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Zhang Y, Du A, Tong L, Yan G, Lu L, Yin Y, Fu X, Yang H, Li H, Huang W, Cai D, Song Z, Zhang X, He Y, Tu S. Genome Resequencing for Autotetraploid Rice and Its Closest Relatives Reveals Abundant Variation and High Potential in Rice Breeding. Int J Mol Sci 2024; 25:9012. [PMID: 39201698 PMCID: PMC11354466 DOI: 10.3390/ijms25169012] [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: 07/05/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Polyploid rice and its reverted diploid show rich phenotypic variation and strong heterosis, showing great breeding value. However, the genomic differences among tetraploids, counterpart common diploids, tetraploid-revertant diploids, and hybrid descendants are unclear. In this work, we bred a new excellent two-line hybrid rice variety, Y Liang You Duo Hui 14 (HTRM12), using Haitian tetraploid self-reverted diploid (HTRM2). Furthermore, we comparatively analyzed the important agronomic traits and genome-wide variations of those closest relatives, Haitian diploid (HT2), Haitian tetraploid (HT4), HTRM2, and HTRM12 in detail, based on multiple phenotypic investigations, genome resequencing, and bioinformatics analysis. The results of agronomic traits analysis and genome-wide variation analysis of single nucleotide polymorphism (SNP), insertion-deletion (InDel), and copy number variation (CNV) show that HT4 and HTRM2 had abundant phenotypic and genomic variations compared to HT2. HTRM2 can inherit important traits and variations from HT4. This implies that tetraploid self-reverted diploid has high potential in creating excellent breeding materials and in breeding breakthrough hybrid rice varieties. Our study verifies the feasibility that polyploid rice could be used as a mutation carrier for creating variations and provides genomic information, new breeding materials, and a new way of application for tetraploid rice breeding.
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Affiliation(s)
- Yachun Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Anping Du
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
| | - Liqi Tong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Gui Yan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Longxiang Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanni Yin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Xingyue Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huixin Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
| | - Weizao Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
| | - Detian Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Zhaojian Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Yuchi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (L.T.); (G.Y.); (Y.Y.); (D.C.); (Z.S.); (X.Z.)
| | - Shengbin Tu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; (Y.Z.); (A.D.); (L.L.); (X.F.); (H.Y.); (H.L.); (W.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Li X, Huang X, Wen M, Yin W, Chen Y, Liu Y, Liu X. Cytological observation and RNA-seq analysis reveal novel miRNAs high expression associated with the pollen fertility of neo-tetraploid rice. BMC PLANT BIOLOGY 2023; 23:434. [PMID: 37723448 PMCID: PMC10506311 DOI: 10.1186/s12870-023-04453-y] [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: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Neo-tetraploid rice lines exhibit high fertility and strong heterosis and harbor novel specific alleles, which are useful germplasm for polyploid rice breeding. However, the mechanism of the fertility associated with miRNAs remains unknown. In this study, a neo-tetraploid rice line, termed Huaduo21 (H21), was used. Cytological observation and RNA-sequencing were employed to identify the fertility-related miRNAs in neo-tetraploid rice. RESULTS H21 showed high pollen fertility (88.08%), a lower percentage of the pollen mother cell (PMC) abnormalities, and lower abnormalities during double fertilization and embryogenesis compared with autotetraploid rice. A total of 166 non-additive miRNAs and 3108 non-additive genes were detected between H21 and its parents. GO and KEGG analysis of non-additive genes revealed significant enrichments in the DNA replication, Chromosome and associated proteins, and Replication and repair pathways. Comprehensive multi-omics analysis identified 32 pairs of miRNA/target that were associated with the fertility in H21. Of these, osa-miR408-3p and osa-miR528-5p displayed high expression patterns, targeted the phytocyanin genes, and were associated with high pollen fertility. Suppression of osa-miR528-5p in Huaduo1 resulted in a low seed set and a decrease in the number of grains. Moreover, transgenic analysis implied that osa-MIR397b-p3, osa-miR5492, and osa-MIR5495-p5 might participate in the fertility of H21. CONCLUSION Taken together, the regulation network of fertility-related miRNAs-targets pairs might contribute to the high seed setting in neo-tetraploid rice. These findings enhance our understanding of the regulatory mechanisms of pollen fertility associated with miRNAs in neo-tetraploid rice.
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Affiliation(s)
- Xiang Li
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.
- College of Biology and Agriculture, Shaoguan University, Shaoguan, China.
| | - Xu Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Minsi Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Wei Yin
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yuanmou Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.
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Kamara N, Jiao Y, Huang W, Cao L, Zhu L, Zhao C, Huang X, Shivute FN, Liu X, Wu J, Shahid MQ. Comparative cytological and transcriptome analyses of ny2 mutant delayed degeneration of tapetal cells and promotes abnormal microspore development in neo-tetraploid rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1229870. [PMID: 37528969 PMCID: PMC10387629 DOI: 10.3389/fpls.2023.1229870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
We aimed to investigate the genetic defects related to pollen development and infertility in NY2, a novel tetraploid rice germplasm known as Neo-tetraploid rice. This rice variety was created through the crossbreeding and selective breeding of various autotetraploid rice lines and has previously shown high fertility. Our previous research has revealed that the NY2 gene, encoding a eukaryotic translation initiation factor 3 subunit E, regulates pollen fertility. However, the underlying mechanism behind this fertility is yet to be understood. To shed light on this matter, we performed a combined cytological and transcriptome analysis of the NY2 gene. Cytological analysis indicated that ny2 underwent abnormal tapetal cells, microspore, and middle layer development, which led to pollen abortion and ultimately to male sterility. Genetic analysis revealed that the F1 plants showed normal fertility and an obvious advantage for seed setting compared to ny2. Global gene expression analysis in ny2 revealed a total of 7545 genes were detected at the meiosis stage, and 3925 and 3620 displayed upregulation and downregulation, respectively. The genes were significantly enriched for the gene ontology (GO) term "carbohydrate metabolic process. Moreover, 9 genes related to tapetum or pollen fertility showed down-regulation, such as OsABCG26 (ATP Binding Cassette G26), TMS9-1 (Thermosensitive Male Sterility), EAT1 (Programmed cell death regulatory), KIN14M (Kinesin Motor), OsMT1a (Metallothionein), and OsSTRL2 (Atypical strictosidine synthase), which were validated by qRT-PCR. Further analyses of DEGs identified nine down-regulated transcription factor genes related to pollen development. NY2 is an important regulator of the development of tapetum and microspore. The regulatory gene network described in this study may offer important understandings into the molecular processes that underlie fertility control in tetraploid rice.
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Affiliation(s)
- Nabieu Kamara
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Crop Improvement Programme, Rokupr Agricultural Research Center, Rokupr - Sierra Leone Agricultural Research Institute (SLARI), Freetown, Sierra Leone
| | - Yamin Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Weicong Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lichong Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lianjun Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Chongchong Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Fimanekeni Ndaitavela Shivute
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Multi-disciplinary Research Services, University of Namibia, Windhoek, Namibia
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
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Zhang J, Yu H, Li J. De novo domestication: retrace the history of agriculture to design future crops. Curr Opin Biotechnol 2023; 81:102946. [PMID: 37080109 DOI: 10.1016/j.copbio.2023.102946] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Certain crops were domesticated from their wild progenitors and have served as the major staple food since then, but now suffered from the limited genetic diversity in breeding. Enormous wild species possess unique advantages such as stress tolerance, polyploidy, perennial habit, and natural nutrition. However, it remains a big challenge to utilize wild species in conventional breeding. With recent advances in biotechnologies, one new breeding strategy, de novo domestication, has emerged and been demonstrated by pioneer work. Here, we review the emergence and milestone progress of de novo domestication and discuss how wild relatives could be exploited into new types of crops. With the understanding of the genetic basis of crop domestication and the development of biotechnologies, various elite wild germplasms will be designed and practiced to fulfill particular breeding goals and create new types of crops. De novo domestication is paving a new way for breeding the future.
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Affiliation(s)
- Jingkun Zhang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China; Hainan Yazhou Bay Seed Laboratory, China.
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Mangena P. Impact of Polyploidy Induction for Salinity Stress Mitigation in Soybean ( Glycine max L. Merrill). PLANTS (BASEL, SWITZERLAND) 2023; 12:1356. [PMID: 36987050 PMCID: PMC10051967 DOI: 10.3390/plants12061356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Polyploidy induction is recognized as one of the major evolutionary processes leading to remarkable morphological, physiological, and genetic variations in plants. Soybean (Glycine max L.), also known as soja bean or soya bean, is an annual leguminous crop of the pea family (Fabaceae) that shares a paleopolypoidy history, dating back to approximately 56.5 million years ago with other leguminous crops such as cowpea and other Glycine specific polyploids. This crop has been documented as one of the polyploid complex species among legumes whose gene evolution and resultant adaptive growth characteristics following induced polyploidization has not been fully explored. Furthermore, no successfully established in vivo or in vitro based polyploidy induction protocols have been reported to date, particularly, with the intention to develop mutant plants showing strong resistance to abiotic salinity stress. This review, therefore, describes the role of synthetic polyploid plant production in soybean for the mitigation of high soil salt stress levels and how this evolving approach could be used to further enhance the nutritional, pharmaceutical and economic industrial value of soybeans. This review also addresses the challenges involved during the polyploidization process.
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Affiliation(s)
- Phetole Mangena
- Department of Biodiversity, School of Molecular and Life Sciences, Faculty of Science and Agriculture, University of Limpopo, Sovenga, Private Bag X1106, Polokwane 0727, South Africa
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DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication. J Adv Res 2022; 42:41-53. [PMID: 35933090 PMCID: PMC9788948 DOI: 10.1016/j.jare.2022.07.007] [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: 03/28/2022] [Revised: 07/05/2022] [Accepted: 07/23/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Polyploidy is a major force in plant evolution and the domestication of cultivated crops. OBJECTIVES The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication. METHODS The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication. RESULTS We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes. CONCLUSION The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.
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Ku T, Gu H, Li Z, Tian B, Xie Z, Shi G, Chen W, Wei F, Cao G. Developmental Differences between Anthers of Diploid and Autotetraploid Rice at Meiosis. PLANTS (BASEL, SWITZERLAND) 2022; 11:1647. [PMID: 35807599 PMCID: PMC9268837 DOI: 10.3390/plants11131647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/18/2022] [Accepted: 06/19/2022] [Indexed: 11/25/2022]
Abstract
Newly synthetic autotetraploid rice shows lower pollen fertility and seed setting rate relative to diploid rice, which hinders its domestication and breeding. In this study, cytological analysis showed that at meiosis I stage, an unbalanced segregation of homologous chromosomes, occurred as well as an early degeneration of tapetal cells in autotetraploid rice. We identified 941 differentially expressed proteins (DEPs) in anthers (meiosis I), including 489 upregulated and 452 downregulated proteins. The DEPs identified were related to post-translational modifications such as protein ubiquitination. These modifications are related to chromatin remodeling and homologous recombination abnormalities during meiosis. In addition, proteins related to the pentose phosphate pathway (BGIOSGA016558, BGIOSGA022166, and BGIOSGA028743) were downregulated. This may be related to the failure of autotetraploid rice to provide the energy needed for cell development after polyploidization, which then ultimately leads to the early degradation of the tapetum. Moreover, we also found that proteins (BGIOSGA017346 and BGIOSGA027368) related to glutenin degradation were upregulated, indicating that a large loss of glutenin cannot provide nutrition for the development of tapetum, resulting in early degradation of tapetum. Taken together, these evidences may help to understand the differences in anther development between diploid and autotetraploid rice during meiosis.
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Affiliation(s)
| | | | | | | | | | | | | | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.K.); (H.G.); (Z.L.); (B.T.); (Z.X.); (G.S.); (W.C.)
| | - Gangqiang Cao
- Henan International Joint Laboratory of Crop Gene Resources and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (T.K.); (H.G.); (Z.L.); (B.T.); (Z.X.); (G.S.); (W.C.)
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Thermo-Sensitive Genic Male Sterile Lines of Neo-Tetraploid Rice Developed through Gene Editing Technology Revealed High Levels of Hybrid Vigor. PLANTS 2022; 11:plants11111390. [PMID: 35684163 PMCID: PMC9182671 DOI: 10.3390/plants11111390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 11/18/2022]
Abstract
Neo-tetraploid rice, which developed from the progenies of autotetraploid hybrid by our research group, is a useful germplasm with high fertility and strong heterosis when they crossed with other autotetraploid rice lines. The CRISPR/Cas9-mediated TMS5 gene editing system has been widely used in diploid rice, but there are few reports in tetraploid rice. Here, we used CRISPR/Cas9 technology to edit the TMS5 gene, which is a temperature sensitive gene controlling the fertility in diploid rice, in neo-tetraploid rice to develop male sterile lines. Two mutant lines, H2s and H3s, were developed from the gene editing and displayed characteristics of thermo-sensitive genic male sterility. The daily mean temperatures of 23 °C to 26 °C were found to be critical for sterility (restrictive temperature) in H2s and H3s under both controlled (growth chambers) and natural growing conditions (field). Cytological observation showed the anther dysplasia appeared later in H2s and H3s than that of the TMS5 mutant of diploid rice (E285s) under the same conditions. Then these mutant lines, H2s and H3s, were crossed with tetraploid rice to generate F1 hybrids, which exhibited obvious advantages for effective number of panicles, total grains and seed setting. The high levels of hybrids heterosis were maintained for several generations that can save seed cost. Our research provides an effective way of developing thermo-sensitive genic male sterility (TGMS) lines of tetraploid rice using gene editing, which will accelerate the utilization of polyploid heterosis.
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Zhao K, Jin N, Madadi M, Wang Y, Wu L, Xu Z, Wang J, Dong J, Tang SW, Wang Y, Peng L, Xiong Z. Incomplete genome doubling enables to consistently enhance plant growth for maximum biomass production by altering multiple transcript co-expression networks in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:461-472. [PMID: 34731273 DOI: 10.1007/s00122-021-03976-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Cytochimera potato plants, which mixed with diploid and tetraploid cells, could cause the highest and significantly increased biomass yield than the polyploid and diploid potato plants. Polyploidization is an important approach in crop breeding for agronomic trait improvement, especially for biomass production. Cytochimera contains two or more mixed cells with different levels of ploidy, which is considered a failure in whole genome duplication. Using colchicine treatment with diploid (Dip) potato (Solanum chacoense) plantlets, this study generated tetraploid (Tet) and cytochimera (Cyt) lines, which, respectively, contained complete and partial cells with genome duplication. Compared to the Dip potato, we observed remarkably enhanced plant growth and biomass yields in Tet and Cyt lines. Notably, the Cyt potato straw, which was generated from incomplete genome doubling, was of significantly higher biomass yield than that of the Tet with a distinctively altered cell wall composition. Meanwhile, we observed that one layer of the tetraploid cells (about 30%) in Cyt plants was sufficient to trigger a gene expression pattern similar to that of Tet, suggesting that the biomass dominance of Cyt may be related to the proportion of different ploidy cells. Further genome-wide analyses of co-expression networks indicated that down-regulation (against Dip) of spliceosomal-related transcripts might lead to differential alternative splicing for specifically improved agronomic traits such as plant growth, biomass yield, and lignocellulose composition in Tet and Cyt plants. In addition, this work examined that the genome of Cyt line was relatively stable after years of asexual reproduction. Hence, this study has demonstrated that incomplete genome doubling is a promising strategy to maximize biomass production in potatoes and beyond.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Nengzhou Jin
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Meysam Madadi
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Youmei Wang
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Zhijun Xu
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Jinxuan Wang
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Jing Dong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Shang-Wen Tang
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Yanting Wang
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Liangcai Peng
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China.
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10
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Wang W, Tu Q, Chen R, Lv P, Xu Y, Xie Q, Song Z, He Y, Cai D, Zhang X. Polyploidization Increases the Lipid Content and Improves the Nutritional Quality of Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:132. [PMID: 35009135 PMCID: PMC8747249 DOI: 10.3390/plants11010132] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Plant polyploidization is frequently associated with changes in nutrient contents. However, the possible contribution of metabolites to this change has not been investigated by characterizing the metabolite contents of diploid and tetraploid forms of rice (Oryza sativa L.). We compared the metabolites of a group of diploid-tetraploid japonica brown rice and a group of diploid-tetraploid indica brown rice based on liquid chromatography-tandem mass spectrometry. In total, 401 metabolites were identified; of these, between the two diploid-tetraploid groups, 180 showed opposite expression trends, but 221 showed the same trends (147 higher abundance vs. 74 lower abundance). Hierarchical cluster analysis of differential metabolites between diploid and tetraploid species showed a clear grouping pattern, in which the expression abundance of lipids, amino acids and derivatives, and phenolic acids increased in tetraploids. Further analysis revealed that the lipids in tetraploid rice increased significantly, especially unsaturated fatty acids and phospholipids. This study provides further basis for understanding the changes in rice nutritional quality following polyploidization and may serve as a new theoretical reference for breeding eutrophic or functional rice varieties via polyploidization.
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11
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Madadi M, Zhao K, Wang Y, Wang Y, Tang SW, Xia T, Jin N, Xu Z, Li G, Qi Z, Peng L, Xiong Z. Modified lignocellulose and rich starch for complete saccharification to maximize bioethanol in distinct polyploidy potato straw. Carbohydr Polym 2021; 265:118070. [PMID: 33966834 DOI: 10.1016/j.carbpol.2021.118070] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 01/09/2023]
Abstract
Potato is a major food crop with enormous biomass straw, but lignocellulose recalcitrance causes a costly bioethanol conversion. Here, we selected the cytochimera (Cyt) potato samples showing significantly-modified lignocellulose and much increased soluble sugars and starch by 2-4 folds in mature straws. Under two pretreatments (8 min liquid hot water; 5% CaO) at minimized conditions, the potato Cyt straw showed complete enzymatic saccharification. Further performing yeast fermentation with all hexoses released from soluble sugars, starch and lignocellulose in the Cyt straw, this study achieved a maximum bioethanol yield of 24 % (% dry matter), being higher than those of other bioenergy crops as previously reported. Hence, this study has proposed a novel mechanism model on the reduction of major lignocellulose recalcitrance and regulation of carbon assimilation to achieve cost-effective bioethanol production under optimal pretreatments. This work also provides a sustainable strategy for utilization of potato straws with minimum waste release.
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Affiliation(s)
- Meysam Madadi
- Biomass & Bioenergy Research Center, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China.
| | - Kanglu Zhao
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Youmei Wang
- Biomass & Bioenergy Research Center, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yanting Wang
- Biomass & Bioenergy Research Center, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China.
| | - Shang-Wen Tang
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China.
| | - Tao Xia
- Biomass & Bioenergy Research Center, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Nengzhou Jin
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Zhijun Xu
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Guanhua Li
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Zhi Qi
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Liangcai Peng
- Biomass & Bioenergy Research Center, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China; Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China.
| | - Zhiyong Xiong
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
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12
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Gan L, Huang B, Song Z, Zhang Y, Zhang Y, Chen S, Tong L, Wei Z, Yu L, Luo X, Zhang X, Cai D, He Y. Unique Glutelin Expression Patterns and Seed Endosperm Structure Facilitate Glutelin Accumulation in Polyploid Rice Seed. RICE (NEW YORK, N.Y.) 2021; 14:61. [PMID: 34224013 PMCID: PMC8257881 DOI: 10.1186/s12284-021-00500-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/06/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice is not only an essential food but also a source of high quality protein. Polyploidy is an evolutionary trajectory in plants, and enhancing glutelin by polyploidization is an attractive strategy for improving the nutritional value of rice seeds and presents a great potential for enhancing the commercial value of rice. Elucidating the mechanisms underlying glutelin synthesis and accumulation in tetraploid rice is of great significance. RESULTS To enhance the nutritional value of rice, we developed tetraploid rice and evaluated the contents of various nutrient elements in mature seeds. The results revealed a significant increase in protein contents, including the total seed storage proteins, glutelins, and amino acids in tetraploid rice when compared with those in diploid rice. Tandem mass tag-based quantitative proteomic analyses of seeds revealed that glutelins regulated by several glutelin genes in 9311-4x were significantly up-regulated (≥1.5-fold), which was further verified by immunoblot analyses. In addition, temporal expression patterns of various glutelin subunits in different rice lines were investigated. The results revealed significant differences in the expression patterns between diploid and tetraploid rice seeds. Cytohistological analyses results revealed that the thickness of aleurone cell layers increased significantly by 32% in tetraploid rice, the structures of protein storage vacuoles (PSVs) in sub-aleurone cells were more diverse and abundant than those of diploid rice. Temporal expression and proteomic analyses results revealed that protein disulfide isomerase-like 1-1 expression levels were higher in tetraploid rice than in diploid rice, and that the gene responded to oxidative folding with increased levels of proglutelin and appropriate distribution of seed glutelins in tetraploid rice. CONCLUSION The results of the present study revealed that polyploidization increased glutelin content by influencing glutelin biosynthesis, transport, and deposition, while variations in glutelin accumulation between tetraploid and diploid rice were largely manifested in the initial time, duration, and relative levels of various glutelin gene expressions during seed filling stages. These findings provide novel insights into improving the protein quality and nutritional value of rice seeds by polyploid breeding.
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Affiliation(s)
- Lu Gan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- School of Chemistry & Environmental Engineering, Hanjiang Normal University, Shiyan, China
| | - Baosheng Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhaojian Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
| | - Yachun Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yujie Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Si Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Liqi Tong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhisong Wei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Lingxiang Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiangbo Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
| | - Detian Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China
| | - Yuchi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China.
- Wuhan Polyploid Biology Technology Co. Ltd, Wuhan, China.
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13
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Xian L, Long Y, Yang M, Chen Z, Wu J, Liu X, Wang L. iTRAQ-based quantitative glutelin proteomic analysis reveals differentially expressed proteins in the physiological metabolism process during endosperm development and their impacts on yield and quality in autotetraploid rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 306:110859. [PMID: 33775365 DOI: 10.1016/j.plantsci.2021.110859] [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: 11/04/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Autotetraploid rice, which is developed through chromosome set doubling using diploid rice, produces high-quality kernels that are rich in storage proteins. However, little information is available about the content of different proteins in autotetraploid rice and their proteomic analysis. The dynamic changes in four storage proteins, namely, albumin, globulin, prolamin, and glutelin, were analyzed in the endosperm of autotetraploid rice (AJNT-4x) and in that of its diploid counterpart (AJNT-2x) for comparison. The contents of the four proteins were all higher during endosperm development in AJNT-4x than in AJNT-2x, but their change and composition were almost the same in the two materials. Then, iTRAQ was employed to analyze the glutelin profiles of AJNT-4x and AJNT-2x at 10 DAF, 15 DAF, and 20 DAF. A total of 1326 proteins were identified in AJNT-4x and AJNT-2x using high-throughput LC-MS/MS. Among the 1326 identified proteins, there were 362 DEPs in AJNT-4x compared with AJNT-2x and 372 DEPs between different developmental stages in AJNT-4x. Eight important upregulated proteins were identified by qRT-PCR, including B8AM24, B8ARJ0, B8AQM6, A2ZCE6, and P37833. Among them, B8AM24 and B8ARJ0 were related to the lysine biosynthesis process. GO enrichment analysis revealed that the critical functions of DEPs exhibited little overlap between the 10, 15, and 20 DAF groups. Endosperm glutelin accumulation was regulated mainly by different DEPs during the early stage, and 15 DAF was a critical regulating point for glutelin accumulation. KEGG pathway analysis showed that ribosomal proteins were significantly higher in AJNT-4x than in AJNT-2x at 10 DAF, and protein processing, biosynthesis, and metabolism of amino acids were higher and more active in AJNT-4x at 15 DAF, while the peroxisome was richer in AJNT-4x at 20 DAF. The PPI network showed that ribosomal proteins gradually decreased with increasing endosperm development. These results provide new insights into dynamic glutelin expression differences during endosperm development in autotetraploid rice, which will aid in the development of rice cultivars with increased yield and improved grain nutritional quality.
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Affiliation(s)
- Lin Xian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanxi Long
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Meng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhixiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Lan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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14
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El-Mowafi HF, AlKahtani MDF, El-Hity MA, Reda AM, Husnain LA, El-Degwy ES, Abdallah RM, AlGwaiz HIM, Hadifa AA, Attia KA. Characterization of fertility alteration and marker validation for male sterility genes in novel PTGMS lines hybrid rice. Saudi J Biol Sci 2021; 28:4109-4116. [PMID: 34354389 PMCID: PMC8324962 DOI: 10.1016/j.sjbs.2021.04.058] [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: 03/21/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
Photoperiod and thermosensitive genetic male sterile (PTGMS) lines have become one of the main sources of global rice production increasing. This study was conducted to evaluate the fertility alteration and validate the male sterility genes using validation markers in novel Egyptian Indica and Japonica PTGMS lines under natural conditions. The study revealed that the new genetic male sterile lines belong to the type of photo–thermosensitive genetic male sterility (PTGMS). The fertility alteration of these lines has influenced by photoperiod and temperature interaction. The new PTGMS lines have three sensitive periods of fertility alteration; transformation, sterility, and fertility period. Furthermore, the sensitive stage of fertility transformation might be from secondary branch primordial to pollen mother cells (PMC) meiosis. Under the natural Sakha condition, the new PTGMS lines were stable sterile under the condition of day length upper 13,75 h and temperature over 25 °C, while its convert to fertile under day length under 13 h, and temperature lower than 24 °C. The co-dominant markers identified the pms3 and tms5 genes in the new PTGMS lines, indicated that the fertility alteration in these lines controlled by photoperiod and thermosensitive stages.
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Affiliation(s)
- Hamdi F El-Mowafi
- Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh 33717, Egypt
| | - Muneera D F AlKahtani
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 102275, Riyadh 11675, Saudi Arabia
| | - Mahmoud A El-Hity
- Agronomy Department, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33512, Egypt
| | - Amr M Reda
- Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh 33717, Egypt
| | - Latifa Al Husnain
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 102275, Riyadh 11675, Saudi Arabia
| | - E S El-Degwy
- Agronomy Department, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33512, Egypt
| | - Rizk M Abdallah
- Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh 33717, Egypt
| | - Hussah I M AlGwaiz
- Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh 33717, Egypt
| | - A A Hadifa
- Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh 33717, Egypt
| | - Kotb A Attia
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh POX 2455-11451, Saudi Arabia.,Rice Department, Field Crops Research Institute, ARC, Sakha, Kafr El-Sheikh 33717, Egypt
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15
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Chen R, Feng Z, Zhang X, Song Z, Cai D. A New Way of Rice Breeding: Polyploid Rice Breeding. PLANTS 2021; 10:plants10030422. [PMID: 33668223 PMCID: PMC7996342 DOI: 10.3390/plants10030422] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/23/2022]
Abstract
Polyploid rice, first discovered by Japanese scientist Eiiti Nakamori in 1933, has a history of nearly 90 years. In the following years, polyploid rice studies have mainly focused on innovations in breeding theory, induction technology and the creation of new germplasm, the analysis of agronomic traits and nutritional components, the study of gametophyte development and reproduction characteristics, DNA methylation modification and gene expression regulation, distant hybridization and utilization among subspecies, species and genomes. In recent years, PMeS lines and neo-tetraploid rice lines with stable high seed setting rate characteristics have been successively selected, breaking through the bottleneck of low seed setting rate of polyploid rice. Following, a series of theoretical and applied studies on high seed setting rate tetraploid rice were carried out. This has pushed research on polyploid rice to a new stage, opening new prospects for polyploid rice breeding.
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Affiliation(s)
- Rongrong Chen
- School of Life Sciences, Hubei University, Wuhan 430062, China; (R.C.); (Z.F.); (Z.S.); (D.C.)
| | - Ziyi Feng
- School of Life Sciences, Hubei University, Wuhan 430062, China; (R.C.); (Z.F.); (Z.S.); (D.C.)
| | - Xianhua Zhang
- School of Life Sciences, Hubei University, Wuhan 430062, China; (R.C.); (Z.F.); (Z.S.); (D.C.)
- Correspondence: ; Tel.: +86-027-88663882
| | - Zhaojian Song
- School of Life Sciences, Hubei University, Wuhan 430062, China; (R.C.); (Z.F.); (Z.S.); (D.C.)
| | - Detian Cai
- School of Life Sciences, Hubei University, Wuhan 430062, China; (R.C.); (Z.F.); (Z.S.); (D.C.)
- Wuhan Polyploid Bio-Technology Co., Ltd., Wuhan 430345, China
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16
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Yu H, Lin T, Meng X, Du H, Zhang J, Liu G, Chen M, Jing Y, Kou L, Li X, Gao Q, Liang Y, Liu X, Fan Z, Liang Y, Cheng Z, Chen M, Tian Z, Wang Y, Chu C, Zuo J, Wan J, Qian Q, Han B, Zuccolo A, Wing RA, Gao C, Liang C, Li J. A route to de novo domestication of wild allotetraploid rice. Cell 2021; 184:1156-1170.e14. [PMID: 33539781 DOI: 10.1016/j.cell.2021.01.013] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 12/02/2020] [Accepted: 01/11/2021] [Indexed: 12/25/2022]
Abstract
Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.
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Affiliation(s)
- Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tao Lin
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingkun Zhang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangdong Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhilan Fan
- National Field Genebank for Wild Rice (Guangzhou), Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuntao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixi Tian
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - 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
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Caixia Gao
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China.
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Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice. Int J Mol Sci 2021; 22:ijms22020841. [PMID: 33467721 PMCID: PMC7830325 DOI: 10.3390/ijms22020841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
Neo-tetraploid rice with high fertility is a useful germplasm for polyploid rice breeding, which was developed from the crossing of different autotetraploid rice lines. However, little information is available on the molecular mechanism underlying the fertility of neo-tetraploid rice. Here, two contrasting populations of tetraploid rice, including one with high fertility (hereafter referred to as JG) and another with low fertility (hereafter referred to as JD), were generated by crossing Huaduo 3 (H3), a high fertility neo-tetraploid rice that was developed by crossing Jackson-4x with 96025-4x, and Huajingxian74-4x (T452), a low fertility autotetraploid rice parent. Cytological, global genome sequencing-based bulked-segregant (BSA-seq) and CRISPR/Cas9 technology were employed to study the genes associated with pollen fertility in neo-tetraploid rice. The embryo sacs of JG and JD lines were normal; however, pollen fertility was low in JD, which led to scarce fertilization and low seed setting. Cytological observations displayed low pollen fertility (25.1%) and approximately 31.3 and 27.2% chromosome lagging at metaphase I and II, and 28.8 and 24.8% chromosome straggling at anaphase I and II in JD, respectively. BSA-seq of F2–3 generations and RNA-seq of F4 generation detected a common fragment, i.e., 18,915,234–19,500,000, at chromosome 7, which was comprised of 78 genes associated with fertility. Among 78 genes, 9 genes had been known to be involved in meiosis and pollen development. Two mutants ny1 (LOC_Os07g32406) and ny2 (LOC_Os07g32040) were generated by CRISPR/Cas9 knockout in neo-tetraploid rice, and which exhibited low pollen fertility and abnormal chromosome behavior. Our study revealed that two unknown genes, LOC_Os07g32406 (NY1) and LOC_Os07g32040 (NY2) play an important role in pollen development of neo-tetraploid rice and provides a new perspective about the genetic mechanisms of fertility in polyploid rice.
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Lu Z, Guo X, Huang Z, Xia J, Li X, Wu J, Yu H, Shahid MQ, Liu X. Transcriptome and Gene Editing Analyses Reveal MOF1a Defect Alters the Expression of Genes Associated with Tapetum Development and Chromosome Behavior at Meiosis Stage Resulting in Low Pollen Fertility of Tetraploid Rice. Int J Mol Sci 2020; 21:ijms21207489. [PMID: 33050591 PMCID: PMC7589589 DOI: 10.3390/ijms21207489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 01/07/2023] Open
Abstract
Autotetraploid rice is a useful rice germplasm for polyploid rice breeding. However, low fertility limits its commercial production. A neo-tetraploid rice with high fertility was developed from the progenies of crossing between autotetraploid lines by our research group. Our previous study showed that a myeloblastosis (MYB) transcription factor, MOF1, might be associated with the pollen development in tetraploid rice. However, little information is available about its role in pollen development in tetraploid rice. Here, we identified a new haplotype of MOF1 from neo-tetraploid rice and marked it as MOF1a. Transcriptome and qRT-PCR analysis demonstrated that MOF1a highly expressed in anthers, and displayed differential expression in neo-tetraploid rice compared to tetraploid rice line with low pollen fertility. The mutant (mof1a) of MOF1a, which was generated by CRISPR/Cas9 knockout in neo-tetraploid rice, showed low pollen fertility, and also exhibited abnormal tapetum and middle layer development, and defective chromosome behaviors during meiosis. A total of 13 tapetal related genes were found to be up-regulated in meiotic anthers of MOF1a compared with wild type plants by RNA-seq analysis, including CYP703A3, PTC1, and OsABCG26, which had been demonstrated to affect tapetal development. Moreover, 335 meiosis-related genes displayed differential expression patterns at same stage, including nine important meiosis-related genes, such as metallothionein OsMT1a. These results demonstrated that MOF1a plays an important role in pollen development and provides a foundation for understanding the molecular mechanism underlying MOF1a in reproduction of tetraploid rice.
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Affiliation(s)
- Zijun Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiyu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Juan Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (M.Q.S.); (X.L.); Tel./Fax: +86-208-528-0205 (M.Q.S. & X.L.)
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (X.G.); (Z.H.); (J.X.); (X.L.); (J.W.); (H.Y.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (M.Q.S.); (X.L.); Tel./Fax: +86-208-528-0205 (M.Q.S. & X.L.)
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Svačina R, Sourdille P, Kopecký D, Bartoš J. Chromosome Pairing in Polyploid Grasses. FRONTIERS IN PLANT SCIENCE 2020; 11:1056. [PMID: 32733528 PMCID: PMC7363976 DOI: 10.3389/fpls.2020.01056] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Polyploids are species in which three or more sets of chromosomes coexist. Polyploidy frequently occurs in plants and plays a major role in their evolution. Based on their origin, polyploid species can be divided into two groups: autopolyploids and allopolyploids. The autopolyploids arise by multiplication of the chromosome sets from a single species, whereas allopolyploids emerge from the hybridization between distinct species followed or preceded by whole genome duplication, leading to the combination of divergent genomes. Having a polyploid constitution offers some fitness advantages, which could become evolutionarily successful. Nevertheless, polyploid species must develop mechanism(s) that control proper segregation of genetic material during meiosis, and hence, genome stability. Otherwise, the coexistence of more than two copies of the same or similar chromosome sets may lead to multivalent formation during the first meiotic division and subsequent production of aneuploid gametes. In this review, we aim to discuss the pathways leading to the formation of polyploids, the occurrence of polyploidy in the grass family (Poaceae), and mechanisms controlling chromosome associations during meiosis, with special emphasis on wheat.
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Affiliation(s)
- Radim Svačina
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Pierre Sourdille
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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Koide Y, Kuniyoshi D, Kishima Y. Fertile Tetraploids: New Resources for Future Rice Breeding? FRONTIERS IN PLANT SCIENCE 2020; 11:1231. [PMID: 32849760 PMCID: PMC7432136 DOI: 10.3389/fpls.2020.01231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/27/2020] [Indexed: 05/02/2023]
Abstract
Ploidy manipulation is an efficient technique for the development of novel phenotypes in plant breeding. However, in rice (Oryza sativa L.), severe seed sterility has been considered a barrier preventing cultivation of autotetraploids since the 1930s. Recently, a series of studies identified two fertile autotetraploids, identified herein as the PMeS (Polyploid Meiosis Stability) and Neo-Tetraploid lines. Here, we summarize their characteristics, focusing on the recovery of seed fertility, and discuss potential future directions of study in this area, providing a comprehensive understanding of current progress in the study of fertile tetraploid rice, a classical, but promising, concept for rice breeding.
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Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
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Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
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22
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Breeding and study of two new photoperiod- and thermo-sensitive genic male sterile lines of polyploid rice (Oryza sativa L.). Sci Rep 2017; 7:14744. [PMID: 29116179 PMCID: PMC5677125 DOI: 10.1038/s41598-017-15241-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 10/23/2017] [Indexed: 11/22/2022] Open
Abstract
Male sterile lines play an important role in the utilization of heterosis. To explore and exploit the heterosis of polyploid hybrid rice, two photoperiod- and thermo-sensitive genic male sterile lines of polyploid rice, PS006 and PS012, were bred via chromosome doubling, complex hybridization and self-breeding. The characteristics of these two lines, including the agronomic traits, growth, development, fertility transformation and combining ability, were investigated. Both lines had good agronomic characteristics and flowering habits, a high outcrossing rate, obvious fertility alterations and good combining abilities. Their hybrids showed strong heterosis and great potential for increasing rice productivity and quality. The new polyploid rice photoperiod- and thermo-sensitive genic male sterile lines will provide material for further research into polyploidy and hybrid vigour in rice and promote the exploitation of polyploid hybrid rice.
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23
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Tu Y, Jiang A, Gan L, Hossain M, Zhang J, Peng B, Xiong Y, Song Z, Cai D, Xu W, Zhang J, He Y. Genome duplication improves rice root resistance to salt stress. RICE (NEW YORK, N.Y.) 2014; 7:15. [PMID: 25184027 PMCID: PMC4151024 DOI: 10.1186/s12284-014-0015-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/15/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Salinity is a stressful environmental factor that limits the productivity of crop plants, and roots form the major interface between plants and various abiotic stresses. Rice is a salt-sensitive crop and its polyploid shows advantages in terms of stress resistance. The objective of this study was to investigate the effects of genome duplication on rice root resistance to salt stress. RESULTS Both diploid rice (HN2026-2x and Nipponbare-2x) and their corresponding tetraploid rice (HN2026-4x and Nipponbare-4x) were cultured in half-strength Murashige and Skoog medium with 150 mM NaCl for 3 and 5 days. Accumulations of proline, soluble sugar, malondialdehyde (MDA), Na(+) content, H(+) (proton) flux at root tips, and the microstructure and ultrastructure in rice roots were examined. We found that tetraploid rice showed less root growth inhibition, accumulated higher proline content and lower MDA content, and exhibited a higher frequency of normal epidermal cells than diploid rice. In addition, a protective gap appeared between the cortex and pericycle cells in tetraploid rice. Next, ultrastructural analysis showed that genome duplication improved membrane, organelle, and nuclei stability. Furthermore, Na(+) in tetraploid rice roots significantly decreased while root tip H(+) efflux in tetraploid rice significantly increased. CONCLUSIONS Our results suggest that genome duplication improves root resistance to salt stress, and that enhanced proton transport to the root surface may play a role in reducing Na(+) entrance into the roots.
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Affiliation(s)
- Yi Tu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
| | - Aiming Jiang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
- Faculty of Biochemistry and Environmental Engineering, Yunyang Teachers’ College, Shiyan 442000, P.R. China
| | - Lu Gan
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
- Faculty of Biochemistry and Environmental Engineering, Yunyang Teachers’ College, Shiyan 442000, P.R. China
| | - Mokter Hossain
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jinming Zhang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
| | - Bo Peng
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
| | - Yuguo Xiong
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
| | - Zhaojian Song
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
| | - Detian Cai
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
| | - Weifeng Xu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuchi He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, P.R. China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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He Y, Wei Q, Ge J, Jiang A, Gan L, Song Z, Cai D. Genome duplication effects on pollen development and the interrelated physiological substances in tetraploid rice with polyploid meiosis stability. PLANTA 2010; 232:1219-28. [PMID: 20717831 DOI: 10.1007/s00425-010-1249-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/29/2010] [Indexed: 05/07/2023]
Abstract
The breeding of polyploid rice made no breakthrough for a long time because of low seed set. The discovery and application of polyploid meiosis stability (PMeS) material played a pivotal role in solving this problem. Our results indicated that genome duplication led to different outcomes in different rice cultivars in terms of pollen fertility, viability, and the accumulation of important physiological substances such as free proline and endogenous hormones. Pollen from the PMeS HN2026-4X lines showed a high fertility and viability similar to those of HN2026-2X (4X indicates tetraploid while 2X indicates the diploid), whereas both rates decreased dramatically in Balilla-4X. The results of pollen microstructure and ultrastructure investigations suggested that the pollen development pattern in HN2026-4X appeared normal at all stages, but a lot of changes were discovered in Balilla-4X. Stable meiosis, timely tapetum degradation, and normal mitochondria development were critical factors insuring the high frequency pollen fertility of PMeS rice. The free proline content increased markedly in HN2026-4X as compared to HN2026-2X, but it was decreased for Balilla-4X. Genome duplication effects on regulating endogenous hormones accumulation in pollen were evident, resulting in the clear difference between PMeS HN2026-4X and Balilla-4X. The accumulation of IAA, ZR, and GA in mature pollen distinguished HN2026-4X from Balilla-4X, which was linked to normal pollen development. In particular, the excessive accumulation of ABA at the meiosis stage may be correlated to disorganized meiosis in Balilla-4X. All the results provided unequivocal evidence that genome duplication played specific roles in the normal pollen development of PMeS HN2026-4X.
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Affiliation(s)
- Yuchi He
- Faculty of Life Science, Hubei University, Wuhan, People's Republic of China.
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Peng H, Zhang J, Wu X. The ploidy effects in plant gene expression: progress, problems and prospects. ACTA ACUST UNITED AC 2008; 51:295-301. [PMID: 18368306 DOI: 10.1007/s11427-008-0039-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 12/18/2007] [Indexed: 12/26/2022]
Abstract
Polyploidy and haploid are widely employed in the studies of genetics and evolution, and great progress has been made in these fields, inspiring the enthusiasm of scientists to explore the ploidy effects in gene expression. In this paper, we review the gene expression and its regulation in polyploids, especially in autopolyploids. We summarize some limitations in previous reports on polyploidy gene expression and its regulation, especially the limitations in the research materials. We propose an idea to create homologous ploidy series with twin-seedlings and to employ high-throughput techniques to investigate the polyploidy transcriptome and its regulation.
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Affiliation(s)
- Hai Peng
- Laboratory of Germplasm and Genetics, College of Life Science, Jianghan University, Wuhan 430056, China
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