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Jiang C, Wang Y, He Y, Peng Y, Xie L, Li Y, Sun W, Zhou J, Zheng C, Xie X. Identification and Characterization of miRNAs and lncRNAs Associated with Salinity Stress in Rice Panicles. Int J Mol Sci 2024; 25:8247. [PMID: 39125819 PMCID: PMC11311799 DOI: 10.3390/ijms25158247] [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: 06/02/2024] [Revised: 07/11/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Salinity is a common abiotic stress that limits crop productivity. Although there is a wealth of evidence suggesting that miRNA and lncRNA play important roles in the response to salinity in rice seedlings and reproductive stages, the mechanism by which competing endogenous RNAs (ceRNAs) influence salt tolerance and yield in rice has been rarely reported. In this study, we conducted full whole-transcriptome sequencing of rice panicles during the reproductive period to clarify the role of ceRNAs in the salt stress response and yield. A total of 214 lncRNAs, 79 miRNAs, and 584 mRNAs were identified as differentially expressed RNAs under salt stress. Functional analysis indicates that they play important roles in GO terms such as response to stress, biosynthesis processes, abiotic stimuli, endogenous stimulus, and response to stimulus, as well as in KEGG pathways such as secondary metabolite biosynthesis, carotenoid biosynthesis, metabolic pathways, and phenylpropanoid biosynthesis. A ceRNA network comprising 95 lncRNA-miRNA-mRNA triplets was constructed. Two lncRNAs, MSTRG.51634.2 and MSTRG.48576.1, were predicted to bind to osa-miR172d-5p to regulate the expression of OsMYB2 and OsMADS63, which have been reported to affect salt tolerance and yield, respectively. Three lncRNAs, MSTRG.30876.1, MSTRG.44567.1, and MSTRG.49308.1, may bind to osa-miR5487 to further regulate the expression of a stress protein (LOC_Os07g48460) and an aquaporin protein (LOC_Os02g51110) to regulate the salt stress response. This study is helpful for understanding the underlying molecular mechanisms of ceRNA that drive the response of rice to salt stress and provide new genetic resources for salt-resistant rice breeding.
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Affiliation(s)
- Conghui Jiang
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Yulong Wang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yanan He
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Yongbin Peng
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Lixia Xie
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Yaping Li
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Wei Sun
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Jinjun Zhou
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chongke Zheng
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
| | - Xianzhi Xie
- Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (C.J.)
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Lu Z, Huang W, Ge Q, Liang G, Sun L, Wu J, Ghouri F, Shahid MQ, Liu X. Seed development-related genes contribute to high yield heterosis in integrated utilization of elite autotetraploid and neo-tetraploid rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1421207. [PMID: 38933462 PMCID: PMC11204133 DOI: 10.3389/fpls.2024.1421207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Introduction Autotetraploid rice holds high resistance to abiotic stress and substantial promise for yield increase, but it could not be commercially used because of low fertility. Thus, our team developed neo-tetraploid rice with high fertility and hybrid vigor when crossed with indica autotetraploid rice. Despite these advances, the molecular mechanisms underlying this heterosis remain poorly understood. Methods An elite indica autotetraploid rice line (HD11) was used to cross with neo-tetraploid rice, and 34 hybrids were obtained to evaluate agronomic traits related to yield. WE-CLSM, RNA-seq, and CRISPR/Cas9 were employed to observe endosperm structure and identify candidate genes from two represent hybrids. Results and discussion These hybrids showed high seed setting and an approximately 55% increase in 1000-grain weight, some of which achieved grain yields comparable to those of the diploid rice variety. The endosperm observations indicated that the starch grains in the hybrids were more compact than those in paternal lines. A total of 119 seed heterosis related genes (SHRGs) with different expressions were identified, which might contribute to high 1000-grain weight heterosis in neo-tetraploid hybrids. Among them, 12 genes had been found to regulate grain weight formation, including OsFl3, ONAC023, OsNAC024, ONAC025, ONAC026, RAG2, FLO4, FLO11, OsISA1, OsNF-YB1, NF-YC12, and OsYUC9. Haplotype analyses of these 12 genes revealed the various effects on grain weight among different haplotypes. The hybrids could polymerize more dominant haplotypes of above grain weight regulators than any homozygous cultivar. Moreover, two SHRGs (OsFl3 and SHRG2) mutants displayed a significant reduction in 1000-grain weight and an increase in grain chalkiness, indicating that OsFl3 and SHRG2 positively regulate grain weight. Our research has identified a valuable indica autotetraploid germplasm for generating strong yield heterosis in combination with neo-tetraploid lines and gaining molecular insights into the regulatory processes of heterosis in tetraploid rice.
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Affiliation(s)
- Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- School of Biology and Agriculture, Shaoguan University, Shaoguan, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Weicong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Qi Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Guobin Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lixia Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Guangdong Base Bank for Lingnan Rice Germplasm Resources, College of Agriculture, South China Agricultural University, Guangzhou, China
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Wang SS, Tsai PH, Cheng SF, Chen RK, Chen KY. Identification of genomic regions controlling spikelet degeneration under FRIZZLE PANICLE (FZP) defect genetic background in rice. Sci Rep 2024; 14:12451. [PMID: 38816469 PMCID: PMC11139880 DOI: 10.1038/s41598-024-63362-8] [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: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
The FZP gene plays a critical role in the formation of lateral branches and spikelets in rice panicle architecture. This study investigates the qSBN7 allele, a hypomorphic variant of FZP, and its influence on panicle architectures in different genetic backgrounds. We evaluated two backcross inbred lines (BILs), BC5_TCS10sbn and BC3_TCS10sbn, each possessing the homozygous qSBN7 allele but demonstrating differing degrees of spikelet degeneration. Our analysis revealed that BC5_TCS10sbn had markedly low FZP expression, which corresponded with an increase in axillary branches and severe spikelet degeneration. Conversely, BC3_TCS10sbn exhibited significantly elevated FZP expression, leading to fewer secondary and tertiary branches, and consequently decreased spikelet degeneration. Compared to BC5_TCS10sbn, BC3_TCS10sbn carries three additional chromosomal substitution segments from its donor parent, IR65598-112-2. All three segments significantly enhance the expression of FZP and reduce the occurrence of tertiary branch and spikelet degeneration. These findings enhance our understanding of the mechanisms regulating FZP and aid rice breeding efforts.
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Affiliation(s)
- Sheng-Shan Wang
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan.
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| | - Pei-Hua Tsai
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan
| | - Shu-Fang Cheng
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan
| | - Rong-Kuen Chen
- Tainan District Agricultural Research and Extension Station, No. 70, Muchang, Xinhua, Tainan, 71246, Taiwan
| | - Kai-Yi Chen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
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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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Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
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Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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6
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Dai D, Huang L, Zhang X, Zhang S, Yuan Y, Wu G, Hou Y, Yuan X, Chen X, Xue C. Identification of a Branch Number Locus in Soybean Using BSA-Seq and GWAS Approaches. Int J Mol Sci 2024; 25:873. [PMID: 38255945 PMCID: PMC10815202 DOI: 10.3390/ijms25020873] [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: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The determination of the soybean branch number plays a pivotal role in plant morphogenesis and yield components. This polygenic trait is subject to environmental influences, and despite its significance, the genetic mechanisms governing the soybean branching number remain incompletely understood. To unravel these mechanisms, we conducted a comprehensive investigation employing a genome-wide association study (GWAS) and bulked sample analysis (BSA). The GWAS revealed 18 SNPs associated with the soybean branch number, among which qGBN3 on chromosome 2 emerged as a consistently detected locus across two years, utilizing different models. In parallel, a BSA was executed using an F2 population derived from contrasting cultivars, Wandou35 (low branching number) and Ruidou1 (high branching number). The BSA results pinpointed a significant quantitative trait locus (QTL), designated as qBBN1, located on chromosome 2 by four distinct methods. Importantly, both the GWAS and BSA methods concurred in co-locating qGBN3 and qBBN1. In the co-located region, 15 candidate genes were identified. Through gene annotation and RT-qPCR analysis, we predicted that Glyma.02G125200 and Glyma.02G125600 are candidate genes regulating the soybean branch number. These findings significantly enhance our comprehension of the genetic intricacies regulating the branch number in soybeans, offering promising candidate genes and materials for subsequent investigations aimed at augmenting the soybean yield. This research represents a crucial step toward unlocking the full potential of soybean cultivation through targeted genetic interventions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China (S.Z.); (Y.Y.); (Y.H.)
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China (S.Z.); (Y.Y.); (Y.H.)
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7
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Chun Y, Fang J, Savelieva EM, Lomin SN, Shang J, Sun Y, Zhao J, Kumar A, Yuan S, Yao X, Liu CM, Arkhipov DV, Romanov GA, Li X. The cytokinin receptor OHK4/OsHK4 regulates inflorescence architecture in rice via an IDEAL PLANT ARCHITECTURE1/WEALTHY FARMER'S PANICLE-mediated positive feedback circuit. THE PLANT CELL 2023; 36:40-64. [PMID: 37811656 PMCID: PMC10734611 DOI: 10.1093/plcell/koad257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/07/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023]
Abstract
Inflorescence architecture is important for rice (Oryza sativa) grain yield. The phytohormone cytokinin (CK) has been shown to regulate rice inflorescence development; however, the underlying mechanism mediated by CK perception is still unclear. Employing a forward genetic approach, we isolated an inactive variant of the CK receptor OHK4/OsHK4 gene named panicle length1, which shows decreased panicle size due to reduced inflorescence meristem (IM) activity. A 2-amino acid deletion in the long α-helix stalk of the sensory module of OHK4 impairs the homodimerization and ligand-binding capacity of the receptor, even though the residues do not touch the ligand-binding domain or the dimerization interface. This deletion impairs CK signaling that occurs through the type-B response regulator OsRR21, which acts downstream of OHK4 in controlling inflorescence size. Meanwhile, we found that IDEAL PLANT ARCHITECTURE1(IPA1)/WEALTHY FARMER'S PANICLE (WFP), encoding a positive regulator of IM development, acts downstream of CK signaling and is directly activated by OsRR21. Additionally, we revealed that IPA1/WFP directly binds to the OHK4 promoter and upregulates its expression through interactions with 2 TCP transcription factors, forming a positive feedback circuit. Altogether, we identified the OHK4-OsRR21-IPA1 regulatory module, providing important insights into the role of CK signaling in regulating rice inflorescence architecture.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Xueyong Li
- Author for correspondence: (X.L.), (G.A.R.)
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8
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Feng G, Xu X, Liu W, Hao F, Yang Z, Nie G, Huang L, Peng Y, Bushman S, He W, Zhang X. Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes. Int J Mol Sci 2023; 24:16370. [PMID: 38003564 PMCID: PMC10671593 DOI: 10.3390/ijms242216370] [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: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wen Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Feigxiang Hao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaun Bushman
- Forage and Range Research Laboratory, United States Department of Agriculture, 695 North 1100 East, Logan, UT 84322-6300, USA
| | - Wei He
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Liu E, Zhu S, Du M, Lyu H, Zeng S, Liu Q, Wu G, Jiang J, Dang X, Dong Z, Hong D. LAX1, functioning with MADS-box genes, determines normal palea development in rice. Gene 2023; 883:147635. [PMID: 37442304 DOI: 10.1016/j.gene.2023.147635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Normal floral organ development in rice is necessary for grain formation. Many MADS-box family genes that belong to ABCDE model have been widely implicated in rice flower development. The LAX1 allele encodes a plant-specific basic helix-loop-helix (bHLH) transcription factor, which is the main regulator of axillary meristem formation in rice. However, the molecular mechanisms of LAX1 allele together with MADS-box family genes underlying palea development have not been reported. We found a short palea mutant plant in a population of indica rice variety 9311 treated with cobalt 60. We report the map-based cloning and characterization of lax1-7, identified as a new mutant allele of the LAX1 locus, and the role of its wild-type allele LAX1 in rice palea development. Through complementary experiments, combined with genetic and molecular biological analyses, the function of the LAX1 allele was determined. We showed that LAX1 allele is expressed specifically in young spikelets and encodes a nucleus-localized protein. In vitro and in vivo experiments revealed that the LAX1 protein physically interacts with OsMADS1, OsMADS6 and OsMADS7. The LAX1 allele is pleiotropic for the maintenance of rice palea identity via cooperation with MADS-box genes and other traits, including axillary meristem initiation, days to heading, plant height, panicle length and spikelet fertility.
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Affiliation(s)
- Erbao Liu
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Shangshang Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyu Du
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Huineng Lyu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyuan Zeng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiangming Liu
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Guocan Wu
- Ningde Institute of Agricultural Sciences, Ningde 355017, China
| | - Jianhua Jiang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Xiaojing Dang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Zhiyao Dong
- College of Life Sciences, Jilin Normal University, Jilin 136000, China
| | - Delin Hong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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10
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Adam H, Gutiérrez A, Couderc M, Sabot F, Ntakirutimana F, Serret J, Orjuela J, Tregear J, Jouannic S, Lorieux M. Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture. BMC Genomics 2023; 24:587. [PMID: 37794325 PMCID: PMC10548634 DOI: 10.1186/s12864-023-09695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.
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Affiliation(s)
- Hélène Adam
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | | | - Marie Couderc
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - François Sabot
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | | | - Julien Serret
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Julie Orjuela
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - James Tregear
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Stefan Jouannic
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | - Mathias Lorieux
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Cali, Colombia.
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11
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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [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: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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12
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Lv Y, Zhang X, Hu Y, Liu S, Yin Y, Wang X. BOS1 is a basic helix-loop-helix transcription factor involved in regulating panicle development in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1162828. [PMID: 37180398 PMCID: PMC10169713 DOI: 10.3389/fpls.2023.1162828] [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: 02/10/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023]
Abstract
Panicle development is crucial to increase the grain yield of rice (Oryza sativa). The molecular mechanisms of the control of panicle development in rice remain unclear. In this study, we identified a mutant with abnormal panicles, termed branch one seed 1-1 (bos1-1). The bos1-1 mutant showed pleiotropic defects in panicle development, such as the abortion of lateral spikelets and the decreased number of primary panicle branches and secondary panicle branches. A combined map-based cloning and MutMap approach was used to clone BOS1 gene. The bos1-1 mutation was located in chromosome 1. A T-to-A mutation in BOS1 was identified, which changed the codon from TAC to AAC, resulting in the amino acid change from tyrosine to asparagine. BOS1 gene encoded a grass-specific basic helix-loop-helix transcription factor, which is a novel allele of the previously cloned LAX PANICLE 1 (LAX1) gene. Spatial and temporal expression profile analyses showed that BOS1 was expressed in young panicles and was induced by phytohormones. BOS1 protein was mainly localized in the nucleus. The expression of panicle development-related genes, such as OsPIN2, OsPIN3, APO1, and FZP, was changed by bos1-1 mutation, suggesting that the genes may be the direct or indirect targets of BOS1 to regulate panicle development. The analysis of BOS1 genomic variation, haplotype, and haplotype network showed that BOS1 gene had several genomic variations and haplotypes. These results laid the foundation for us to further dissect the functions of BOS1.
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Affiliation(s)
| | | | | | | | | | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
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13
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Xu T, Fu D, Xiong X, Zhu J, Feng Z, Liu X, Wu C. OsbHLH067, OsbHLH068, and OsbHLH069 redundantly regulate inflorescence axillary meristem formation in rice. PLoS Genet 2023; 19:e1010698. [PMID: 37053298 PMCID: PMC10128955 DOI: 10.1371/journal.pgen.1010698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 04/25/2023] [Accepted: 03/08/2023] [Indexed: 04/15/2023] Open
Abstract
Rice axillary meristems (AMs) are essential to the formation of tillers and panicle branches in rice, and therefore play a determining role in rice yield. However, the regulation of inflorescence AM development in rice remains elusive. In this study, we identified no spikelet 1-Dominant (nsp1-D), a sparse spikelet mutant, with obvious reduction of panicle branches and spikelets. Inflorescence AM deficiency in nsp1-D could be ascribed to the overexpression of OsbHLH069. OsbHLH069 functions redundantly with OsbHLH067 and OsbHLH068 in panicle AM formation. The Osbhlh067 Osbhlh068 Osbhlh069 triple mutant had smaller panicles and fewer branches and spikelets. OsbHLH067, OsbHLH068, and OsbHLH069 were preferentially expressed in the developing inflorescence AMs and their proteins could physically interact with LAX1. Both nsp1-D and lax1 showed sparse panicles. Transcriptomic data indicated that OsbHLH067/068/069 may be involved in the metabolic pathway during panicle AM formation. Quantitative RT-PCR results demonstrated that the expression of genes involved in meristem development and starch/sucrose metabolism was down-regulated in the triple mutant. Collectively, our study demonstrates that OsbHLH067, OsbHLH068, and OsbHLH069 have redundant functions in regulating the formation of inflorescence AMs during panicle development in rice.
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Affiliation(s)
- Tingting Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaohu Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Junkai Zhu
- Jiangsu Kingearth Seed Co., Ltd., Yangzhou, China
| | - Zhiyun Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xiaobin Liu
- Jiangsu Kingearth Seed Co., Ltd., Yangzhou, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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14
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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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15
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Wang N, Shu X, Zhang F, Wang Z. Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA. FRONTIERS IN PLANT SCIENCE 2023; 13:975530. [PMID: 36704164 PMCID: PMC9872026 DOI: 10.3389/fpls.2022.975530] [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: 06/22/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.
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16
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Deblieck M, Szilagyi G, Andrii F, Saranga Y, Lauterberg M, Neumann K, Krugman T, Perovic D, Pillen K, Ordon F. Dissection of a grain yield QTL from wild emmer wheat reveals sub-intervals associated with culm length and kernel number. Front Genet 2022; 13:955295. [DOI: 10.3389/fgene.2022.955295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic diversity in wheat has been depleted due to domestication and modern breeding. Wild relatives are a valuable source for improving drought tolerance in domesticated wheat. A QTL region on chromosome 2BS of wild emmer wheat (Triticum turgidum ssp. dicoccoides), conferring high grain yield under well-watered and water-limited conditions, was transferred to the elite durum wheat cultivar Uzan (T. turgidum ssp. durum) by a marker-assisted backcross breeding approach. The 2B introgression line turned out to be higher yielding but also exhibited negative traits that likely result from trans-, cis-, or linkage drag effects from the wild emmer parent. In this study, the respective 2BS QTL was subjected to fine-mapping, and a set of 17 homozygote recombinants were phenotyped at BC4F5 generation under water-limited and well-watered conditions at an experimental farm in Israel and at a high-throughput phenotyping platform (LemnaTec-129) in Germany. In general, both experimental setups allowed the identification of sub-QTL intervals related to culm length, kernel number, thousand kernel weight, and harvest index. Sub-QTLs for kernel number and harvest index were detected specifically under either drought stress or well-watered conditions, while QTLs for culm length and thousand-kernel weight were detected in both conditions. Although no direct QTL for grain yield was identified, plants with the sub-QTL for kernel number showed a higher grain yield than the recurrent durum cultivar Uzan under well-watered and mild drought stress conditions. We, therefore, suggest that this sub-QTL might be of interest for future breeding purposes.
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17
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Zhang YJ, Zhang Y, Zhang LL, He JX, Xue HW, Wang JW, Lin WH. The transcription factor OsGATA6 regulates rice heading date and grain number per panicle. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6133-6149. [PMID: 35662326 DOI: 10.1093/jxb/erac247] [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: 11/29/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Heading date, panicle architecture, and grain size are key traits that affect the yield of rice (Oryza sativa). Here, we identified a new gene, OsGATA6, whose product regulates heading date. Overexpression of OsGATA6 resulted in delayed heading, increased grain number, and decreased grain size. Knockdown lines generated by artificial microRNA (amiRNA) and CRISPR genome-edited lines of OsGATA6 both showed earlier heading, decreased grain number, and increased grain size. These results suggested that OsGATA6 negatively regulates heading date, positively regulates panicle development, and affects grain size. OsGATA6 was found to be constitutively expressed in rice, and strongly expressed in young leaves and panicles. In situ hybridization analyses showed that OsGATA6 was specifically localized in superficial cells of the panicle primordium. Overexpression lines show decreased expression of RFT1 and Hd3a, which promote heading. OsMFT1, which delays heading date and increases grain number, was down-regulated in amiRNA lines. Further analyses showed that OsGATA6 could bind to the promoter of OsMFT1 and induce its expression, thereby regulating heading date and panicle development. Overexpression of OsGATA6 in Arabidopsis resulted in repressed expression of AtFT and late flowering, suggesting that its function is similar. Taken together, we have identified a new GATA regulator that influences rice heading date and grain number, which potentially increases rice yield.
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Affiliation(s)
- Yan-Jie Zhang
- The Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- State Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Liang-Li Zhang
- State Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Hong-Wei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Hui Lin
- The Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China
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18
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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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19
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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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20
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Shaw BP, Sekhar S, Panda BB, Sahu G, Chandra T, Parida AK. Genes determining panicle morphology and grain quality in rice ( Oryza sativa). FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:673-688. [PMID: 35598893 DOI: 10.1071/fp21346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The world's increase in rice (Oryza sativa L.) production is not keeping up with the increase in its population. To boost the introduction of new high-yielding cultivars, knowledge is being gained on the genes and quantitative trait loci (QTLs) determining the panicle phenotype. The important are those determining yield of the crop, such as grain numbers per panicle and size and weight of the grains. Biochemical and molecular functions of many of them are understood in some details. Among these, OsCKX2 and OsSPL14 have been shown to increase panicle branching and grain numbers when overexpressed. Furthermore, miRNAs appear to play an important role in determining the panicle morphology by regulating the expressions of the genes like OsSPL14 and GRF4 involved in panicle branching and grain numbers and length. Mutations also greatly influence the grain shape and size. However, the information gained so far on the genetic regulation of grain filling and panicle morphology has not been successfully put into commercial application. Furthermore, the identification of the gene(s)/QTLs regulating panicle compactness is still lacking, which may enable the researchers to convert a compact-panicle cultivar into a lax/open one, and thereby increasing the chances of enhancing the yield of a desired compact-panicle cultivar obtained by the breeding effort.
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Affiliation(s)
| | - Sudhanshu Sekhar
- Institute of Life Sciences, Nalco Square, Bhubaneswar-751023, Odisha, India
| | | | - Gyanasri Sahu
- Institute of Life Sciences, Nalco Square, Bhubaneswar-751023, Odisha, India
| | - Tilak Chandra
- Institute of Life Sciences, Nalco Square, Bhubaneswar-751023, Odisha, India
| | - Ajay Kumar Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar-751023, Odisha, India
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21
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Combined Analysis of BSA-Seq Based Mapping, RNA-Seq, and Metabolomic Unraveled Candidate Genes Associated with Panicle Grain Number in Rice (Oryza sativa L.). Biomolecules 2022; 12:biom12070918. [PMID: 35883474 PMCID: PMC9313402 DOI: 10.3390/biom12070918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
Rice grain yield is a complex and highly variable quantitative trait consisting of several key components, including the grain weight, the effective panicles per unit area, and the grain number per panicle (GNPP). The GNPP is a significant contributor to grain yield controlled by multiple genes (QTL) and is crucial for improvement. Attempts have been made to find genes for this trait, which has always been a challenging and arduous task through conventional methods. We combined a BSA analysis, RNA profiling, and a metabolome analysis in the present study to identify new candidate genes involved in the GNPP. The F2 population from crossing R4233 (high GNPP) and Ce679 (low GNPP) revealed a frequency distribution fitting two segregated genes. Three pools, including low, middle, and high GNPP, were constructed and a BSA analysis revealed six candidate regions spanning 5.38 Mb, containing 739 annotated genes. Further, a conjunctive analysis of BSA-Seq and RNA-Seq showed 31 differentially expressed genes (DEGs) in the candidate intervals. Subsequently, a metabolome analysis showed 1024 metabolites, with 71 significantly enriched, including 44 up and 27 downregulated in Ce679 vs. R4233. A KEGG enrichment analysis of these 31 DEGs and 71 differentially enriched metabolites (DEMs) showed two genes, Os12g0102100 and Os01g0580500, significantly enriched in the metabolic pathways’ biosynthesis of secondary metabolites, cysteine and methionine metabolism, and fatty acid biosynthesis. Os12g0102100, which encodes for the alcohol dehydrogenase superfamily and a zinc-containing protein, is a novel gene whose contribution to the GNPP is not yet elucidated. This gene coding for mitochondrial trans-2-enoyl-CoA reductase is involved in the biosynthesis of myristic acid, also known as tetradecanoic acid. The Os01g0580500 coding for the enzyme 1-aminoclopropane-1-carboxylate oxidase (OsACO7) is responsible for the final step of the ethylene biosynthesis pathway through the conversion of 1-aminocyclopropane-1-carboxylic acid (ACC) into ethylene. Unlike Os12g0102100, this gene was significantly upregulated in R4233, downregulated in Ce679, and significantly enriched in two of the three metabolite pathways. This result pointed out that these two genes are responsible for the difference in the GNPP in the two cultivars, which has never been identified. Further validation studies may disclose the physiological mechanisms through which they regulate the GNPP in rice.
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22
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Parida AK, Sekhar S, Panda BB, Sahu G, Shaw BP. Effect of Panicle Morphology on Grain Filling and Rice Yield: Genetic Control and Molecular Regulation. Front Genet 2022; 13:876198. [PMID: 35620460 PMCID: PMC9127237 DOI: 10.3389/fgene.2022.876198] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022] Open
Abstract
The demand for rice is likely to increase approximately 1.5 times by the year 2050. In contrast, the rice production is stagnant since the past decade as the ongoing rice breeding program is unable to increase the production further, primarily because of the problem in grain filling. Investigations have revealed several reasons for poor filling of the grains in the inferior spikelets of the compact panicle, which are otherwise genetically competent to develop into well-filled grains. Among these, the important reasons are 1) poor activities of the starch biosynthesizing enzymes, 2) high ethylene production leading to inhibition in expressions of the starch biosynthesizing enzymes, 3) insufficient division of the endosperm cells and endoreduplication of their nuclei, 4) low accumulation of cytokinins and indole-3-acetic acid (IAA) that promote grain filling, and 5) altered expressions of the miRNAs unfavorable for grain filling. At the genetic level, several genes/QTLs linked to the yield traits have been identified, but the information so far has not been put into perspective toward increasing the rice production. Keeping in view the genetic competency of the inferior spikelets to develop into well-filled grains and based on the findings from the recent research studies, improving grain filling in these spikelets seems plausible through the following biotechnological interventions: 1) spikelet-specific knockdown of the genes involved in ethylene synthesis and overexpression of β-CAS (β-cyanoalanine) for enhanced scavenging of CN− formed as a byproduct of ethylene biosynthesis; 2) designing molecular means for increased accumulation of cytokinins, abscisic acid (ABA), and IAA in the caryopses; 3) manipulation of expression of the transcription factors like MYC and OsbZIP58 to drive the expression of the starch biosynthesizing enzymes; 4) spikelet-specific overexpression of the cyclins like CycB;1 and CycH;1 for promoting endosperm cell division; and 5) the targeted increase in accumulation of ABA in the straw during the grain filling stage for increased carbon resource remobilization to the grains. Identification of genes determining panicle compactness could also lead to an increase in rice yield through conversion of a compact-panicle into a lax/open one. These efforts have the ability to increase rice production by as much as 30%, which could be more than the set production target by the year 2050.
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Affiliation(s)
- Ajay Kumar Parida
- Crop Improvement Group, Institute of Life Sciences, Bhubaneswar, India
| | - Sudhanshu Sekhar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Binay Bhushan Panda
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, India
| | - Gyanasri Sahu
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Bhubaneswar, India
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23
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Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. PLANT COMMUNICATIONS 2022; 3:100325. [PMID: 35576158 PMCID: PMC9251437 DOI: 10.1016/j.xplc.2022.100325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maomao Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jianchang Sun
- Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China
| | - Xianju Wang
- Rice Research Institute of Liaoning Province, Shenyang 110161, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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24
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Prakash S, Rai R, Zamzam M, Ahmad O, Peesapati R, Vijayraghavan U. OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:865928. [PMID: 35498659 PMCID: PMC9044032 DOI: 10.3389/fpls.2022.865928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Stem cell homeostasis by the WUSCHEL-CLAVATA (WUS-CLV) feedback loop is generally conserved across species; however, its links with other meristem regulators can be species-specific, rice being an example. We characterized the role of rice OsbZIP47 in vegetative and reproductive development. The knockdown (KD) transgenics showed meristem size abnormality and defects in developmental progression. The size of the shoot apical meristem (SAM) in 25-day OsbZIP47KD plants was increased as compared to the wild-type (WT). Inflorescence of KD plants showed reduced rachis length, number of primary branches, and spikelets. Florets had defects in the second and third whorl organs and increased organ number. OsbZIP47KD SAM and panicles had abnormal expression for CLAVATA peptide-like signaling genes, such as FON2-LIKE CLE PROTEIN1 (FCP1), FLORAL ORGAN NUMBER 2 (FON2), and hormone pathway genes, such as cytokinin (CK) ISOPENTEYLTRANSFERASE1 (OsIPT1), ISOPENTEYLTRANSFERASE 8 (OsIPT8), auxin biosynthesis OsYUCCA6, OsYUCCA7 and gibberellic acid (GA) biosynthesis genes, such as GRAIN NUMBER PER PANICLE1 (GNP1/OsGA20OX1) and SHORTENED BASAL INTERNODE (SBI/OsGA2ox4). The effects on ABBERANT PANICLE ORGANIZATION1 (APO1), OsMADS16, and DROOPING LEAF (DL) relate to the second and third whorl floret phenotypes in OsbZIP47KD. Protein interaction assays showed OsbZIP47 partnerships with RICE HOMEOBOX1 (OSH1), RICE FLORICULA/LEAFY (RFL), and OsMADS1 transcription factors. The meta-analysis of KD panicle transcriptomes in OsbZIP47KD, OsMADS1KD, and RFLKD transgenics, combined with global OSH1 binding sites divulge potential targets coregulated by OsbZIP47, OsMADS1, OSH1, and RFL. Further, we demonstrate that OsbZIP47 redox status affects its DNA binding affinity to a cis element in FCP1, a target locus. Taken together, we provide insights on OsbZIP47 roles in SAM development, inflorescence branching, and floret development.
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Wang H, Tong X, Tang L, Wang Y, Zhao J, Li Z, Liu X, Shu Y, Yin M, Adegoke TV, Liu W, Wang S, Xu H, Ying J, Yuan W, Yao J, Zhang J. RLB (RICE LATERAL BRANCH) recruits PRC2-mediated H3K27 tri-methylation on OsCKX4 to regulate lateral branching. PLANT PHYSIOLOGY 2022; 188:460-476. [PMID: 34730827 PMCID: PMC8774727 DOI: 10.1093/plphys/kiab494] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 09/24/2021] [Indexed: 05/26/2023]
Abstract
Lateral branches such as shoot and panicle are determining factors and target traits for rice (Oryza sativa L.) yield improvement. Cytokinin promotes rice lateral branching; however, the mechanism underlying the fine-tuning of cytokinin homeostasis in rice branching remains largely unknown. Here, we report the map-based cloning of RICE LATERAL BRANCH (RLB) encoding a nuclear-localized, KNOX-type homeobox protein from a rice cytokinin-deficient mutant showing more tillers, sparser panicles, defected floret morphology as well as attenuated shoot regeneration from callus. RLB directly binds to the promoter and represses the transcription of OsCKX4, a cytokinin oxidase gene with high abundance in panicle branch meristem. OsCKX4 over-expression lines phenocopied rlb, which showed upregulated OsCKX4 levels. Meanwhile, RLB physically binds to Polycomb repressive complex 2 (PRC2) components OsEMF2b and co-localized with H3K27me3, a suppressing histone modification mediated by PRC2, in the OsCKX4 promoter. We proposed that RLB recruits PRC2 to the OsCKX4 promoter to epigenetically repress its transcription, which suppresses the catabolism of cytokinin, thereby promoting rice lateral branching. Moreover, antisense inhibition of OsCKX4 under the LOG promoter successfully increased panicle size and spikelet number per plant without affecting other major agronomic traits. This study provides insight into cytokinin homeostasis, lateral branching in plants, and also promising target genes for rice genetic improvement.
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Affiliation(s)
- Huimei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Juan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Xixi Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yazhou Shu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Man Yin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Tosin Victor Adegoke
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Wanning Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Shuang Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Huayu Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Jiezheng Ying
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
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Xiong Y, Zhang C, Zhou H, Sun W, Wang P, Wang D, Qiu X, Ali J, Yu S. Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice. RICE (NEW YORK, N.Y.) 2021; 14:97. [PMID: 34826005 PMCID: PMC8626550 DOI: 10.1186/s12284-021-00539-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/17/2021] [Indexed: 05/27/2023]
Abstract
Heterosis denotes the superiority of a hybrid plant over its parents. The use of heterosis has contributed significantly to yield improvement in crops. However, the genetic and molecular bases on heterosis are not fully understood. A large number of heterotic loci were identified for 12 yield-related traits in one parental population of chromosome segment substitution lines (CSSLs) and two test populations, which were interconnected by CSSLs derived from two rice genome-sequenced cultivars, Nipponbare and Zhenshan 97. Seventy-five heterotic loci were identified in both homozygous background of Zhenshan 97 and heterogeneous background of an elite hybrid cultivar Shanyou 63. Among the detected loci, at least 11 were colocalized in the same regions encompassing previously reported heterosis-associated genes. Furthermore, a heterotic locus Ghd8NIP for yield advantage was verified using transgenic experiments. Various allelic interaction at Ghd8 exhibited different heterosis levels in hetero-allelic combinations of five near-isogenic lines that contain a particular allele. The significant overdominance effects from some hetero-allelic combinations were found to improve yield heterosis in hybrid cultivars. Our findings support the role of allelic interaction at heterotic loci in the improvement of yield potential, which will be helpful for dissecting the genetic basis of heterosis and provide an optional strategy for the allele replacement in molecular breeding programs in hybrid rice.
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Affiliation(s)
- Yin Xiong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongju Zhou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianjin Qiu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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27
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Zhou X, Nong C, Wu B, Zhou T, Zhang B, Liu X, Gao G, Mi J, Zhang Q, Liu H, Liu S, Li Z, He Y, Mou T, Guo S, Li S, Yang Y, Zhang Q, Xing Y. Combinations of Ghd7, Ghd8, and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6963-6976. [PMID: 34283218 DOI: 10.1093/jxb/erab344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Heterosis of grain yield is closely associated with heading date in crops. Gene combinations of the major heading date genes Ghd7, Ghd8, and Hd1 play important roles in enhancing grain yield and adaptation to ecological regions in rice. However, the predominant three-gene combinations for a specific ecological region remain unclear in both three-line and two-line hybrids. In this study, we sequenced these three genes of 50 cytoplasmic male sterile/maintainer lines, 31 photo-thermo-sensitive genic male sterile lines, and 109 restorer lines. Sequence analysis showed that hybrids carrying strong functional alleles of Ghd7 and Hd1 and non-functional Ghd8 are predominant in three-line hybrids and are recommended for rice production in the subtropics around 30°N/S. Hybrids carrying strong functional Ghd7 and Ghd8 and non-functional Hd1 are predominant in two-line hybrids and are recommended for low latitude areas around 23.5°N/S rich in photothermal resources. Hybrids carrying strong functional Ghd7 and Ghd8 and functional Hd1 were not identified in commercial hybrids in the middle and lower reaches of the Yangtze River, but they have high yield potential in tropical regions because they have the strongest photoperiod sensitivity. Based on these findings, two genic sterile lines, Xiangling 628S and C815S, whose hybrids often head very late, were diagnosed with these three genes, and Hd1 was targeted to be knocked out in Xiangling 628S and replaced with hd1 in C815S. The hybrids developed from both modified sterile lines in turn had appropriate heading dates and significantly improved grain yield. This study provides new insights for breeding design to develop hybrids for various regions.
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Affiliation(s)
- Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Chunxiao Nong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Tianhao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Xingshao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou 434023,China
| | - Shisheng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Zhixin Li
- College of Agriculture, Yangtze University, Jingzhou 434023,China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Sibin Guo
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Naning 530007,China
| | - Shaoqing Li
- College of Life Science, Wuhan University, Wuhan 430072,China
| | - Yuanzhu Yang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha 410128,China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
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28
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Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio. Sci Rep 2021; 11:19751. [PMID: 34611187 PMCID: PMC8492636 DOI: 10.1038/s41598-021-98402-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/06/2021] [Indexed: 02/08/2023] Open
Abstract
We developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.
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Bai S, Hong J, Li L, Su S, Li Z, Wang W, Zhang F, Liang W, Zhang D. Dissection of the Genetic Basis of Rice Panicle Architecture Using a Genome-wide Association Study. RICE (NEW YORK, N.Y.) 2021; 14:77. [PMID: 34487253 PMCID: PMC8421479 DOI: 10.1186/s12284-021-00520-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/26/2021] [Indexed: 05/26/2023]
Abstract
Panicle architecture is one of the major factors influencing productivity of rice crops. The regulatory mechanisms underlying this complex trait are still unclear and genetic resources for rice breeders to improve panicle architecture are limited. Here, we have performed a genome-wide association study (GWAS) to analyze and identify genetic determinants underlying three panicle architecture traits. A population of 340 rice accessions from the 3000 Rice Genomes Project was phenotyped for panicle length, primary panicle number and secondary branch number over two years; GWAS was performed across the whole panel, and also across the japonica and indica sub-panels. A total of 153 quantitative trait loci (QTLs) were detected, of which 5 were associated with multiple traits, 8 were unique to either indica or japonica sub-panels, while 37 QTLs were stable across both years. Using haplotype and expression analysis, we reveal that genetic variations in the OsSPL18 promoter significantly affect gene expression and correlate with panicle length phenotypes. Three new candidate genes with putative roles in determining panicle length were also identified. Haplotype analysis of OsGRRP and LOC_Os03g03480 revealed high association with panicle length variation. Gene expression of DSM2, involved in abscisic acid biosynthesis, was up-regulated in long panicle accessions. Our results provide valuable information and resources for further unravelling the genetic basis determining rice panicle architecture. Identified candidate genes and molecular markers can be used in marker-assisted selection to improve rice panicle architecture through molecular breeding.
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Affiliation(s)
- Shaoxing Bai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ling Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Fengli Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, 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 Jiao Tong University, Shanghai, 200240, China.
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, SA, 5064, Australia.
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Zhi H, He Q, Tang S, Yang J, Zhang W, Liu H, Jia Y, Jia G, Zhang A, Li Y, Guo E, Gao M, Li S, Li J, Qin N, Zhu C, Ma C, Zhang H, Chen G, Zhang W, Wang H, Qiao Z, Li S, Cheng R, Xing L, Wang S, Liu J, Liu J, Diao X. Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3023-3036. [PMID: 34081150 DOI: 10.1007/s00122-021-03875-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Multi-environment QTL mapping identified 23 stable loci and 34 co-located QTL clusters for panicle architecture and grain yield-related traits, which provide a genetic basis for foxtail millet yield improvement. Panicle architecture and grain weight, both of which are influenced by genetic and environmental factors, have significant effects on grain yield potential. Here, we used a recombinant inbred line (RIL) population of 333 lines of foxtail millet, which were grown in 13 trials with varying environmental conditions, to identify quantitative trait loci (QTL) controlling nine agronomic traits related to panicle architecture and grain yield. We found that panicle weight, grain weight per panicle, panicle length, panicle diameter, and panicle exsertion length varied across different geographical locations. QTL mapping revealed 159 QTL for nine traits. Of the 159 QTL, 34 were identified in 2 to 12 environments, suggesting that the genetic control of panicle architecture in foxtail millet is sensitive to photoperiod and/or other environmental factors. Eighty-eight QTL controlling different traits formed 34 co-located QTL clusters, including the triple QTL cluster qPD9.2/qPL9.5/qPEL9.3, which was detected 23 times in 13 environments. Several candidate genes, including Seita.2G388700, Seita.3G136000, Seita.4G185300, Seita.5G241500, Seita.5G243100, Seita.9G281300, and Seita.9G342700, were identified in the genomic intervals of multi-environmental QTL or co-located QTL clusters. Using available phenotypic and genotype data, we conducted haplotype analysis for Seita.2G002300 and Seita.9G064000,which showed high correlations with panicle weight and panicle exsertion length, respectively. These results not only provided a basis for further fine mapping, functional studies and marker-assisted selection of traits related to panicle architecture in foxtail millet, but also provide information for comparative genomics analyses of cereal crops.
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Affiliation(s)
- Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Junjun Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Huifang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Yanchao Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Aiying Zhang
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Yuhui Li
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Erhu Guo
- Institute of Millet Crops, Shanxi Agricultural University, Changzhi, 046000, Shanxi, China
| | - Ming Gao
- Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, Jilin, China
| | - Shujie Li
- Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, Jilin, China
| | - Junxia Li
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Na Qin
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Cancan Zhu
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Chunye Ma
- Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Haijin Zhang
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Guoqiu Chen
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Wenfei Zhang
- Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Shunguo Li
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Lu Xing
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Suying Wang
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinrong Liu
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China.
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Chang Z, Xu R, Xun Q, Liu J, Zhong T, Ding Y, Ding C. OsmiR164-targeted OsNAM, a boundary gene, plays important roles in rice leaf and panicle development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:41-55. [PMID: 33368800 DOI: 10.1111/tpj.15143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 12/10/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
The CUP-SHAPED COTYLEDON (CUC) genes (CUC1, CUC2 and CUC3) regulate organ boundary formation in Arabidopsis. However, the functions of their homologous genes in rice (Oryza sativa) are still unknown. Here, we have identified an orthologous gene of CUC1 and CUC2 in rice, named OsNAM. Subcellular localization and yeast two-hybrid assay results have suggested that OsNAM encodes a conserved nuclear NAC (NAM/ATAF1/CUC2) protein with a transcriptional activator. The null mutant osnam-1 presented a fused leaf structure, small panicles, reduced branches and aberrant floral organ identities when compared with those of the wild type. Beta-glucuronidase staining and GFP reporter lines indicated that OsNAM was expressed in young tissues and that its boundary enrichment expression was regulated by OsmiR164. Loss-of-function mutants for OsCUC3 resulted in no obvious defects throughout rice development. The osnam oscuc3 double mutant, however, resulted in severe leaf fusion of the first two leaves, while the osnam single mutant showed a similar phenotype from the seventh leaf. These results indicated that OsNAM and OsCUC3 act redundantly for boundary specification during post-embryonic development. Overall, we describe the biological functions of OsNAM and OsCUC3 in rice development and the expression characteristics of OsNAM. This work reveals the important role of CUC genes in rice.
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Affiliation(s)
- Zhongyuan Chang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ruihan Xu
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jiajun Liu
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Tianhui Zhong
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, People's Republic of China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, People's Republic of China
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Molecular and Genetic Aspects of Grain Number Determination in Rice ( Oryza sativa L.). Int J Mol Sci 2021; 22:ijms22020728. [PMID: 33450933 PMCID: PMC7828406 DOI: 10.3390/ijms22020728] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Rice grain yield is a complex trait determined by three components: panicle number, grain number per panicle (GNPP) and grain weight. GNPP is the major contributor to grain yield and is crucial for its improvement. GNPP is determined by a series of physiological and biochemical steps, including inflorescence development, formation of rachis branches such as primary rachis branches and secondary rachis branches, and spikelet specialisation (lateral and terminal spikelets). The molecular genetic basis of GNPP determination is complex, and it is regulated by numerous interlinked genes. In this review, panicle development and the determination of GNPP is described briefly, and GNPP-related genes that influence its determination are categorised according to their regulatory mechanisms. We introduce genes related to rachis branch development and their regulation of GNPP, genes related to phase transition (from rachis branch meristem to spikelet meristem) and their regulation of GNPP, and genes related to spikelet specialisation and their regulation of GNPP. In addition, we describe other GNPP-related genes and their regulation of GNPP. Research on GNPP determination suggests that it is possible to cultivate rice varieties with higher grain yield by modifying GNPP-related genes.
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Ke Q, Tao W, Li T, Pan W, Chen X, Wu X, Nie X, Cui L. Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley ( Hordeum vulgare L.). Curr Genomics 2021; 21:621-644. [PMID: 33414683 PMCID: PMC7770637 DOI: 10.2174/1389202921999201102165537] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/17/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022] Open
Abstract
Background The basic helix-loop-helix (bHLH) transcription factor is one of the most important gene families in plants, playing a key role in diverse metabolic, physiological, and developmental processes. Although it has been well characterized in many plants, the significance of the bHLH family in barley is not well understood at present. Methods Through a genome-wide search against the updated barley reference genome, the genomic organization, evolution and expression of the bHLH family in barley were systematically analyzed. Results We identified 141 bHLHs in the barley genome (HvbHLHs) and further classified them into 24 subfamilies based on phylogenetic analysis. It was found that HvbHLHs in the same subfamily shared a similar conserved motif composition and exon-intron structures. Chromosome distribution and gene duplication analysis revealed that segmental duplication mainly contributed to the expansion of HvbHLHs and the duplicated genes were subjected to strong purifying selection. Furthermore, expression analysis revealed that HvbHLHs were widely expressed in different tissues and also involved in response to diverse abiotic stresses. The co-expression network was further analyzed to underpin the regulatory function of HvbHLHs. Finally, 25 genes were selected for qRT-PCR validation, the expression profiles of HvbHLHs showed diverse patterns, demonstrating their potential roles in relation to stress tolerance regulation. Conclusion This study reported the genome organization, evolutionary characteristics and expression profile of the bHLH family in barley, which not only provide the targets for further functional analysis, but also facilitate better understanding of the regulatory network bHLH genes involved in stress tolerance in barley.
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Affiliation(s)
- Qinglin Ke
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenjing Tao
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tingting Li
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenqiu Pan
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaoyun Chen
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaoyu Wu
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaojun Nie
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Licao Cui
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
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Zhou D, Shen W, Cui Y, Liu Y, Zheng X, Li Y, Wu M, Fang S, Liu C, Tang M, Yi Y, Zhao M, Chen L. APICAL SPIKELET ABORTION (ASA) Controls Apical Panicle Development in Rice by Regulating Salicylic Acid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:636877. [PMID: 33719311 PMCID: PMC7947001 DOI: 10.3389/fpls.2021.636877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/22/2021] [Indexed: 05/11/2023]
Abstract
Panicle degradation causes severe yield reduction in rice. There are two main types of panicle degradation: apical spikelet abortion and basal degeneration. In this study, we isolated and characterized the apical panicle abortion mutant apical spikelet abortion (asa), which exhibits degeneration and defects in the apical spikelets. This mutant had a pleiotropic phenotype, characterized by reduced plant height, increased tiller number, and decreased pollen fertility. Map-based cloning revealed that OsASA encodes a boric acid channel protein that showed the highest expression in the inflorescence, peduncle, and anther. RNA-seq analysis of the asa mutant vs wild-type (WT) plants revealed that biological processes related to reactive oxygen species (ROS) homeostasis and salicylic acid (SA) metabolism were significantly affected. Furthermore, the asa mutants had an increased SA level and H2O2 accumulation in the young panicles compared to the WT plants. Moreover, the SA level and the expression of OsPAL3, OsPAL4, and OsPAL6 genes (related to SA biosynthesis) were significantly increased under boron-deficient conditions in the asa mutant and in OsASA-knockout plants. Collectively, these results suggest that the boron distribution maintained by OsASA is required for normal panicle development in a process that involves modulating ROS homeostasis and SA biosynthesis.
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Affiliation(s)
- Dan Zhou
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Weifeng Shen
- Rice Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuqin Liu
- Rice Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Xijun Zheng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yan Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Minliang Wu
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanru Fang
- Rice Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Chunhong Liu
- Rice Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Ming Tang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwestern, School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwestern, School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mingfu Zhao
- Rice Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
- *Correspondence: Mingfu Zhao,
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Liang Chen,
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Deveshwar P, Prusty A, Sharma S, Tyagi AK. Phytohormone-Mediated Molecular Mechanisms Involving Multiple Genes and QTL Govern Grain Number in Rice. Front Genet 2020; 11:586462. [PMID: 33281879 PMCID: PMC7689023 DOI: 10.3389/fgene.2020.586462] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/09/2020] [Indexed: 11/13/2022] Open
Abstract
Increasing the grain number is the most direct route toward enhancing the grain yield in cereals. In rice, grain number can be amplified through increasing the shoot branching (tillering), panicle branching, panicle length, and seed set percentage. Phytohormones have been conclusively shown to control the above characteristics by regulating molecular factors and their cross-interactions. The dynamic equilibrium of cytokinin levels in both shoot and inflorescence meristems, maintained by the regulation of its biosynthesis, activation, and degradation, determines the tillering and panicle branching, respectively. Auxins and gibberellins are known broadly to repress the axillary meristems, while jasmonic acid is implicated in the determination of reproductive meristem formation. The balance of auxin, gibberellin, and cytokinin determines meristematic activities in the inflorescence. Strigolactones have been shown to repress the shoot branching but seem to regulate panicle branching positively. Ethylene, brassinosteroids, and gibberellins regulate spikelet abortion and grain filling. Further studies on the optimization of endogenous hormonal levels can help in the expansion of the grain yield potential of rice. This review focuses on the molecular machinery, involving several genes and quantitative trait loci (QTL), operational in the plant that governs hormonal control and, in turn, gets governed by the hormones to regulate grain number and yield in rice.
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Affiliation(s)
- Priyanka Deveshwar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Ankita Prusty
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Shivam Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns. Nat Commun 2020; 11:4778. [PMID: 32963241 PMCID: PMC7508829 DOI: 10.1038/s41467-020-18608-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders. Hybrid rice cultivars are widely planted around the world. Here, the authors resequence 1,143 indica accessions, focusing on the parents of superior hybrid rice lines in China, and reveal genetic loci that are associated with heterosis via measuring frequency of parental variation difference (FPVD).
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Wu H, Xie D, Tang Z, Shi D, Yang W. PINOID regulates floral organ development by modulating auxin transport and interacts with MADS16 in rice. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1778-1795. [PMID: 31950589 PMCID: PMC7336374 DOI: 10.1111/pbi.13340] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 12/14/2019] [Accepted: 12/26/2019] [Indexed: 05/12/2023]
Abstract
In rice (Oryza sativa L.), floral organ development is an important trait. Although a role for PINOID in regulating floral organ development was reported recently, the underlying molecular mechanism remains unclear. Here, we isolated and characterized an abnormal floral organ mutant and mapped the causative gene through an improved MutMap method. Molecular study revealed that the observed phenotype is caused by a point mutation in OsPINOID (OsPID) gene; therefore, we named the mutation as ospid-4. Our data demonstrate that OsPID interacts with OsPIN1a and OsPIN1b to regulate polar auxin transport as shown previously. Additionally, OsPID also interacts with OsMADS16 to regulate transcription during floral organ development in rice. Together, we propose a model that OsPID regulates floral organ development by modulating auxin polar transport and interaction with OsMADS16 and/or LAX1 in rice. These results provide a novel insight into the role of OsPID in regulating floral organ development of rice, especially in stigma development, which would be useful for genetic improvement of high-yield breeding of rice.
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Affiliation(s)
- Hua‐Mao Wu
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Dong‐Jiang Xie
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Zuo‐Shun Tang
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Dong‐Qiao Shi
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Wei‐Cai Yang
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
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Gouda G, Gupta MK, Donde R, Mohapatra T, Vadde R, Behera L. Marker-assisted selection for grain number and yield-related traits of rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:885-898. [PMID: 32377039 PMCID: PMC7196572 DOI: 10.1007/s12298-020-00773-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 05/11/2023]
Abstract
Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.
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Affiliation(s)
- Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Trilochan Mohapatra
- Secretary (DARE) and Director General (ICAR), Government of India, New Delhi, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
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OsbHLH073 Negatively Regulates Internode Elongation and Plant Height by Modulating GA Homeostasis in Rice. PLANTS 2020; 9:plants9040547. [PMID: 32340222 PMCID: PMC7238965 DOI: 10.3390/plants9040547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 11/16/2022]
Abstract
Internode elongation is one of the key agronomic traits determining a plant’s height and biomass. However, our understanding of the molecular mechanisms controlling internode elongation is still limited in crop plant species. Here, we report the functional identification of an atypical basic helix-loop-helix transcription factor (OsbHLH073) through gain-of-function studies using overexpression (OsbHLH073-OX) and activation tagging (osbhlh073-D) lines of rice. The expression of OsbHLH073 was significantly increased in the osbhlh073-D line. The phenotype of osbhlh073-D showed semi-dwarfism due to deficient elongation of the first internode and poor panicle exsertion. Transgenic lines overexpressing OsbHLH073 confirmed the phenotype of the osbhlh073-D line. Exogenous gibberellic acid (GA3) treatment recovered the semi-dwarf phenotype of osbhlh073-D plants at the seedling stage. In addition, quantitative expression analysis of genes involving in GA biosynthetic and signaling pathway revealed that the transcripts of rice ent-kaurene oxidases 1 and 2 (OsKO1 and OsKO2) encoding the GA biosynthetic enzyme were significantly downregulated in osbhlh073-D and OsbHLH073-OX lines. Yeast two-hybrid and localization assays showed that the OsbHLH073 protein is a nuclear localized-transcriptional activator. We report that OsbHLH073 participates in regulating plant height, internode elongation, and panicle exsertion by regulating GA biosynthesis associated with the OsKO1 and OsKO2 genes.
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Nutan KK, Rathore RS, Tripathi AK, Mishra M, Pareek A, Singla-Pareek SL. Integrating the dynamics of yield traits in rice in response to environmental changes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:490-506. [PMID: 31410470 DOI: 10.1093/jxb/erz364] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.
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Affiliation(s)
- Kamlesh Kant Nutan
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ray Singh Rathore
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Amit Kumar Tripathi
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Manjari Mishra
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Harrop TWR, Mantegazza O, Luong AM, Béthune K, Lorieux M, Jouannic S, Adam H. A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5617-5629. [PMID: 31346594 PMCID: PMC6812710 DOI: 10.1093/jxb/erz340] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/15/2019] [Indexed: 05/25/2023]
Abstract
Rice yield is influenced by inflorescence size and architecture, and inflorescences from domesticated rice accessions produce more branches and grains. Neither the molecular control of branching nor the developmental differences between wild and domesticated rice accessions are fully understood. We surveyed phenotypes related to branching, size, and grain yield across 91 wild and domesticated African and Asian accessions. Characteristics related to axillary meristem identity were the main phenotypic differences between inflorescences from wild and domesticated accessions. We used whole transcriptome sequencing in developing inflorescences to measure gene expression before and after the transition from branching axillary meristems to determinate spikelet meristems. We identified a core set of genes associated with axillary meristem identity in Asian and African rice, and another set associated with phenotypic variability between wild and domesticated accessions. AP2/EREBP-like genes were enriched in both sets, suggesting that they are key factors in inflorescence branching and rice domestication. Our work has identified new candidates in the molecular control of inflorescence development and grain yield, and provides a detailed description of the effects of domestication on phenotype and gene expression.
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Affiliation(s)
- Thomas W R Harrop
- Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Dunedin, Aotearoa, New Zealand
| | | | - Ai My Luong
- University of Montpellier, DIADE, IRD, France
| | | | - Mathias Lorieux
- Rice genetics and Genomics Laboratory, International Center for Tropical Agriculture, Cali 6713, Colombia
| | | | - Hélène Adam
- University of Montpellier, DIADE, IRD, France
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Nomura T, Arakawa N, Yamamoto T, Ueda T, Adachi S, Yonemaru JI, Abe A, Takagi H, Yokoyama T, Ookawa T. Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1. PLoS One 2019; 14:e0221424. [PMID: 31437205 PMCID: PMC6705783 DOI: 10.1371/journal.pone.0221424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/06/2019] [Indexed: 12/30/2022] Open
Abstract
During late 1960s Green Revolution, researchers utilized semidwarf 1 (sd1) to improve the yield and lodging resistance in rice (Oryza sativa L.). However, sd1 has a negative effect to culm strength and biomass production. To increase yield dramatically in 21th century, development of next generation long-culm rice for non-lodging and high grain yield independent of sd1 has been needed. The present study developed Monster Rice 1, a long-culm and heavy-panicle type of rice line and compared it with Takanari, a high-yielding semidwarf rice variety about yield and lodging resistance associated traits. Brown rice yield and bending moment at breaking of the basal elongated internode were higher in Monster Rice 1 than those in Takanari due to a large number of spikelets per panicle and thicker culm. Furthermore, to identify QTLs with superior alleles for these traits, QTL and haplotype analyses were performed using F2 population and recombinant inbred lines derived from a cross between Monster Rice 1 and Takanari. The results from this study suggest that long-culm and heavy-panicle type of rice with a superior lodging resistance by culm strength can perform its high yield potential by using these identified QTLs contributing yield and lodging resistance.
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Affiliation(s)
- Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Naoya Arakawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Tadamasa Ueda
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | | | - Akira Abe
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Tadashi Yokoyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- * E-mail:
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Joint RNA-Seq and miRNA Profiling Analyses to Reveal Molecular Mechanisms in Regulating Thickness of Pod Canopy in Brassica napus. Genes (Basel) 2019; 10:genes10080591. [PMID: 31387302 PMCID: PMC6722711 DOI: 10.3390/genes10080591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 07/31/2019] [Indexed: 12/14/2022] Open
Abstract
Oilseed rape (Brassica napus) is the second largest oilseed crop worldwide. As an architecture component of B. napus, thickness of pod canopy (TPC) plays an important role in yield formation, especially under high-density cultivation conditions. However, the mechanisms underlying the regulation of TPC remain unclear. RNA and microRNA (miRNA) profiling of two groups of B. napus lines with significantly different TPC at the bolting with a tiny bud stage revealed differential expressions of numerous genes involved in nitrogen-related pathways. Expression of several nitrogen-related response genes, including ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15, was dramatically changed in the thick TPC lines compared to those in the thin TPC lines. Differentially expressed miRNAs also included many involved in nitrogen-related pathways. Expression of most target genes was negatively associated with corresponding miRNAs, such as miR159, miR6029, and miR827. In addition, 12 (including miR319, miR845, and miR158) differentially expressed miRNAs between two plant tissues sampled (stem apex and flower bud) were identified, implying that they might have roles in determining overall plant architecture. These results suggest that nitrogen signaling may play a pivotal role in regulating TPC in B. napus.
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Yang X, Wang J, Dai Z, Zhao X, Miao X, Shi Z. miR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways. RICE (NEW YORK, N.Y.) 2019; 12:40. [PMID: 31147794 PMCID: PMC6542935 DOI: 10.1186/s12284-019-0299-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/16/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice (Oryza sativa) panicle architecture is the major determinant of the ideal plant architecture that directly influence yield potential. Many genes influencing development of primary branches, secondary branches, spikelet and pedicel would also influence panicle architecture, which is thus a complex trait regulated by genes from various aspects. miR156, an extensively studied miRNA, has recently emerged as promising target for crop improvement because of its role in plant architecture regulation, such as the number of tillers, plant height and the panicle architecture. Increasing evidence suggests that miR156 might play an important role in panicle architecture regulation. MAIN BODY To study the detailed function of miR156 in rice panicle architecture regulation, we examined the genetic interaction or transcriptional regulation of miR156/OsSPL to other panicle regulating genes. Our results revealed that expression of many panicle related genes were influenced by miR156. Through biochemical analysis, we further proved that miR156 directly regulated the axillary meristem regulating gene, LAX1, at the transcription level. And the intimate relations between miR156 and LAX1, and miR156 and LAX2 were also uncovered by genetic analysis. On the other hand, a tight genetic linkage between miR156 and RCN2, the panicle branch promoting gene, was also detected, which suggested a buffering mechanism for the miR156 mediated panicle architecture regulation. Furthermore, genetic analysis also demonstrated that miR156 functioned in the same pathway with OsRA2 to regulate pedicel length. SHORT CONCLUSION Altogether, miR156 integrates several genetic pathways mediated by genes such as LAX1, LAX2, RCN2 and OsRA2, and comprehensively regulates panicle development in rice. Based on these analysis, we concluded that miR156 acts as an important regulator for panicle architecture through influencing various aspects of panicle development.
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Affiliation(s)
- Xiaofang Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jiang Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhengyan Dai
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xiaoling Zhao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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Basile A, Fambrini M, Tani C, Shukla V, Licausi F, Pugliesi C. The
Ha‐ROXL
gene is required for initiation of axillary and floral meristems in sunflower. Genesis 2019; 57:e23307. [DOI: 10.1002/dvg.23307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Alice Basile
- Institute of Life SciencesScuola Superiore Sant'Anna Pisa Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE)University of Pisa Pisa Italy
| | - Camilla Tani
- Department of Agriculture, Food and Environment (DAFE)University of Pisa Pisa Italy
| | - Vinay Shukla
- Institute of Life SciencesScuola Superiore Sant'Anna Pisa Italy
| | - Francesco Licausi
- Institute of Life SciencesScuola Superiore Sant'Anna Pisa Italy
- Department of BiologyUniversity of Pisa Pisa Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE)University of Pisa Pisa Italy
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Jiang Q, Zeng Y, Yu B, Cen W, Lu S, Jia P, Wang X, Qin B, Cai Z, Luo J. The rice pds1 locus genetically interacts with partner to cause panicle exsertion defects and ectopic tillers in spikelets. BMC PLANT BIOLOGY 2019; 19:200. [PMID: 31092192 PMCID: PMC6521401 DOI: 10.1186/s12870-019-1805-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is a staple food crop worldwide. Its yield and quality are affected by its tillering pattern and spikelet development. Although many genes involved in the vegetative and reproductive development of rice have been characterized in previous studies, the genetic mechanisms that control axillary tillering, spikelet development, and panicle exsertion remain incompletely understood. RESULTS Here, we characterized a novel rice recombinant inbred line (RIL), panicle exsertion defect and aberrant spikelet (pds). It was derived from a cross between two indica varieties, S142 and 430. Intriguingly, no abnormal phenotypes were observed in the parents of pds. This RIL exhibited sheathed panicles at heading stage. Still, a small number of tillers in pds plants were fully exserted from the flag leaves. Elongated sterile lemmas and rudimentary glumes (occurred occasionally) were observed in the spikelets of the exserted panicles and were transformed into palea/lemma-like structures. Furthermore, more interestingly, tillers occasionally grew from the axils of the elongated rudimentary glumes. Via genetic linkage analysis, we found that the abnormal phenotype of pds manifesting as genetic incompatibility or hybrid weakness was caused by genetic interaction between a recessive locus, pds1, which was derived from S142 and mapped to chromosome 8, and a locus pds2, which not yet mapped from 430. We fine-mapped pds1 to an approximately 55-kb interval delimited by the markers pds-4 and 8 M3.51. Six RGAP-annotated ORFs were included in this genomic region. qPCR analysis revealed that Loc_Os080595 might be the target of pds1 locus, and G1 gene might be involved in the genetic mechanism underlying the pds phenotype. CONCLUSIONS In this study, histological and genetic analyses revealed that the pyramided pds loci resulted in genetic incompatibility or hybrid weakness in rice might be caused by a genetic interaction between pds loci derived from different rice varieties. Further isolation of pds1 and its interactor pds2, would provide new insight into the molecular regulation of grass inflorescence development and exsertion, and the evolution history of the extant rice.
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Affiliation(s)
- Qigui Jiang
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
| | - Yindi Zeng
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
| | - Baiyang Yu
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
| | - Weijian Cen
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
- Agriculture College, Guangxi University, Nanning, 530004 China
| | - Siyuan Lu
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
| | - Peilong Jia
- Agriculture College, Guangxi University, Nanning, 530004 China
| | - Xuan Wang
- Agriculture College, Guangxi University, Nanning, 530004 China
| | - Baoxiang Qin
- Agriculture College, Guangxi University, Nanning, 530004 China
| | - Zhongquan Cai
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
- Institute of New Rural Development, Guangxi University, Nanning, 530004 China
- Agriculture College, Guangxi University, Nanning, 530004 China
| | - Jijing Luo
- College of Life Science and technology (State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources), Guangxi University, Nanning, 530004 China
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Yu J, Ai G, Shen D, Chai C, Jia Y, Liu W, Dou D. Bioinformatical analysis and prediction of Nicotiana benthamiana bHLH transcription factors in Phytophthora parasitica resistance. Genomics 2019; 111:473-482. [PMID: 29522799 DOI: 10.1016/j.ygeno.2018.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/26/2018] [Accepted: 03/04/2018] [Indexed: 01/18/2023]
Abstract
The basic helix-loop-helix (bHLH) family, one of the largest transcription factor groups in plants, regulates many critical developmental processes. However, their functions in plant defense have not been extensively studied in Nicotiana benthamiana, an important model plant species for phytopathology. Here, we identified N. benthamiana bHLH genes (NbbHLHs) using a whole-genome searching approach, and found that the NbbHLHs are highly enriched and some subfamilies are selectively expanded in N. benthamiana. The results showed that gene duplication may be responsible for bHLH family expansion in this plant. Furthermore, we analyzed their expression profiles upon infection with Phytophthora parasitica. Finally, 28 candidate NbbHLHs may play important roles in Phytophthora pathogen resistance using cis-element analysis and protein-interaction network prediction. Taken together, our results established a platform for future studies of the gene family and provide molecular insights into plant immune responses against P. parasitica.
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Affiliation(s)
- Jing Yu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Gan Ai
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunyue Chai
- College of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Yuling Jia
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Liu
- College of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
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Chen E, Huang X, Tian Z, Wing RA, Han B. The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:639-665. [PMID: 31035826 DOI: 10.1146/annurev-arplant-050718-100320] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.
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Affiliation(s)
- Erwang Chen
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;
| | - Bin Han
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
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Ali A, Xu P, Riaz A, Wu X. Current Advances in Molecular Mechanisms and Physiological Basis of Panicle Degeneration in Rice. Int J Mol Sci 2019; 20:ijms20071613. [PMID: 30939720 PMCID: PMC6479839 DOI: 10.3390/ijms20071613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/22/2022] Open
Abstract
Panicle degeneration, also known as panicle abortion, is a serious defect and causes heavy losses to reproductive yield in cereals. Several mutants have been reported to display the phenotype of spikelet abortion in rice. Recent findings have resulted in significant breakthroughs, but comprehensive understanding about the molecular pathways and physiological basis of panicle degeneration still remain a dilemma. In this review, we have summarized all the responsible genes and mechanisms underlying the panicle development with a special focus on degeneration. Here, we hypothesized a model by using knowledge and coherent logic in order to understand the molecular regulation of panicle degeneration. In addition to this, we included all the previous discoveries, schools of thoughts, ancient working theories, and crosstalk of phytohormones and provided new insights for future studies.
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Affiliation(s)
- Asif Ali
- Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Chengdu 611130, China.
| | - Peizhou Xu
- Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Chengdu 611130, China.
| | - Asad Riaz
- Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xianjun Wu
- Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Chengdu 611130, China.
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Ni S, Li Z, Ying J, Zhang J, Chen H. Decreased Spikelets 4 Encoding a Novel Tetratricopeptide Repeat Domain-Containing Protein Is Involved in DNA Repair and Spikelet Number Determination in Rice. Genes (Basel) 2019; 10:genes10030214. [PMID: 30871267 PMCID: PMC6471630 DOI: 10.3390/genes10030214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Spikelet number per panicle is a determinative factor of rice yield. DNA repair epigenetically alters the DNA accessibility, which can eventually regulate the transcription of the target genes. However, what and how DNA repair genes are related to rice spikelet development remains unknown. Here, we report the map-based cloning of a novel spikelet number gene DES4 encoding a tetratricopeptide domain-containing protein. DES4 is a close ortholog of Arabidopsis BRU1, which is functionally related to axillary meristem development. A single base pair deletion in the last exon of DES4 caused a premature stop of the resulting protein. The des4 mutant exhibited dwarf, reduced tiller, and spikelet numbers phenotypes, as well as hypersensitivity to genotoxic stresses, suggesting its essential role in DNA repair. DES4 is predominantly expressed in young panicles and axillary meristems, and DES4 protein is localized in nucleus. A set of DNA repair genes such as cyclins, KUs (KD subunits) and recombinases were differentially regulated in des4. Meanwhile, rice spikelet number genes LAX1, LAX2, and MOC1 were significantly down-regulated in des4. In morphology, des4 showed more severe reduction of spikelet numbers than lax1, lax2, and moc1, suggesting that DES4 may work upstream of the three genes.
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Affiliation(s)
- Shen Ni
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Zongzhu Li
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC 20037, USA.
| | - Jiancheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Hongqi Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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