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Huang K, Wang Y, Li Y, Zhang B, Zhang L, Duan P, Xu R, Wang D, Liu L, Zhang G, Zhang H, Wang C, Guo N, Hao J, Luo Y, Zhu X, Li Y. Modulation of histone acetylation enables fully mechanized hybrid rice breeding. NATURE PLANTS 2024; 10:954-970. [PMID: 38831046 DOI: 10.1038/s41477-024-01720-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024]
Abstract
Hybrid rice has achieved high grain yield and greatly contributes to food security, but the manual-labour-intensive hybrid seed production process limits fully mechanized hybrid rice breeding. For next-generation hybrid seed production, the use of small-grain male sterile lines to mechanically separate small hybrid seeds from mixed harvest is promising. However, it is difficult to find ideal grain-size genes for breeding ideal small-grain male sterile lines without penalties in the number of hybrid seeds and hybrid rice yield. Here we report that the use of small-grain alleles of the ideal grain-size gene GSE3 in male sterile lines enables fully mechanized hybrid seed production and dramatically increases hybrid seed number in three-line and two-line hybrid rice systems. The GSE3 gene encodes a histone acetyltransferase that binds histones and influences histone acetylation levels. GSE3 is recruited by the transcription factor GS2 to the promoters of their co-regulated grain-size genes and influences the histone acetylation status of their co-regulated genes. Field trials demonstrate that genome editing of GSE3 can be used to immediately improve current elite male sterile lines of hybrid rice for fully mechanized hybrid rice breeding, providing a new perspective for mechanized hybrid breeding in other crops.
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Affiliation(s)
- Ke Huang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Hainan Seed Industry Laboratory, Sanya, China
| | - Yuexing Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yingjie Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Hainan Seed Industry Laboratory, Sanya, China
| | - Baolan Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Limin Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Penggen Duan
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ran Xu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dekai Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lijie Liu
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - Guozheng Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hao Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - Chenjie Wang
- School of Breeding and Multiplication, Hainan University, Sanya, China
| | - Nian Guo
- School of Breeding and Multiplication, Hainan University, Sanya, China
| | - Jianqin Hao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuehua Luo
- School of Breeding and Multiplication, Hainan University, Sanya, China
| | - Xudong Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
| | - Yunhai Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agriculture, University of Chinese Academy of Sciences, Beijing, China.
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2
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You J, Ye L, Wang D, Zhang Y, Xiao W, Wei M, Wu R, Liu J, He G, Zhao F, Zhang T. Mapping and candidate gene analysis of QTLs for grain shape in a rice chromosome segment substitution line Z485 and breeding of SSSLs. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:39. [PMID: 38766512 PMCID: PMC11099003 DOI: 10.1007/s11032-024-01480-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01480-x.
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Affiliation(s)
- Jing You
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Li Ye
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Dachuan Wang
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Yi Zhang
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Wenwen Xiao
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Mi Wei
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Ruhui Wu
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Jinyan Liu
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Guanghua He
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Fangming Zhao
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
| | - Ting Zhang
- Key Laboratory of Crop Molecular Improvement, College of Agronomy and Biotechnology, Rice Research InstituteAcademy of Agricultural SciencesSouthwest University, Chongqing, 400715 China
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3
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Wen Y, Hu P, Fang Y, Tan Y, Wang Y, Wu H, Wang J, Wu K, Chai B, Zhu L, Zhang G, Gao Z, Ren D, Zeng D, Shen L, Dong G, Zhang Q, Li Q, Xiong G, Xue D, Qian Q, Hu J. GW9 determines grain size and floral organ identity in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:915-928. [PMID: 37983630 PMCID: PMC10955487 DOI: 10.1111/pbi.14234] [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: 02/20/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/22/2023]
Abstract
Grain weight is an important determinant of grain yield. However, the underlying regulatory mechanisms for grain size remain to be fully elucidated. Here, we identify a rice mutant grain weight 9 (gw9), which exhibits larger and heavier grains due to excessive cell proliferation and expansion in spikelet hull. GW9 encodes a nucleus-localized protein containing both C2H2 zinc finger (C2H2-ZnF) and VRN2-EMF2-FIS2-SUZ12 (VEFS) domains, serving as a negative regulator of grain size and weight. Interestingly, the non-frameshift mutations in C2H2-ZnF domain result in increased plant height and larger grain size, whereas frameshift mutations in both C2H2-ZnF and VEFS domains lead to dwarf and malformed spikelet. These observations indicated the dual functions of GW9 in regulating grain size and floral organ identity through the C2H2-ZnF and VEFS domains, respectively. Further investigation revealed the interaction between GW9 and the E3 ubiquitin ligase protein GW2, with GW9 being the target of ubiquitination by GW2. Genetic analyses suggest that GW9 and GW2 function in a coordinated pathway controlling grain size and weight. Our findings provide a novel insight into the functional role of GW9 in the regulation of grain size and weight, offering potential molecular strategies for improving rice yield.
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Affiliation(s)
- Yi Wen
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Peng Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Yunxia Fang
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Yiqing Tan
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yueying Wang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Hao Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Junge Wang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Bingze Chai
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Li Zhu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Deyong Ren
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Dali Zeng
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Lan Shen
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guojun Dong
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Qing Li
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guosheng Xiong
- Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina
| | - Dawei Xue
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Qian Qian
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Jiang Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
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4
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Sun Z, Mei T, Tan X, Feng T, Li R, Duan S, Zhao H, Ye Y, Liu B, Zhou A, Ai H, Huang X. The ldp1 Mutation Affects the Expression of Auxin-Related Genes and Enhances SAM Size in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:759. [PMID: 38592751 PMCID: PMC10975181 DOI: 10.3390/plants13060759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Panicle type is one of the important factors affecting rice (Oryza sativa L.) yield, and the identification of regulatory genes in panicle development can provide significant insights into the molecular network involved. This study identified a large and dense panicle 1 (ldp1) mutant produced from the Wuyunjing 7 (WYJ7) genotype, which displayed significant relative increases in panicle length, number of primary and secondary branches, number of grains per panicle, grain width, and grain yield per plant. Scanning electron microscopy results showed that the shoot apical meristem (SAM) of ldp1 was relatively larger at the bract stage (BM), with a significantly increased number of primary (PBM) and secondary branch (SBM) meristematic centers, indicating that the ldp1 mutation affects early stages in SAM development Comparative RNA-Seq analysis of meristem tissues from WYJ7 and ldp1 at the BM, PBM, and SBM developmental stages indicated that the number of differentially expressed genes (DEGs) were highest (1407) during the BM stage. Weighted gene coexpression network analysis (WGCNA) revealed that genes in one module (turquoise) are associated with the ldp1 phenotype and highly expressed during the BM stage, suggesting their roles in the identity transition and branch differentiation stages of rice inflorescences. Hub genes involved in auxin synthesis and transport pathways, such as OsAUX1, OsAUX4, and OsSAUR25, were identified. Moreover, GO and KEGG analysis of the DEGs in the turquoise module and the 1407 DEGs in the BM stage revealed that a majority of genes involved in tryptophan metabolism and auxin signaling pathway were differentially expressed between WYJ and ldp1. The genetic analysis indicated that the ldp1 phenotype is controlled by a recessive monogene (LDP1), which was mapped to a region between 16.9 and 18.1 Mb on chromosome seven. This study suggests that the ldp1 mutation may affect the expression of key genes in auxin synthesis and signal transduction, enhance the size of SAM, and thus affect panicle development. This study provides insights into the molecular regulatory network underlying rice panicle morphogenesis and lays an important foundation for further understanding the function and molecular mechanism of LDP1 during panicle development.
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Affiliation(s)
- Zhanglun Sun
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Tianrun Mei
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Xuan Tan
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Tingting Feng
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Ruining Li
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Sumei Duan
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Yafeng Ye
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230001, China; (Y.Y.); (B.L.)
| | - Binmei Liu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230001, China; (Y.Y.); (B.L.)
| | - Aifeng Zhou
- Anhui Xin Fu Xiang Tian Ecological Agriculture Co., Ltd., Maanshan 238200, China;
| | - Hao Ai
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou 239000, China; (Z.S.); (T.M.); (X.T.); (T.F.); (R.L.); (S.D.); (H.Z.)
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5
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Wang P, Ma L, Li D, Zhang B, Zhou T, Zhou X, Xing Y. Fine mapping of the panicle length QTL qPL5 in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:6. [PMID: 38261843 PMCID: PMC10794681 DOI: 10.1007/s11032-024-01443-2] [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: 11/08/2023] [Accepted: 12/02/2023] [Indexed: 01/25/2024]
Abstract
Panicle length is a crucial trait tightly associated with spikelets per panicle and grain yield in rice. To dissect the genetic basis of panicle length, a population of 161 recombinant inbred lines (RILs) was developed from the cross between an aus variety Chuan 7 (C7) and a tropical Geng variety Haoboka (HBK). C7 has a panicle length of 30 cm, 7 cm longer than that of HBK, and the panicle length was normally distributed in the RIL population. A total of six quantitative trait loci (QTLs) for panicle length were identified, and single QTLs explained the phenotypic variance from 4.9 to 18.1%. Among them, three QTLs were mapped to the regions harbored sd1, DLT, and Ehd1, respectively. To validate the genetic effect of a minor QTL qPL5, a near-isogenic F2 (NIF2) population segregated at qPL5 was developed. Interestingly, panicle length displayed bimodal distribution, and heading date also exhibited significant variation in the NIF2 population. qPL5 accounted for 66.5% of the panicle length variance. The C7 allele at qPL5 increased panicle length by 2.4 cm and promoted heading date by 5 days. Finally, qPL5 was narrowed down to an 80-kb region flanked by markers M2197 and M2205 using a large NIF2 population of 7600 plants. LOC_Os05g37540, encoding a phytochrome signal protein whose homolog in Arabidopsis enlarges panicle length, is regarded as the candidate gene because a single-nucleotide mutation (C1099T) caused a premature stop codon in HBK. The characterization of qPL5 with enlarging panicle length but promoting heading date makes its great value in breeding early mature varieties without yield penalty in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01443-2.
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Affiliation(s)
- Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Daoyang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tianhao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
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6
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Wang Y, Lv Y, Yu H, Hu P, Wen Y, Wang J, Tan Y, Wu H, Zhu L, Wu K, Chai B, Liu J, Zeng D, Zhang G, Zhu L, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Li Q, Guo L, Xiong G, Qian Q, Hu J. GR5 acts in the G protein pathway to regulate grain size in rice. PLANT COMMUNICATIONS 2024; 5:100673. [PMID: 37596786 PMCID: PMC10811372 DOI: 10.1016/j.xplc.2023.100673] [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: 02/24/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Grain size is an important determinant of grain yield in rice. Although dozens of grain size genes have been reported, the molecular mechanisms that control grain size remain to be fully clarified. Here, we report the cloning and characterization of GR5 (GRAIN ROUND 5), which is allelic to SMOS1/SHB/RLA1/NGR5 and encodes an AP2 transcription factor. GR5 acts as a transcriptional activator and determines grain size by influencing cell proliferation and expansion. We demonstrated that GR5 physically interacts with five Gγ subunit proteins (RGG1, RGG2, DEP1, GS3, and GGC2) and acts downstream of the G protein complex. Four downstream target genes of GR5 in grain development (DEP2, DEP3, DRW1, and CyCD5;2) were revealed and their core T/CGCAC motif identified by yeast one-hybrid, EMSA, and ChIP-PCR experiments. Our results revealed that GR5 interacts with Gγ subunits and cooperatively determines grain size by regulating the expression of downstream target genes. These findings provide new insight into the genetic regulatory network of the G protein signaling pathway in the control of grain size and provide a potential target for high-yield rice breeding.
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Affiliation(s)
- Yueying Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yang Lv
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Haiping Yu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Peng Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yi Wen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Junge Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Yiqing Tan
- Nanjing Agricultural University, Nan Jing 210000, Jiangsu, China
| | - Hao Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Lixin Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Bingze Chai
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Jialong Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Lan Shen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Qing Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China
| | - Guosheng Xiong
- Nanjing Agricultural University, Nan Jing 210000, Jiangsu, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, Hainan, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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7
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He L, Chen T, Liang W, Zhao C, Zhao L, Yao S, Zhou L, Zhu Z, Zhao Q, Lu K, Wang C, Zhu L, Zhang Y. The RING-Type Domain-Containing Protein GNL44 Is Essential for Grain Size and Quality in Rice ( Oryza sativa L.). Int J Mol Sci 2024; 25:589. [PMID: 38203760 PMCID: PMC10779214 DOI: 10.3390/ijms25010589] [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: 11/22/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Grain size in rice (Oryza sativa L.) shapes yield and quality, but the underlying molecular mechanism is not fully understood. We functionally characterized GRAIN NUMBER AND LARGE GRAIN SIZE 44 (GNL44), encoding a RING-type protein that localizes to the cytoplasm. The gnl44 mutant has fewer but enlarged grains compared to the wild type. GNL44 is mainly expressed in panicles and developing grains. Grain chalkiness was higher in the gnl44 mutant than in the wild type, short-chain amylopectin content was lower, middle-chain amylopectin content was higher, and appearance quality was worse. The amylose content and gel consistency of gnl44 were lower, and protein content was higher compared to the wild type. Rapid Visco Analyzer results showed that the texture of cooked gnl44 rice changed, and that the taste value of gnl44 was lower, making the eating and cooking quality of gnl44 worse than that of the wild type. We used gnl44, qgl3, and gs3 monogenic and two-gene near-isogenic lines to study the effects of different combinations of genes affecting grain size on rice quality-related traits. Our results revealed additive effects for these three genes on grain quality. These findings enrich the genetic resources available for rice breeders.
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Affiliation(s)
- Lei He
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Tao Chen
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Wenhua Liang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Chunfang Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Ling Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Shu Yao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Lihui Zhou
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Zhen Zhu
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Qingyong Zhao
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Kai Lu
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Cailin Wang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yadong Zhang
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice, Jiangsu Academy of Agricultural Science, Nanjing 210014, China (C.W.)
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
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8
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [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: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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9
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Wu J, Sun LQ, Song Y, Bai Y, Wan GY, Wang JX, Xia JQ, Zhang ZY, Zhang ZS, Zhao Z, Xiang CB. The OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice. THE NEW PHYTOLOGIST 2023; 240:2404-2418. [PMID: 37845836 DOI: 10.1111/nph.19318] [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: 03/15/2023] [Accepted: 09/16/2023] [Indexed: 10/18/2023]
Abstract
Rice panicles, a major component of yield, are regulated by phytohormones and nutrients. How mineral nutrients promote panicle architecture remains largely unknown. Here, we report that NIN-LIKE PROTEIN3 and 4 (OsNLP3/4) are crucial positive regulators of rice panicle architecture in response to nitrogen (N). Loss-of-function mutants of either OsNLP3 or OsNLP4 produced smaller panicles with reduced primary and secondary branches and fewer grains than wild-type, whereas their overexpression plants showed the opposite phenotypes. The OsNLP3/4-regulated panicle architecture was positively correlated with N availability. OsNLP3/4 directly bind to the promoter of OsRFL and activate its expression to promote inflorescence meristem development. Furthermore, OsRFL activates OsMOC1 expression by binding to its promoter. Our findings reveal the novel N-responsive OsNLP3/4-OsRFL-OsMOC1 module that integrates N availability to regulate panicle architecture, shedding light on how N nutrient signals regulate panicle architecture and providing candidate targets for the improvement of crop yield.
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Affiliation(s)
- Jie Wu
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Liang-Qi Sun
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Ying Song
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Yu Bai
- Experimental Center of Engineering and Materials Science, University of Science and Technology of China, Hefei, 230027, China
| | - Guang-Yu Wan
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Jing-Xian Wang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Jin-Qiu Xia
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zheng-Yi Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zi-Sheng Zhang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Zhong Zhao
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
| | - Cheng-Bin Xiang
- Division of Life Sciences and Medicine, Division of Molecular & Cell Biophysics, Hefei National Science Center for Interdisciplinary Sciences at the Microscale, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China
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10
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Rieu P, Arnoux-Courseaux M, Tichtinsky G, Parcy F. Thinking outside the F-box: how UFO controls angiosperm development. THE NEW PHYTOLOGIST 2023; 240:945-959. [PMID: 37664990 DOI: 10.1111/nph.19234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023]
Abstract
The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Moïra Arnoux-Courseaux
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
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11
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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2023:S2090-1232(23)00265-5. [PMID: 37739122 DOI: 10.1016/j.jare.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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12
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Zheng L, Wu H, Wang A, Zhang Y, Liu Z, Ling HQ, Song XJ, Li Y. The SOD7/DPA4-GIF1 module coordinates organ growth and iron uptake in Arabidopsis. NATURE PLANTS 2023; 9:1318-1332. [PMID: 37550368 DOI: 10.1038/s41477-023-01475-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/03/2023] [Indexed: 08/09/2023]
Abstract
Organ growth is controlled by both intrinsic genetic factors and external environmental signals. However, the molecular mechanisms that coordinate plant organ growth and nutrient supply remain largely unknown. We have previously reported that the B3 domain transcriptional repressor SOD7 (NGAL2) and its closest homologue DPA4 (NGAL3) act redundantly to limit organ and seed growth in Arabidopsis. Here we report that SOD7 represses the interaction between the transcriptional coactivator GRF-INTERACTING FACTOR 1 (GIF1) and growth-regulating factors (GRFs) by competitively interacting with GIF1, thereby limiting organ and seed growth. We further reveal that GIF1 physically interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), which acts as a central regulator of iron uptake and homeostasis. SOD7 can competitively repress the interaction of GIF1 with FIT to influence iron uptake and responses. The sod7-2 dpa4-3 mutant enhances the expression of genes involved in iron uptake and displays high iron accumulation. Genetic analyses support that GIF1 functions downstream of SOD7 to regulate organ and seed growth as well as iron uptake and responses. Thus, our findings define a previously unrecognized mechanism that the SOD7/DPA4-GIF1 module coordinates organ growth and iron uptake by targeting key regulators of growth and iron uptake.
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Affiliation(s)
- Leiying Zheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Anbin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yueying Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zupei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, China.
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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13
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Niu F, Liu M, Dong S, Dong X, Wang Y, Cheng C, Chu H, Hu Z, Ma F, Yan P, Lan D, Zhang J, Zhou J, Sun B, Zhang A, Hu J, Zhang X, He S, Cui J, Yuan X, Yang J, Cao L, Luo X. RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice. Int J Mol Sci 2023; 24:10303. [PMID: 37373450 DOI: 10.3390/ijms241210303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.
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Affiliation(s)
- Fuan Niu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Mingyu Liu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shiqing Dong
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xianxin Dong
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Can Cheng
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huangwei Chu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Zejun Hu
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Fuying Ma
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Dengyong Lan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianming Zhang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jihua Zhou
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Bin Sun
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Anpeng Zhang
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jian Hu
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinwei Zhang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shicong He
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinhao Cui
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinyu Yuan
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Liming Cao
- Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
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14
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Li Y, Wu S, Huang Y, Ma X, Tan L, Liu F, Lv Q, Zhu Z, Hu M, Fu Y, Zhang K, Gu P, Xie D, Sun H, Sun C. OsMADS17 simultaneously increases grain number and grain weight in rice. Nat Commun 2023; 14:3098. [PMID: 37248234 DOI: 10.1038/s41467-023-38726-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
During the processes of rice domestication and improvement, a trade-off effect between grain number and grain weight was a major obstacle for increasing yield. Here, we identify a critical gene COG1, encoding the transcription factor OsMADS17, with a 65-bp deletion in the 5' untranslated region (5' UTR) presented in cultivated rice increasing grain number and grain weight simultaneously through decreasing mRNA translation efficiency. OsMADS17 controls grain yield by regulating multiple genes and that the interaction with one of them, OsAP2-39, has been characterized. Besides, the expression of OsMADS17 is regulated by OsMADS1 directly. It indicates that OsMADS1-OsMADS17-OsAP2-39 participates in the regulatory network controlling grain yield, and downregulation of OsMADS17 or OsAP2-39 expression can further improve grain yield by simultaneously increasing grain number and grain weight. Our findings provide insights into understanding the molecular basis co-regulating rice yield-related traits, and offer a strategy for breeding higher-yielding rice varieties.
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Affiliation(s)
- Yuanjie Li
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, 100084, China
| | - Sheng Wu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, 100084, China
| | - Yongyu Huang
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xin Ma
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Lubin Tan
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Fengxia Liu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zuofeng Zhu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Meixia Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Yongcai Fu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Kun Zhang
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Ping Gu
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Key Laboratory of Bioinformatics, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, 100084, China
| | - Hongying Sun
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
| | - Chuanqing Sun
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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15
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Francis N, Rajasekaran R, Rajagopalan VR, Bakya SV, Muthurajan R, Kumar AG, Alagarswamy S, Krishnamoorthy I, Thiyagarajan C. Molecular characterization and SNP identification using genotyping-by-sequencing in high-yielding mutants of proso millet. FRONTIERS IN PLANT SCIENCE 2023; 14:1108203. [PMID: 37275247 PMCID: PMC10233037 DOI: 10.3389/fpls.2023.1108203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/07/2023] [Indexed: 06/07/2023]
Abstract
Proso millet (Panicummiliaceum L.) is a short-duration C4 crop that is drought tolerant and nutritionally rich and can grow well in marginal lands. Though the crop has many climate-resilient traits like tolerance to drought and heat, its yield is lower than that of common cereals like rice, wheat, and maize. Being an underutilized crop, the molecular resources in the crop are limited. The main aim of the present study was to develop and characterize contrasting mutants for yield and generate functional genomic information for the trait in proso millet. Gamma irradiation-induced mutant population was screened to identify high-yielding mutants, which were evaluated up to M4 generation. One mutant with a dense panicle and high yield (ATL_hy) and one with a lax panicle and low yield (ATL_ly) along with the wild type were sequenced using the genotyping-by-sequencing approach. The variants detected as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) were annotated against the reference genome of proso millet. Bioinformatic analyses using the National Center for Biotechnology Information (NCBI) and UniProt databases were performed to elucidate genetic information related to the SNP variations. A total of 25,901, 30,335, and 31,488 SNPs, respectively, were detected in the wild type, ATL_hy mutants, and ATL_ly mutants. The total number of functional SNPs identified in high-yielding and low-yielding mutants was 84 and 171, respectively. Two functional SNPs in the high-yielding mutant (ATL_hy) and one in the low-yielding mutant (ATL_ly) corresponded to the gene coding for "E3 ubiquitin-protein ligase UPL7". Pathway mapping of the functional SNPs identified that two SNPs in ATL_ly were involved in the starch biosynthetic pathway coding for the starch synthase enzyme. This information can be further used in identifying genes responsible for various metabolic processes in proso millet and in designing useful genetic markers.
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Affiliation(s)
- Neethu Francis
- Department of Genetics and Plant Breeding, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - S. Vinothini Bakya
- Department of Genetics and Plant Breeding, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | | | | | - Senthil Alagarswamy
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Iyanar Krishnamoorthy
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chitdeshwari Thiyagarajan
- Department of Soil Science and Agricultural Chemistry, Tamil Nadu Agricultural University, Coimbatore, India
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16
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Gu J, Guo F, Lin L, Zhang J, Sun W, Muhammad R, Liang H, Duan D, Deng X, Lin Z, Wang Y, Zhong Y, Xu Z. Microbiological mechanism for "production while remediating" in Cd-contaminated paddy fields: A field experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 885:163896. [PMID: 37146825 DOI: 10.1016/j.scitotenv.2023.163896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
Security utilization measures (SUMs) for "production while remediating" in moderate and mild Cd-polluted paddy fields had been widely used. To investigate how SUMs drove rhizosphere soil microbial communities and reduced soil Cd bioavailability, a field experiment was conducted using soil biochemical analysis and 16S rRNA high-throughput sequencing. Results showed that SUMs improved rice yield by increasing the number of effective panicles and filled grains, while also inhibiting soil acidification and enhancing disease resistance by improving soil enzyme activities. SUMs also reduced the accumulation of harmful Cd in rice grains and transformed it into FeMn oxidized Cd, organic-bound Cd, and residual Cd in rhizosphere soil. This was partly due to the higher degree of soil DOM aromatization, which helped complex the Cd with DOM. Additionally, the study also found that microbial activity was the primary source of soil DOM, and that SUMs increased the diversity of soil microbes and recruited many beneficial microbes (Arthrobacter, Candidatus_Solibacter, Bryobacter, Bradyrhizobium, and Flavisolibacter) associated with organic matter decomposition, plant growth promotion, and pathogen inhibition. Besides, special taxa (Bradyyrhizobium and Thermodesulfovibrio) involved in sulfate/sulfur ion generation and nitrate/nitrite reduction pathway were observably enriched, which effectively reduced the soil Cd bioavailability through adsorption and co-precipitation. Therefore, SUMs not only changed the soil physicochemical properties (e.g., pH), but also drove rhizosphere microbes to participate in the chemical species transformation of soil Cd, thus reducing Cd accumulation in rice grains.
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Affiliation(s)
- Jiguang Gu
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Fang Guo
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Lihong Lin
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jiexiang Zhang
- GRG Metrology& Test Group Co., Ltd., Guangzhou 510656, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Riaz Muhammad
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Haojie Liang
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Dengle Duan
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xingying Deng
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zheng Lin
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yifan Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuming Zhong
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhimin Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300350, China; College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
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17
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Li F, Wang K, Zhang X, Han P, Liu Y, Zhang J, Peng T, Li J, Zhao Y, Sun H, Du Y. BPB1 regulates rice ( Oryza sative L.) panicle length and panicle branch development by promoting lignin and inhibiting cellulose accumulation. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:41. [PMID: 37312745 PMCID: PMC10248638 DOI: 10.1007/s11032-023-01389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/24/2023] [Indexed: 06/15/2023]
Abstract
Panicle structure is one of the most important agronomic traits directly related to rice yield. This study identified a rice mutant basal primary branch 1 (bpb1), which exhibited a phenotype of reduced panicle length and arrested basal primary branch development. In addition, lignin content was found to be increased while cellulose content was decreased in bpb1 young panicles. Map-based cloning methods characterized the gene BPB1, which encodes a peptide transporter (PTR) family transporter. Phylogenetic tree analysis showed that the BPB1 family is highly conserved in plants, especially the PTR2 domain. It is worth noting that BPB1 is divided into two categories based on monocotyledonous and dicotyledonous plants. Transcriptome analysis showed that BPB1 mutation can promote lignin synthesis and inhibit cellulose synthesis, starch and sucrose metabolism, cell cycle, expression of various plant hormones, and some star genes, thereby inhibiting rice panicle length, resulting in basal primary branch development stagnant phenotypes. In this study, BPB1 provides new insights into the molecular mechanism of rice panicle structure regulation by BPB1 by regulating lignin and cellulose content and several transcriptional metabolic pathways. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01389-x.
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Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ke Wang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Peijie Han
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Jing Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
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18
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Beretta VM, Franchini E, Ud Din I, Lacchini E, Van den Broeck L, Sozzani R, Orozco-Arroyo G, Caporali E, Adam H, Jouannic S, Gregis V, Kater MM. The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37009647 DOI: 10.1111/tpj.16229] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.
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Affiliation(s)
- Veronica M Beretta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Emanuela Franchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Israr Ud Din
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Elia Lacchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Lisa Van den Broeck
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gregorio Orozco-Arroyo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
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19
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Guo T, Lu ZQ, Xiong Y, Shan JX, Ye WW, Dong NQ, Kan Y, Yang YB, Zhao HY, Yu HX, Guo SQ, Lei JJ, Liao B, Chai J, Lin HX. Optimization of rice panicle architecture by specifically suppressing ligand-receptor pairs. Nat Commun 2023; 14:1640. [PMID: 36964129 PMCID: PMC10039049 DOI: 10.1038/s41467-023-37326-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
Rice panicle architecture determines the grain number per panicle and therefore impacts grain yield. The OsER1-OsMKKK10-OsMKK4-OsMPK6 pathway shapes panicle architecture by regulating cytokinin metabolism. However, the specific upstream ligands perceived by the OsER1 receptor are unknown. Here, we report that the EPIDERMAL PATTERNING FACTOR (EPF)/EPF-LIKE (EPFL) small secreted peptide family members OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 synergistically contribute to rice panicle morphogenesis by recognizing the OsER1 receptor and activating the mitogen-activated protein kinase cascade. Notably, OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 negatively regulate spikelet number per panicle, but OsEPFL8 also controls rice spikelet fertility. A osepfl6 osepfl7 osepfl9 triple mutant had significantly enhanced grain yield without affecting spikelet fertility, suggesting that specifically suppressing the OsEPFL6-OsER1, OsEPFL7-OsER1, and OsEPFL9-OsER1 ligand-receptor pairs can optimize rice panicle architecture. These findings provide a framework for fundamental understanding of the role of ligand-receptor signaling in rice panicle development and demonstrate a potential method to overcome the trade-off between spikelet number and fertility.
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Affiliation(s)
- Tao Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yehui Xiong
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang-Qin Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie-Jie Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jijie Chai
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Luo L, Xie Y, Yu S, Yang J, Chen S, Yuan X, Guo T, Wang H, Liu Y, Chen C, Xiao W, Chen Z. The DnaJ domain-containing heat-shock protein NAL11 determines plant architecture by mediating gibberellin homeostasis in rice (Oryza sativa). THE NEW PHYTOLOGIST 2023; 237:2163-2179. [PMID: 36564987 DOI: 10.1111/nph.18696] [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: 11/15/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Ideal Plant Architecture 1 (IPA1) is a key regulator of plant architecture. However, knowledge of downstream genes applicable for improving rice plant architecture is very limited. We identified the plant architecture regulatory gene NARROW LEAF 11 (NAL11), which encodes a heat-shock protein (HSP) containing a DnaJ domain. A promising rare allele of NAL11 (NAL11-923del-1552 ) positively selected in Aus cultivars was identified; this allele exhibited increased expression and generated relatively few tillers, thick stems, and large panicles, components of the ideal plant architecture (IPA). NAL11 is involved in regulating the cell cycle and cell proliferation. NAL11 loss-of-function mutants present impaired chloroplast development and gibberellin (GA) defects. Biochemical analyses show that IPA1 directly binds to elements in the missing fragment of the NAL11-923del-1552 promoter and negatively regulates NAL11 expression. Genetic analyses support the hypothesis that NAL11 acts downstream of IPA1 to regulate IPA by modulating GA homeostasis, and NAL11 may be an essential complement for IPA1. Our work revealed that avoidance of the inhibition of NAL11-923del-1552 caused by IPA1 represents a positive strategy for rescuing GA defects accompanied by the upregulation of IPA1 in breeding high-yield rice.
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Affiliation(s)
- Lixin Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yuelan Xie
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- Yangjiang Institute of Agricultural Sciences, Yangjiang, 529500, China
| | - Sijia Yu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- Yunnan Key Laboratory of Potato Biology, Yunnan Normal University, Kunming, 650500, China
| | - Sirong Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Xi Yuan
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Chun Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Wuming Xiao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
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21
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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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22
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Ma X, Jia Q, Li S, Chen Z, Ming X, Zhao Y, Zhou DX. An enhanced network of energy metabolism, lysine acetylation, and growth-promoting protein accumulation is associated with heterosis in elite hybrid rice. PLANT COMMUNICATIONS 2023:100560. [PMID: 36774536 PMCID: PMC10363507 DOI: 10.1016/j.xplc.2023.100560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/08/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Heterosis refers to the superior performance of a hybrid compared with its parental lines. Although several genetic and molecular models have been proposed to explain heterosis, it remains unclear how hybrid cells integrate complementary gene expression or activity to drive heterotic growth. In this work, we show that accumulation of growth-promoting and energy metabolism proteins, enhanced energy metabolism activities, and increased protein lysine acetylation were associated with superior growth of the panicle meristem in the elite hybrid rice Shanyou 63 relative to its parental varieties. Metabolism of nuclear/cytosolic acetyl-coenzyme A was also enhanced in the hybrid, which paralleled increases in histone H3 acetylation to selectively target the expression of growth-promoting and metabolic genes. Lysine acetylation of cellular proteins, including TARGET OF RAPAMYCIN complex 1, ribosomal proteins, and energy metabolism enzymes, was also augmented and/or remodeled to modulate their activities. The data indicate that an enhanced network of energy-producing metabolic activity and growth-promoting histone acetylation/gene expression in the hybrid could contribute to its superior growth rate and may constitute a model to explain heterosis.
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Affiliation(s)
- Xuan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingxiao Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Ming
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, 91405 Orsay, France.
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23
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Rios-Ruiz WF, Tuanama-Reátegui C, Huamán-Córdova G, Valdez-Nuñez RA. Co-Inoculation of Endophytes Bacillus siamensis TUR07-02b and Priestia megaterium SMBH14-02 Promotes Growth in Rice with Low Doses of Nitrogen Fertilizer. PLANTS (BASEL, SWITZERLAND) 2023; 12:524. [PMID: 36771609 PMCID: PMC9919783 DOI: 10.3390/plants12030524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Multiple biotic and abiotic factors influence rice cultivation. These factors limit productivity and yield, as well as an irrational use of agrochemicals in rice cultivation. A sustainable alternative is using selected growth-promoting microorganisms to increase nutritional efficiency. In the present study, the direct mechanisms of growth promotion in two strains of Bacillus, three strains of Priestia, and two strains of Burkholderia endophytes of rice were characterized. Bacillus siamensis TUR07-02b and Priestia megaterium SMBH14-02 were selected to promote Oryza sativa var's growth. "Bellavista" was used at different doses (50, 75, and 100%) of mineral nitrogen (N) using a randomized block design by quintuplicate. Both strains, SMBH14-02 and TUR07-02b, presented outstanding promoter characteristics, including auxin production (123.17 and 335.65 μg mL-1, respectively) and biological nitrogen fixation capacity. Similarly, B. siamensis TUR07-02b could solubilize phosphate-Ca (20.94 μg mL-1), cellulases, and pectinases. Under greenhouse conditions, co-inoculated plants receiving 75% of the total dose of mineral nitrogen showed increased agronomic parameters in relation to panicle length, grains per panicle, grain yield, and harvest index by 25.0, 30.7, 39.5, and 12.5%, respectively, compared to the 75% fertilized treatment without inoculation. The strains of B. siamensis TUR07-02b and P. megaterium SMBH14-02 are potential microbial resources in the formulation of new inoculants to reduce the use of nitrogenous fertilizers. Thus, agronomic validation of the inoculant consortium at the field level will be an essential step in providing an alternative for the sustainable management of rice cultivation and increased productivity of rice farmers in the San Martín region.
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Affiliation(s)
- Winston Franz Rios-Ruiz
- Laboratorio de Microbiología Agrícola, Departamento Académico Agrosilvopastoril, Facultad de Ciencias Agrarias, Universidad Nacional de San Martín, Tarapoto 22202, Perú
| | - Ciceron Tuanama-Reátegui
- Laboratorio de Microbiología Agrícola, Departamento Académico Agrosilvopastoril, Facultad de Ciencias Agrarias, Universidad Nacional de San Martín, Tarapoto 22202, Perú
| | - Gamaniel Huamán-Córdova
- Laboratorio de Microbiología Agrícola, Departamento Académico Agrosilvopastoril, Facultad de Ciencias Agrarias, Universidad Nacional de San Martín, Tarapoto 22202, Perú
| | - Renzo Alfredo Valdez-Nuñez
- Departamento Académico de Ciencias Básicas, Facultad de Ingeniería, Universidad Nacional de Barranca, Barranca 15169, Perú
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24
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Hanlon MT, Vejchasarn P, Fonta JE, Schneider HM, McCouch SR, Brown KM. Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation. BMC PLANT BIOLOGY 2023; 23:6. [PMID: 36597029 PMCID: PMC9811729 DOI: 10.1186/s12870-022-04026-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus, indica, temperate japonica, and tropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets. RESULTS We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and Arabidopsis. CONCLUSIONS Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.
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Affiliation(s)
- Meredith T Hanlon
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, Huck Institutes of the Life Sciences, Penn State University, University Park, PA, 16802, USA
| | - Phanchita Vejchasarn
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Rice Department, Ministry of Agriculture, Ubon Ratchathani Rice Research Center, Ubon Ratchathani, 34000, Thailand
| | - Jenna E Fonta
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, Huck Institutes of the Life Sciences, Penn State University, University Park, PA, 16802, USA
| | - Hannah M Schneider
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA
- Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, the Netherlands
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853-1901, USA
- Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Kathleen M Brown
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16802, USA.
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25
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Zhang Q, Xie J, Wang X, Liu M, Zhu X, Yang T, Khan NU, Sun C, Li J, Zhang Z, Li Z, Zhang H. Natural variation of RGN1a regulates grain number per panicle in japonica rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1097622. [PMID: 36589052 PMCID: PMC9795840 DOI: 10.3389/fpls.2022.1097622] [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: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The grain number per panicle (GNP) is an important yield component. Identifying naturally favorable variations in GNP will benefit high-yield rice breeding. Here, we performed a genome-wide association study using a mini-core collection of 266 cultivated rice accessions with deep sequencing data and investigated the phenotype for three years. Three genes, i.e., TOTOU1 (TUT1), Grain height date 7 (Ghd7), and Days to heading 7/Grain height date 7.1/Pseudo-Response Regulator37 (DTH7/Ghd7.1/OsPRR37), which regulate GNP, were found in the quantitative trait loci (QTL) identified in this study. A stable QTL, qGNP1.3, which showed a strong correlation with variations in GNP, was repeatedly detected. After functional and transgenic phenotype analysis, we identified a novel gene, regulator of grain number 1a (RGN1a), which codes for protein kinase, controlling GNP in rice. The RGN1a mutation caused 37.2%, 27.8%, 51.2%, and 25.5% decreases in grain number, primary branch number per panicle, secondary branch number per panicle, and panicle length, respectively. Furthermore, breeding utilization analysis revealed that the additive effects of the dominant allelic variants of RGN1a and DTH7 played a significant role in increasing the grain number per panicle in japonica rice. Our findings enrich the gene pool and provide an effective strategy for the genetic improvement of grain numbers.
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Affiliation(s)
- Quan Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jianyin Xie
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Xueqiang Wang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Miaosong Liu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Tao Yang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Najeeb Ullah Khan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Chen Sun
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya Nanfan Research Institute of Hainan University, Sanya, China
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26
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Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield. Biomolecules 2022; 12:biom12121772. [PMID: 36551200 PMCID: PMC9775962 DOI: 10.3390/biom12121772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.
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27
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Developing Genetic Engineering Techniques for Control of Seed Size and Yield. Int J Mol Sci 2022; 23:ijms232113256. [PMID: 36362043 PMCID: PMC9655546 DOI: 10.3390/ijms232113256] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.
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28
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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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29
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Chun Y, Kumar A, Li X. Genetic and molecular pathways controlling rice inflorescence architecture. FRONTIERS IN PLANT SCIENCE 2022; 13:1010138. [PMID: 36247571 PMCID: PMC9554555 DOI: 10.3389/fpls.2022.1010138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Rice inflorescence is one of the major organs in determining grain yield. The genetic and molecular regulation on rice inflorescence architecture has been well investigated over the past years. In the present review, we described genes regulating rice inflorescence architecture based on their roles in meristem activity maintenance, meristem identity conversion and branch elongation. We also introduced the emerging regulatory pathways of phytohormones involved in rice inflorescence development. These studies show the intricacies and challenges of manipulating inflorescence architecture for rice yield improvement.
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Affiliation(s)
- Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ashmit Kumar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Fisheries and Forestry, Fiji National University, Nausori, Fiji
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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30
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Ma W, Cui S, Lu Z, Yan X, Cai L, Lu Y, Cai K, Zhou H, Ma R, Zhou S, Wang X. YTH Domain Proteins Play an Essential Role in Rice Growth and Stress Response. PLANTS 2022; 11:plants11172206. [PMID: 36079588 PMCID: PMC9460353 DOI: 10.3390/plants11172206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
As the most prevalent epi-transcriptional modification, m6A modifications play essential roles in regulating RNA fate. The molecular functions of YTH521-B homology (YTH) domain proteins, the most known READER proteins of m6A modifications, have been well-studied in animals. Although plants contain more YTH domain proteins than other eukaryotes, little is known about their biological importance. In dicot species Arabidopsis thaliana, the YTHDFA clade members ECT2/3/4 and CPSF30-L are well-studied and important for cell proliferation, plant organogenesis, and nitrate transport. More emphasis is needed on the biological functions of plant YTH proteins, especially monocot YTHs. Here we presented a detailed phylogenetic relationship of eukaryotic YTH proteins and clustered plant YTHDFC clade into three subclades. To determine the importance of monocot YTH proteins, YTH knockout mutants and RNAi-induced knockdown plants were constructed and used for phenotyping, transcriptomic analysis, and stress treatments. Knocking out or knocking down OsYTHs led to the downregulation of multicellular organismal regulation genes and resulted in growth defects. In addition, loss-of-function ythdfa mutants led to better salinity tolerance whereas ythdfc mutants were more sensitive to abiotic stress. Overall, our study establishes the functional relevance of rice YTH genes in plant growth regulation and stress response.
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Affiliation(s)
- Weiwei Ma
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Lu
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Xiaofeng Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Long Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongfa Lu
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Kefeng Cai
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Huacheng Zhou
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Rongrong Ma
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (S.Z.); (X.W.)
| | - Xiaole Wang
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
- Correspondence: (S.Z.); (X.W.)
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31
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Wittern LM, Barrero JM, Bovill WD, Verbyla KL, Hughes T, Swain SM, Steed G, Webb AAR, Gardner K, Greenland A, Jacobs J, Frohberg C, Schmidt RC, Cavanagh C, Rohde A, Davey MW, Hannah MA. Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat. Sci Rep 2022; 12:14229. [PMID: 35987959 PMCID: PMC9392761 DOI: 10.1038/s41598-022-18614-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTwo homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.
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32
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Lu Y, Chuan M, Wang H, Chen R, Tao T, Zhou Y, Xu Y, Li P, Yao Y, Xu C, Yang Z. Genetic and molecular factors in determining grain number per panicle of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:964246. [PMID: 35991390 PMCID: PMC9386260 DOI: 10.3389/fpls.2022.964246] [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: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tianyun Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Youli Yao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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33
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Miao Y, Xun Q, Taji T, Tanaka K, Yasuno N, Ding C, Kyozuka J. ABERRANT PANICLE ORGANIZATION2 controls multiple steps in panicle formation through common direct-target genes. PLANT PHYSIOLOGY 2022; 189:2210-2226. [PMID: 35556145 PMCID: PMC9342985 DOI: 10.1093/plphys/kiac216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 05/15/2023]
Abstract
At the transition from vegetative to reproductive growth in rice (Oryza sativa), a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor (TF). APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation during reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.
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Affiliation(s)
- Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Naoko Yasuno
- Graduate School of Life Sciences, University of Tokyo, Tokyo 113-8654, Japan
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Smalley S, Hellmann H. Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111275. [PMID: 35487671 DOI: 10.1016/j.plantsci.2022.111275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.
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Affiliation(s)
- Samuel Smalley
- Washington State University, Pullman, WA 99164, United States
| | - Hanjo Hellmann
- Washington State University, Pullman, WA 99164, United States.
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35
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HECT ubiquitin ligases as accessory proteins of the plant proteasome. Essays Biochem 2022; 66:135-145. [PMID: 35635104 PMCID: PMC9400063 DOI: 10.1042/ebc20210064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/21/2022] [Accepted: 04/29/2022] [Indexed: 12/31/2022]
Abstract
The proteasome plays vital roles in eukaryotic cells by orchestrating the regulated degradation of large repertoires of substrates involved in numerous biological processes. Proteasome dysfunction is associated with a wide variety of human pathologies and in plants severely affects growth, development and responses to stress. The activity of E3 ubiquitin ligases marks proteins fated for degradation with chains of the post-translational modifier, ubiquitin. Proteasomal processing of ubiquitinated substrates involves ubiquitin chain recognition, deubiquitination, ATP-mediated unfolding and translocation, and proteolytic digestion. This complex series of steps is made possible not only by the many specialised subunits of the 1.5 MDa proteasome complex but also by a range of accessory proteins that are recruited to the proteasome. A surprising class of accessory proteins are members of the HECT-type family of ubiquitin ligases that utilise a unique mechanism for post-translational attachment of ubiquitin to their substrates. So why do proteasomes that already contain all the necessary machinery to recognise ubiquitinated substrates, harbour HECT ligase activity? It is now clear that some ubiquitin ligases physically relay their substrates to proteasome-associated HECT ligases, which prevent substrate stalling at the proteasome. Moreover, HECT ligases ubiquitinate proteasome subunits, thereby modifying the proteasome's ability to recognise substrates. They may therefore enable proteasomes to be both non-specific and extraordinarily selective in a complex substrate environment. Understanding the relationship between the proteasome and accessory HECT ligases will reveal how the proteasome controls so many diverse plant developmental and stress responses.
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36
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Hu P, Tan Y, Wen Y, Fang Y, Wang Y, Wu H, Wang J, Wu K, Chai B, Zhu L, Zhang G, Gao Z, Ren D, Zeng D, Shen L, Xue D, Qian Q, Hu J. LMPA Regulates Lesion Mimic Leaf and Panicle Development Through ROS-Induced PCD in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:875038. [PMID: 35586211 PMCID: PMC9108926 DOI: 10.3389/fpls.2022.875038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Leaf and panicle are important nutrient and yield organs in rice, respectively. Although several genes controlling lesion mimic leaf and panicle abortion have been identified, a few studies have reported the involvement of a single gene in the production of both the traits. In this study, we characterized a panicle abortion mutant, lesion mimic leaf and panicle apical abortion (lmpa), which exhibits lesions on the leaf and causes degeneration of apical spikelets. Molecular cloning revealed that LMPA encodes a proton pump ATPase protein that is localized in the plasma membrane and is highly expressed in leaves and panicles. The analysis of promoter activity showed that the insertion of a fragment in the promoter of lmpa caused a decrease in the transcription level. Cellular and histochemistry analysis indicated that the ROS accumulated and cell death occurred in lmpa. Moreover, physiological experiments revealed that lmpa was more sensitive to high temperatures and salt stress conditions. These results provide a better understanding of the role of LMPA in panicle development and lesion mimic formation by regulating ROS homeostasis.
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Affiliation(s)
- Peng Hu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiqing Tan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yi Wen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yueying Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hao Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Junge Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Kaixiong Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Bingze Chai
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qian Qian
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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37
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Wang Z, Tao S, Liu S, Jia M, Cui D, Sun G, Deng Z, Wang F, Kong X, Fu M, Che Y, Liao R, Li T, Geng S, Mao L, Li A. A Multi-Omics Approach for Rapid Identification of Large Genomic Lesions at the Wheat Dense Spike ( wds) Locus. FRONTIERS IN PLANT SCIENCE 2022; 13:850302. [PMID: 35498697 PMCID: PMC9043957 DOI: 10.3389/fpls.2022.850302] [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: 01/07/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Optimal spike architecture provides a favorable structure for grain development and yield improvement. However, the number of genes cloned to underlie wheat spike architecture is extremely limited. Here, we obtained a wheat dense spike mutant (wds) induced by 60Co treatment of a common wheat landrace Huangfangzhu that exhibited significantly reduced spike and grain lengths. The shortened spike length was caused by longitudinal reduction in number and length of rachis cells. We adopted a multi-omics approach to identify the genomic locus underlying the wds mutant. We performed Exome Capture Sequencing (ECS) and identified two large deletion segments, named 6BL.1 at 334.8∼424.3 Mb and 6BL.2, 579.4∼717.8 Mb in the wds mutant. RNA-seq analysis confirmed that genes located in these regions lost their RNA expression. We then found that the 6BL.2 locus was overlapping with a known spike length QTL, qSL6B.2. Totally, 499 genes were located within the deleted region and two of them were found to be positively correlated with long spike accessions but not the ones with short spike. One of them, TraesCS6B01G334600, a well-matched homolog of the rice OsBUL1 gene that works in the Brassinosteroids (BR) pathway, was identified to be involved in cell size and number regulation. Further transcriptome analysis of young spikes showed that hormone-related genes were enriched among differentially expressed genes, supporting TraesCS6B01G334600 as a candidate gene. Our work provides a strategy to rapid locate genetic loci with large genomic lesions in wheat and useful resources for future wheat study.
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Affiliation(s)
- Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shu Tao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoshuai Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiling Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dada Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoliang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongyin Deng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingchen Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxue Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqing Che
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruyi Liao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Li
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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38
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Jiang S, Wei J, Li N, Wang Z, Zhang Y, Xu R, Zhou L, Huang X, Wang L, Guo S, Wang Y, Song CP, Qian W, Li Y. The UBP14-CDKB1;1-CDKG2 cascade controls endoreduplication and cell growth in Arabidopsis. THE PLANT CELL 2022; 34:1308-1325. [PMID: 34999895 PMCID: PMC8972217 DOI: 10.1093/plcell/koac002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 05/31/2023]
Abstract
Endoreduplication, a process in which DNA replication occurs in the absence of mitosis, is found in all eukaryotic kingdoms, especially plants, where it is assumed to be important for cell growth and cell fate maintenance. However, a comprehensive understanding of the mechanism regulating endoreduplication is still lacking. We previously reported that UBIQUITIN-SPECIFIC PROTEASE14 (UBP14), encoded by DA3, acts upstream of CYCLIN-DEPENDENT KINASE B1;1 (CDKB1;1) to influence endoreduplication and cell growth in Arabidopsis thaliana. The da3-1 mutant possesses large cotyledons with enlarged cells due to high ploidy levels. Here, we identified a suppressor of da3-1 (SUPPRESSOR OF da3-1 6; SUD6), encoding CYCLIN-DEPENDENT KINASE G2 (CDKG2), which promotes endoreduplication and cell growth. CDKG2/SUD6 physically associates with CDKB1;1 in vivo and in vitro. CDKB1;1 directly phosphorylates SUD6 and modulates its stability. Genetic analysis indicated that SUD6 acts downstream of DA3 and CDKB1;1 to control ploidy level and cell growth. Thus, our study establishes a regulatory cascade for UBP14/DA3-CDKB1;1-CDKG2/SUD6-mediated control of endoreduplication and cell growth in Arabidopsis.
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Affiliation(s)
- Shan Jiang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinwei Wei
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhibiao Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yilan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lixun Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, College of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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39
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Grain Size Associated Genes and the Molecular Regulatory Mechanism in Rice. Int J Mol Sci 2022; 23:ijms23063169. [PMID: 35328589 PMCID: PMC8953112 DOI: 10.3390/ijms23063169] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 01/17/2023] Open
Abstract
Grain size is a quantitative trait that is controlled by multiple genes. It is not only a yield trait, but also an important appearance quality of rice. In addition, grain size is easy to be selected in evolution, which is also a significant trait for studying rice evolution. In recent years, many quantitative trait loci (QTL)/genes for rice grain size were isolated by map-based cloning or genome-wide association studies, which revealed the genetic and molecular mechanism of grain size regulation in part. Here, we summarized the QTL/genes cloned for grain size and the regulation mechanism with a view to provide the theoretical basis for improving rice yield and breeding superior varieties.
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40
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Koppolu R, Chen S, Schnurbusch T. Evolution of inflorescence branch modifications in cereal crops. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102168. [PMID: 35016076 DOI: 10.1016/j.pbi.2021.102168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Grasses are ubiquitous in our daily lives, with gramineous cereal crops such as maize, rice, and wheat constituting a large proportion of our daily staple food intake. Evolutionary forces, especially over the past ∼20 million years, have shaped grass adaptability, inflorescence architecture, and reproductive success. Here, we provide basic information on grass evolution and inflorescence structures mainly related to two inflorescence types: branched panicle- and spike-type inflorescences, the latter of which has highly modified branching. We summarize and compare known genetic pathways underlying each infloresecence type and discuss how the maize RAMOSA, rice ABERRANT PANICLE ORGANIZATION, and Triticeae COMPOSITUM pathways are regulated. Our analyses might lay the foundation for understanding species-specific gene regulatory networks that could result in improved sink capacities.
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Affiliation(s)
- Ravi Koppolu
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - Shulin Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany.
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41
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Wang C, Yang X, Li G. Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops. Int J Mol Sci 2021; 22:3508. [PMID: 33805287 PMCID: PMC8037405 DOI: 10.3390/ijms22073508] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Flowering plants develop new organs throughout their life cycle. The vegetative shoot apical meristem (SAM) generates leaf whorls, branches and stems, whereas the reproductive SAM, called the inflorescence meristem (IM), forms florets arranged on a stem or an axis. In cereal crops, the inflorescence producing grains from fertilized florets makes the major yield contribution, which is determined by the numbers and structures of branches, spikelets and florets within the inflorescence. The developmental progression largely depends on the activity of IM. The proper regulations of IM size, specification and termination are outcomes of complex interactions between promoting and restricting factors/signals. Here, we focus on recent advances in molecular mechanisms underlying potential pathways of IM identification, maintenance and differentiation in cereal crops, including rice (Oryza sativa), maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare), highlighting the researches that have facilitated grain yield by, for example, modifying the number of inflorescence branches. Combinatorial functions of key regulators and crosstalk in IM determinacy and specification are summarized. This review delivers the knowledge to crop breeding applications aiming to the improvements in yield performance and productivity.
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Affiliation(s)
- Chengyu Wang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
| | - Gang Li
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
- School of Agriculture, Food and Wine, Waite Research Institute, Waite Campus, The University of Adelaide, Glen Osmond, SA 5064, Australia;
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