract
The genus Vigna is an agronomically important taxon, with many of its species inhabiting a wide range of environments and offering numerous useful genes for the improvement of the cultivated types. The present study aimed to detect the genomic regions associated with yield-attributing traits by genome-wide association mapping. A diverse panel of 98 wild and cultivated Vigna accessions (acc.) belonging to 13 different species was evaluated for yield and related traits during the kharif season of 2017 and 2018. The panel was also genotyped using 92 cross-genera and cross-species simple sequence repeat markers to study the population genetic structure and useful market-trait associations. The PCA and trait correlation established relationships amongst the traits during both seasons while 100-seed weight (HSW) had a positive correlation with pod length (PL), and days to first flowering (DFF) with days to maturity (DM). The population genetic structure analysis grouped different acc. into three genetically distinct sub-populations with SP-1 comprising 34 acc., SP-2 (24 acc.), and SP-3 (33 acc.) and one admixture group (7 acc.). Mixed linear model analysis revealed an association of 13 markers, namely, VR018, VR039, VR022, CEDG033, GMES0337, MBSSR008, CEDG220, VM27, CP1225, CP08695, CEDG100, CEDG008, and CEDG096A with nine traits. Seven of the aforementioned markers, namely, VR018 for plant height (PH) and terminal leaflet length (TLL), VR022 for HSW and pod length (PL), CEDG033 for DFF and DM, MBSSR008 for DFF and DM, CP1225 for CC at 30 days (CC30), DFF and DM, CEDG100 for PH and terminal leaflet length (TLL), and CEDG096A for CC30 and chlorophyll content at 45 days were associated with multiple traits. The marker CEDG100, associated with HSW, PH, and TLL, is co-localized in gene-encoding histone-lysine N-methyltransferase ATX5. Similarly, VR22, associated with PL and HSW, is co-located in gene-encoding SHOOT GRAVITROPISM 5 in mungbean. These associations may be highly useful for marker-assisted genetic improvement of mungbean and other related Vigna species.
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Affiliation(s)
- Gita Kumari
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - G. Roopa Lavanya
- Sam Higginbottom University of Agricultural Technology and Sciences, Prayagraj, India
| | - Pravin Tiwari
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - P. G. Gore
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Tripathi
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
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Zhang Y, Han E, Peng Y, Wang Y, Wang Y, Geng Z, Xu Y, Geng H, Qian Y, Ma S. Rice co-expression network analysis identifies gene modules associated with agronomic traits. PLANT PHYSIOLOGY 2022; 190:1526-1542. [PMID: 35866684 PMCID: PMC9516743 DOI: 10.1093/plphys/kiac339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Identifying trait-associated genes is critical for rice (Oryza sativa) improvement, which usually relies on map-based cloning, quantitative trait locus analysis, or genome-wide association studies. Here we show that trait-associated genes tend to form modules within rice gene co-expression networks, a feature that can be exploited to discover additional trait-associated genes using reverse genetics. We constructed a rice gene co-expression network based on the graphical Gaussian model using 8,456 RNA-seq transcriptomes, which assembled into 1,286 gene co-expression modules functioning in diverse pathways. A number of the modules were enriched with genes associated with agronomic traits, such as grain size, grain number, tiller number, grain quality, leaf angle, stem strength, and anthocyanin content, and these modules are considered to be trait-associated gene modules. These trait-associated gene modules can be used to dissect the genetic basis of rice agronomic traits and to facilitate the identification of trait genes. As an example, we identified a candidate gene, OCTOPUS-LIKE 1 (OsOPL1), a homolog of the Arabidopsis (Arabidopsis thaliana) OCTOPUS gene, from a grain size module and verified it as a regulator of grain size via functional studies. Thus, our network represents a valuable resource for studying trait-associated genes in rice.
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Affiliation(s)
- Yu Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Ershang Han
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yuming Peng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yuzhou Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yifan Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Zhenxing Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yupu Xu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Haiying Geng
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
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Wang H, Han X, Fu X, Sun X, Chen H, Wei X, Cui S, Liu Y, Guo W, Li X, Xing J, Zhang Y. Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:911993. [PMID: 36212357 PMCID: PMC9533090 DOI: 10.3389/fpls.2022.911993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.
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Affiliation(s)
- Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofeng Fu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xinling Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Hailong Chen
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xirui Wei
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Shubin Cui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yiguo Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Weiwei Guo
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
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Shao P, Peng Y, Wu Y, Wang J, Pan Z, Yang Y, Aini N, Guo C, Shui G, Chao L, Tian X, An Q, Yang Q, You C, Lu L, Zhang X, Wang M, Nie X. Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:988647. [PMID: 36212380 PMCID: PMC9532966 DOI: 10.3389/fpls.2022.988647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.
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Affiliation(s)
- Panxia Shao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Yabin Peng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanlong Wu
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Jing Wang
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhenyuan Pan
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Yang Yang
- Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Nurimanguli Aini
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Chunping Guo
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Guangling Shui
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Lei Chao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaomin Tian
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Qiushuang An
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Qingyong Yang
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyuan You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
- Cotton Research Institute of the Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, China
| | - Lu Lu
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang, China
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Zhao J, Jiang L, Bai H, Dai Y, Li K, Li S, Wang X, Wu L, Fu Q, Yang Y, Dong Q, Yu S, Wang M, Liu H, Peng Z, Zhu H, Zhang X, He X, Lei Y, Liang Y, Guo L, Zhang H, Yu D, Liu Y, Huang H, Liu C, Peng S, Du Y. Characteristics of members of IGT family genes in controlling rice root system architecture and tiller development. FRONTIERS IN PLANT SCIENCE 2022; 13:961658. [PMID: 36147240 PMCID: PMC9487910 DOI: 10.3389/fpls.2022.961658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
Root system architecture (RSA) and tiller are important agronomic traits. However, the mechanisms of the IGT family genes regulate RSA and tiller development in different rice varieties remain unclear. In this study, we demonstrated that 38 rice varieties obtained from Yuanyang Hani's terraced fields with different RSA and could be classified into six groups based on the ratio of root length and width. We found a positive correlation between RSA (including root width, length, and area) and tiller number in most of rice varieties. Furthermore, the IGT family genes Deeper Rooting 1 (DRO1), LAZY1, TAC1, and qSOR1 showed different expression patterns when rice grown under irrigation and drought conditions. Moreover, the qSOR1 gene had higher levels in the roots and tillers, and accompanied with higher levels of PIN1b gene in roots when rice grown under drought environmental condition. DRO1 gene had two single nucleotide polymorphisms (SNPs) in the exon 3 sequences and showed different expression patterns in the roots and tillers of the 38 rice varieties. Overexpression of DRO1 with a deletion of exon 5 caused shorter root length, less lateral roots and lower levels of LAZY1, TAC1, and qSOR1. Further protein interaction network, microRNA targeting and co-expression analysis showed that DRO1 plays a critical role in the root and tiller development associated with auxin transport. These data suggest that the RSA and tiller development are regulated by the IGT family genes in an intricate network way, which is tightly related to rice genetic background in rice adapting to different environmental conditions.
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Affiliation(s)
- Jianping Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Lihui Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Hanrui Bai
- Division of Life Sciences and Medicine, College of Life Sciences, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Yuliang Dai
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Kuixiu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Saijie Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xiaoran Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yanfen Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qian Dong
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Si Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Meixian Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Haiyan Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Ziai Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Haiyan Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xiaoyan Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xie He
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yan Lei
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yan Liang
- Yuguopu District Agricultural Comprehensive Service Center, Mengzi, China
| | - Liwei Guo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Hongji Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Decai Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Sheng Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
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Blocking Rice Shoot Gravitropism by Altering One Amino Acid in LAZY1. Int J Mol Sci 2022; 23:ijms23169452. [PMID: 36012716 PMCID: PMC9409014 DOI: 10.3390/ijms23169452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Tiller angle is an important trait that determines plant architecture and yield in cereal crops. Tiller angle is partially controlled during gravistimulation by the dynamic re-allocation of LAZY1 (LA1) protein between the nucleus and plasma membrane, but the underlying mechanism remains unclear. In this study, we identified and characterized a new allele of LA1 based on analysis of a rice (Oryza sativa L.) spreading-tiller mutant la1G74V, which harbors a non-synonymous mutation in the predicted transmembrane (TM) domain-encoding region of this gene. The mutation causes complete loss of shoot gravitropism, leading to prostrate growth of plants. Our results showed that LA1 localizes not only to the nucleus and plasma membrane but also to the endoplasmic reticulum. Removal of the TM domain in LA1 showed spreading-tiller phenotype of plants similar to la1G74V but did not affect the plasma membrane localization; thus, making it distinct from its ortholog ZmLA1 in Zea mays. Therefore, we propose that the TM domain is indispensable for the biological function of LA1, but this domain does not determine the localization of the protein to the plasma membrane. Our study provides new insights into the LA1-mediated regulation of shoot gravitropism.
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Wang H, Ouyang Q, Yang C, Zhang Z, Hou D, Liu H, Xu H. Mutation of OsPIN1b by CRISPR/Cas9 Reveals a Role for Auxin Transport in Modulating Rice Architecture and Root Gravitropism. Int J Mol Sci 2022; 23:ijms23168965. [PMID: 36012245 PMCID: PMC9409181 DOI: 10.3390/ijms23168965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022] Open
Abstract
The distribution and content of auxin within plant tissues affect a variety of important growth and developmental processes. Polar auxin transport (PAT), mainly mediated by auxin influx and efflux transporters, plays a vital role in determining auxin maxima and gradients in plants. The auxin efflux carrier PIN-FORMED (PIN) family is one of the major protein families involved in PAT. Rice (Oryza sativa L.) genome possesses 12 OsPIN genes. However, the detailed functions of OsPIN genes involved in regulating the rice architecture and gravity response are less well understood. In the present study, OsPIN1b was disrupted by CRISPR/Cas9 technology, and its roles in modulating rice architecture and root gravitropism were investigated. Tissue-specific analysis showed that OsPIN1b was mainly expressed in roots, stems and sheaths at the seedling stage, and the transcript abundance was progressively decreased during the seedling stages. Expression of OsPIN1b could be quickly and greatly induced by NAA, indicating that OsPIN1b played a vital role in PAT. IAA homeostasis was disturbed in ospin1b mutants, as evidenced by the changed sensitivity of shoot and root to NAA and NPA treatment, respectively. Mutation of OsPIN1b resulted in pleiotropic phenotypes, including decreased growth of shoots and primary roots, reduced adventitious root number in rice seedlings, as well as shorter and narrower leaves, increased leaf angle, more tiller number and decreased plant height and panicle length at the late developmental stage. Moreover, ospin1b mutants displayed a curly root phenotype cultured with tap water regardless of lighting conditions, while nutrient solution culture could partially rescue the curly root phenotype in light and almost completely abolish this phenotype in darkness, indicating the involvement of the integration of light and nutrient signals in root gravitropism regulation. Additionally, amyloplast sedimentation was impaired in the peripheral tiers of the ospin1b root cap columella cell, while it was not the main contributor to the abnormal root gravitropism. These data suggest that OsPIN1b not only plays a vital role in regulating rice architecture but also functions in regulating root gravitropism by the integration of light and nutrient signals.
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Affiliation(s)
- Huihui Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Qiqi Ouyang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Chong Yang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Zhuoyan Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Dianyun Hou
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Hao Liu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
| | - Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China
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