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Hu X, Liu Y, Zhong X, Hu R, Li M, Peng B, Pan J, Liang K, Fu Y, Huang N. Optimized nitrogen management improves grain yield of rice by regulating panicle architecture in South China. Heliyon 2024; 10:e34607. [PMID: 39149045 PMCID: PMC11324970 DOI: 10.1016/j.heliyon.2024.e34607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/27/2024] [Accepted: 07/12/2024] [Indexed: 08/17/2024] Open
Abstract
Optimized nitrogen (N) management (OPT), with reduced total N input and more N applied during panicle development, has been proved to increase grain yield of rice through panicle enlargement. However, the changes in panicle architecture and source of variation are not well understood. A hybrid rice variety named Tianyou 3618 was subjected to OPT and farmer's fertilizer practice (FFP) in early cropping seasons of 2016 and 2017. With 16.7 % less N input, OPT increased panicle size by 8.6 % and 27.4 %, and grain yield by 13.8 % and 12.3 % for 2016 and 2017, respectively. OPT had greater dry matter accumulation and N uptake from panicle initiation to heading, which bolstered panicle enlargement. The number of surviving florets per branch was quite constant under different N treatments for all primary, secondary, and tertiary branches, implying that panicle size was mainly determined by the number of branches rather than the number of florets per branch. Little change was observed between OPT and FFP in differentiation, degeneration and survival of primary branches and their florets. Surviving secondary and tertiary branches and their florets were significantly more under OPT than those under FFP. The increase in surviving secondary branches under OPT resulted from both enhanced differentiation and reduced degeneration. While the increase in surviving tertiary branches under OPT was merely from enhanced differentiation though their degeneration was also dramatically increased. Among the increased differentiated florets under OPT, 32.4%-36.3 % and 61.6%-67.7 % came from secondary and tertiary branches, respectively. Among the increased surviving florets under OPT, 62.2%-65.2 % and 32.5%-37.8 % came from secondary and tertiary branches, respectively. Both secondary branches and tertiary branches were principal contributors to the increase in panicle size of OPT. To our knowledge, this is the first report on the detailed changes in panicle architecture and their involvement in panicle enlargement and yield gain under OPT.
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Affiliation(s)
- Xiangyu Hu
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Yanzhuo Liu
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Xuhua Zhong
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Rui Hu
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Meijuan Li
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Bilin Peng
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Junfeng Pan
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Kaiming Liang
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Youqiang Fu
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, China
| | - Nongrong Huang
- Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology for Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, 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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Wu HYL, Jen J, Hsu PY. What, where, and how: Regulation of translation and the translational landscape in plants. THE PLANT CELL 2024; 36:1540-1564. [PMID: 37437121 PMCID: PMC11062462 DOI: 10.1093/plcell/koad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/14/2023]
Abstract
Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Joey Jen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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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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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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Agata A, Ashikari M, Sato Y, Kitano H, Hobo T. Designing rice panicle architecture via developmental regulatory genes. BREEDING SCIENCE 2023; 73:86-94. [PMID: 37168816 PMCID: PMC10165343 DOI: 10.1270/jsbbs.22075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/03/2022] [Indexed: 05/13/2023]
Abstract
Rice panicle architecture displays remarkable diversity in branch number, branch length, and grain arrangement; however, much remains unknown about how such diversity in patterns is generated. Although several genes related to panicle branch number and panicle length have been identified, how panicle branch number and panicle length are coordinately regulated is unclear. Here, we show that panicle length and panicle branch number are independently regulated by the genes Prl5/OsGA20ox4, Pbl6/APO1, and Gn1a/OsCKX2. We produced near-isogenic lines (NILs) in the Koshihikari genetic background harboring the elite alleles for Prl5, regulating panicle rachis length; Pbl6, regulating primary branch length; and Gn1a, regulating panicle branching in various combinations. A pyramiding line carrying Prl5, Pbl6, and Gn1a showed increased panicle length and branching without any trade-off relationship between branch length or number. We successfully produced various arrangement patterns of grains by changing the combination of alleles at these three loci. Improvement of panicle architecture raised yield without associated negative effects on yield-related traits except for panicle number. Three-dimensional (3D) analyses by X-ray computed tomography (CT) of panicles revealed that differences in panicle architecture affect grain filling. Importantly, we determined that Prl5 improves grain filling without affecting grain number.
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Affiliation(s)
- Ayumi Agata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yutaka Sato
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hidemi Kitano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Tokunori Hobo
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Corresponding author (e-mail: )
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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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8
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Dai D, Zhang H, He L, Chen J, Du C, Liang M, Zhang M, Wang H, Ma L. Panicle Apical Abortion 7 Regulates Panicle Development in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms23169487. [PMID: 36012754 PMCID: PMC9409353 DOI: 10.3390/ijms23169487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The number of grains per panicle significantly contributes to rice yield, but the regulatory mechanism remains largely unknown. Here, we reported a loss-of-function mutant, panicle apical abortion 7 (paa7), which exhibited panicle abortion and degeneration of spikelets on the apical panicles during the late stage of young panicle development in rice. High accumulations of H2O2 in paa7 caused programmed cell death (PCD) accompanied by nuclear DNA fragmentation in the apical spikelets. Map-based cloning revealed that the 3 bp "AGC" insertion and 4 bp "TCTC" deletion mutation of paa7 were located in the 3'-UTR regions of LOC_Os07g47330, which was confirmed through complementary assays and overexpressed lines. Interestingly, LOC_Os07g47330 is known as FRIZZY PANICLE (FZP). Thus, PAA7 could be a novel allele of FZP. Moreover, the severe damage for panicle phenotype in paa7/lax2 double mutant indicated that PAA7 could crosstalk with Lax Panicle 2 (LAX2). These findings suggest that PAA7 regulates the development of apical spikelets and interacts with LAX2 to regulate panicle development in rice.
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Affiliation(s)
- Dongqing Dai
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Lei He
- Institute of Food Crops, Key Laboratory of Jiangsu Province for Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Junyu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Chengxing Du
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Minmin Liang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Meng Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Huimei Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Liangyong Ma
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
- Correspondence: ; Tel.: +86-0571-63370323
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9
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Lu Y, Chuan M, Wang H, Chen R, Tao T, Zhou Y, Xu Y, Li P, Yao Y, Xu C, Yang Z. Genetic and molecular factors in determining grain number per panicle of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:964246. [PMID: 35991390 PMCID: PMC9386260 DOI: 10.3389/fpls.2022.964246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tianyun Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Youli Yao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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10
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Kellogg EA. Genetic control of branching patterns in grass inflorescences. THE PLANT CELL 2022; 34:2518-2533. [PMID: 35258600 PMCID: PMC9252490 DOI: 10.1093/plcell/koac080] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/02/2022] [Indexed: 05/13/2023]
Abstract
Inflorescence branching in the grasses controls the number of florets and hence the number of seeds. Recent data on the underlying genetics come primarily from rice and maize, although new data are accumulating in other systems as well. This review focuses on a window in developmental time from the production of primary branches by the inflorescence meristem through to the production of glumes, which indicate the transition to producing a spikelet. Several major developmental regulatory modules appear to be conserved among most or all grasses. Placement and development of primary branches are controlled by conserved auxin regulatory genes. Subtending bracts are repressed by a network including TASSELSHEATH4, and axillary branch meristems are regulated largely by signaling centers that are adjacent to but not within the meristems themselves. Gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators extend along the inflorescence axis and the branches, governing the transition from production of branches to production of spikelets. The relative speed of this transition determines the extent of secondary and higher order branching. This inflorescence regulatory network is modified within individual species, particularly as regards formation of secondary branches. Differences between species are caused both by modifications of gene expression and regulators and by presence or absence of critical genes. The unified networks described here may provide tools for investigating orphan crops and grasses other than the well-studied maize and rice.
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11
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Chen Q, Tian F, Cheng T, Jiang J, Zhu G, Gao Z, Lin H, Hu J, Qian Q, Fang X, Chen F. Translational repression of FZP mediated by CU-rich element/OsPTB interactions modulates panicle development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1319-1331. [PMID: 35293072 DOI: 10.1111/tpj.15737] [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: 06/16/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Panicle development is an important determinant of the grain number in rice. A thorough characterization of the molecular mechanism underlying panicle development will lead to improved breeding of high-yielding rice varieties. Frizzy Panicle (FZP), a critical gene for panicle development, is regulated by OsBZR1 and OsARFs at the transcriptional stage. However, the translational modulation of FZP has not been reported. We reveal that the CU-rich elements (CUREs) in the 3' UTR of the FZP mRNA are crucial for efficient FZP translation. The knockout of CUREs in the FZP 3' UTR or the over-expression of the FZP 3' UTR fragment containing CUREs resulted in an increase in FZP mRNA translation efficiency. Moreover, the number of secondary branches (NSB) and the grain number per panicle (GNP) decreased in the transformed rice plants. The CUREs in the 3' UTR of FZP mRNA were verified as the targets of the polypyrimidine tract-binding proteins OsPTB1 and OsPTB2 in rice. Both OsPTB1 and OsPTB2 were highly expressed in young panicles. The knockout of OsPTB1/2 resulted in an increase in the FZP translational efficiency and a decrease in the NSB and GNP. Furthermore, the over-expression of OsPTB1/2 decreased the translation of the reporter gene fused to FZP 3' UTR in vivo and in vitro. These results suggest that OsPTB1/2 can mediate FZP translational repression by interacting with CUREs in the 3' UTR of FZP mRNA, leading to changes in the NSB and GNP. Accordingly, in addition to transcriptional regulation, FZP expression is also fine-tuned at the translational stage during rice panicle development.
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Affiliation(s)
- Qiong Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Fa'an Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Cheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun'e Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanlin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Haiyan Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaohua Fang
- Genetic Resource R&D Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chang Zhou, 213001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
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12
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RNA-binding proteins and their role in translational regulation in plants. Essays Biochem 2022; 66:87-97. [PMID: 35612383 DOI: 10.1042/ebc20210069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022]
Abstract
Translation is a fundamental process for life that needs to be finely adapted to the energetical, developmental and environmental conditions; however, the molecular mechanisms behind such adaptation are not yet fully understood. By directly recognizing and binding to cis-elements present in their target mRNAs, RBPs govern all post-transcriptional regulatory processes. They orchestrate the balance between mRNA stability, storage, decay, and translation of their client mRNAs, playing a crucial role in the modulation of gene expression. In the last years exciting discoveries have been made regarding the roles of RBPs in fine-tuning translation. In this review, we focus on how these RBPs recognize their targets and modulate their translation, highlighting the complex and diverse molecular mechanisms implicated. Since the repertoire of RBPs keeps growing, future research promises to uncover new fascinating means of translational modulation, and thus, of gene expression.
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13
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Pasion EA, Badoni S, Misra G, Anacleto R, Parween S, Kohli A, Sreenivasulu N. OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1396-1411. [PMID: 33544455 PMCID: PMC8313136 DOI: 10.1111/pbi.13560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 06/02/2023]
Abstract
To address the future food security in Asia, we need to improve the genetic gain of grain yield while ensuring the consumer acceptance. This study aimed to identify novel genes influencing the number of upper secondary rachis branches (USRB) to elevate superior grains without compromising grain quality by studying the genetic variance of 310 diverse O. sativa var. indica panel using single- and multi-locus genome-wide association studies (GWAS), gene set analyses and gene regulatory network analysis. GWAS of USRB identified 230 significant (q-value < 0.05) SNPs from chromosomes 1 and 2. GWAS targets narrowed down using gene set analyses identified large effect association on an important locus LOC_Os02g50790/LOC_Os02g50799 encoding a nuclear-pore anchor protein (OsTPR). The superior haplotype derived from non-synonymous SNPs identified in OsTPR was specifically associated with increase in USRB with superior grains being low chalk. Through haplotype mining, we further demonstrated the synergy of offering added yield advantage due to superior allele of OsTPR in elite materials with low glycaemic index (GI) property. We further validated the importance of OsTPR using recombinant inbred lines (RILs) population by introgressing a superior allele of OsTPR into elite materials resulted in raise in productivity in high amylose background. This confirmed a critical role for OsTPR in influencing yield while maintaining grain and nutritional quality.
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Affiliation(s)
- Erstelle A. Pasion
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Saurabh Badoni
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Gopal Misra
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Roslen Anacleto
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Ajay Kohli
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
| | - Nese Sreenivasulu
- Applied Functional Genomics ClusterGrain Quality and Nutrition CentreStrategic Innovation PlatformInternational Rice Research InstituteLos BañosPhilippines
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14
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Khong GN, Le NT, Pham MT, Adam H, Gauron C, Le HQ, Pham DT, Colonges K, Pham XH, Do VN, Lebrun M, Jouannic S. A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice. PLoS Genet 2021; 17:e1009594. [PMID: 34097698 PMCID: PMC8211194 DOI: 10.1371/journal.pgen.1009594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/17/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022] Open
Abstract
The number of grains per panicle is an important yield-related trait in cereals which depends in part on panicle branching complexity. One component of this complexity is the number of secondary branches per panicle. Previously, a GWAS site associated with secondary branch and spikelet numbers per panicle in rice was identified. Here we combined gene capture, bi-parental genetic population analysis, expression profiling and transgenic approaches in order to investigate the functional significance of a cluster of 6 ANK and ANK-TPR genes within the QTL. Four of the ANK and ANK-TPR genes present a differential expression associated with panicle secondary branch number in contrasted accessions. These differential expression patterns correlate in the different alleles of these genes with specific deletions of potential cis-regulatory sequences in their promoters. Two of these genes were confirmed through functional analysis as playing a role in the control of panicle architecture. Our findings indicate that secondary branching diversity in the rice panicle is governed in part by differentially expressed genes within this cluster encoding ANK and ANK-TPR domain proteins that may act as positive or negative regulators of panicle meristem’s identity transition from indeterminate to determinate state. Grain yield is one of the most important indexes in rice breeding, which is controlled in part by panicle branching complexity. A new QTL with co-location of spikelet number (SpN) and secondary branch number (SBN) traits was identified by genome-wide association study in a Vietnamese rice landrace panel. A set of four Ankyrin and Tetratricopeptide repeat domain-encoding genes was identified from this QTL based on their difference of expression levels between two contrasted haplotypes for the SpN and SBN traits. The differential expression is correlated with deletions in the promoter regions of these genes. Two of the genes act as negative regulators of the panicle meristem’s identity transition from indeterminate to determinate state while the other two act as positive regulators of this meristem fate transition. Based on the different phenotypes between overexpressed and mutant plants, two of these genes were confirmed as playing a role in the control of panicle architecture. These findings can be directly used to assist selection for grain yield improvement.
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Affiliation(s)
- Giang Ngan Khong
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- * E-mail: (GNK); (SJ)
| | - Nhu Thi Le
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Mai Thi Pham
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Helene Adam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Carole Gauron
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Hoa Quang Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Dung Tien Pham
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Kelly Colonges
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Xuan Hoi Pham
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Vinh Nang Do
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Michel Lebrun
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR LSTM, University of Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France
| | - Stefan Jouannic
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
- * E-mail: (GNK); (SJ)
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15
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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16
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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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17
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Panda D, Sahu N, Behera PK, Lenka K. Genetic variability of panicle architecture in indigenous rice landraces of Koraput region of Eastern Ghats of India for crop improvement. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1961-1971. [PMID: 33088042 PMCID: PMC7548273 DOI: 10.1007/s12298-020-00871-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Panicle architecture is an important character that influence reproductive success and contributes directly to grain yield. In the present study, we evaluated diversity of panicle traits in 77 indigenous rice landraces from Koraput and compared with three popularity cultivated hybrid varieties of the locality for possibility of using in crop improvement program. Significant morphological variations of panicle traits such as panicle number, panicle angle, panicle weight, panicle length, grain number and grain weight were recorded in studied rice landraces. Based on the principal component analysis, first two axis of principal component captures 56.34% of the total variation and indicated significant variability of panicle traits among the genotypes. Panicle length, panicle weight, grain number and flag leaf area are the major determinants of phenotypic diversity. Multiple correlation between traits indicated that panicle weight in studied rice landraces were positively correlated with panicle number, grain number and leaf area and negatively associated with panicle length, panicle angle and chaff number. The genetic advance as percentage of mean (GAM) ranged from 22.19% for panicle length to 147.02% for panicle angle. High GAM along with heritability was observed for panicle number, panicle weight, grain number and chaff number and are important traits for selection during crop improvement. Some of the landraces such as Matidhan, Bhatagurumukhi, Chiklakoli and Kamuntana remarkably showed superior panicle weight along with higher grain number and length of panicle, which can be used in the future rice breeding program.
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Affiliation(s)
- Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput, Odisha 764021 India
| | - Neelamadhab Sahu
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput, Odisha 764021 India
| | - Prafulla K. Behera
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput, Odisha 764021 India
| | - Kartik Lenka
- MS Swaminathan Research Foundation, Jeypore, Koraput, Odisha 764002 India
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18
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Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles. Commun Biol 2020; 3:302. [PMID: 32528064 PMCID: PMC7289860 DOI: 10.1038/s42003-020-1036-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 05/26/2020] [Indexed: 12/02/2022] Open
Abstract
Panicle architecture directly affects crop productivity and is a key target of high-yield rice breeding. Panicle length strongly affects panicle architecture, but the underlying regulatory mechanisms are largely unknown. Here, we show that two quantitative trait loci (QTLs), PANICLE RACHIS LENGTH5 (Prl5) and PRIMARY BRANCH LENGTH6 (Pbl6), independently regulate panicle length in rice. Prl5 encodes a gibberellin biosynthesis enzyme, OsGA20ox4. The expression of Prl5 was higher in young panicles resulting in panicle rachis elongation. Pbl6 is identical to ABERRANT PANICLE ORGANIZATION 1 (APO1), encoding an F-box-containing protein. We found a novel function that higher expression of Pbl6 is responsible for primary branch elongation. RNA-seq analysis revealed that these two genes independently regulate panicle length at the level of gene expression. QTL pyramiding of both genes increased panicle length and productivity. By combining these two genes in various combinations, we designed numerous panicle architecture without trade-off relationship. Ayumi Agata et al. study the molecular mechanisms regulating panicle length which directly affects crop yield. They identify QTLs Prl5 and Pbl6 that independently regulate panicle length in rice at the gene expression level. By designing different allelic combinations, they generate desired panicle architecture and confirm their positive effect on yield in the field.
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19
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Zhu Y, Wagner D. Plant Inflorescence Architecture: The Formation, Activity, and Fate of Axillary Meristems. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a034652. [PMID: 31308142 DOI: 10.1101/cshperspect.a034652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The above-ground plant body in different plant species can have very distinct forms or architectures that arise by recurrent redeployment of a finite set of building blocks-leaves with axillary meristems, stems or branches, and flowers. The unique architectures of plant inflorescences in different plant families and species, on which this review focuses, determine the reproductive success and yield of wild and cultivated plants. Major contributors to the inflorescence architecture are the activity and developmental trajectories adopted by axillary meristems, which determine the degree of branching and the number of flowers formed. Recent advances in genetic and molecular analyses in diverse flowering plants have uncovered both common regulatory principles and unique players and/or regulatory interactions that underlie inflorescence architecture. Modulating activity of these regulators has already led to yield increases in the field. Additional insight into the underlying regulatory interactions and principles will not only uncover how their rewiring resulted in altered plant form, but will also enhance efforts at optimizing plant architecture in desirable ways in crop species.
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Affiliation(s)
- Yang Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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20
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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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