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Chen L, Ma Y, He T, Chen T, Pan Y, Zhou D, Li X, Lu Y, Wu Q, Wang L. Integrated transcriptome and metabolome analysis unveil the response mechanism in wild rice ( Zizania latifolia griseb.) against sheath rot infection. Front Genet 2023; 14:1163464. [PMID: 37359383 PMCID: PMC10289006 DOI: 10.3389/fgene.2023.1163464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Sheath rot disease (SRD) is one of the most devastating diseases of Manchurian wild rice (MWR) (Zizania latifolia Griseb). Pilot experiments in our laboratory have shown that an MWR cultivar "Zhejiao NO.7"exhibits signs of SRD tolerance. To explore the responses of Zhejiao No. 7 to SRD infection, we used a combined transcriptome and metabolome analysis approach. A total of 136 differentially accumulated metabolites (DAMs, 114 up- and 22 down-accumulated in FA compared to CK) were detected. These up-accumulated metabolites were enriched in tryptophan metabolism, amino acid biosynthesis, flavonoids, and phytohormone signaling. Transcriptome sequencing results showed the differential expression of 11,280 genes (DEGs, 5,933 up-, and 5,347 downregulated in FA compared to CK). The genes expressed in tryptophan metabolism, amino acid biosynthesis, phytohormone biosynthesis and signaling, and reactive oxygen species homeostasis confirmed the metabolite results. In addition, genes related to the cell wall, carbohydrate metabolism, and plant-pathogen interaction (especially hypersensitive response) showed changes in expression in response to SRD infection. These results provide a basis for understanding the response mechanisms in MWR to FA attack that can be used for breeding SRD-tolerant MWR.
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Affiliation(s)
- Limin Chen
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yamin Ma
- Agricultural and Rural Bureau of Jinyun County, Jinyun, Zhejiang, China
| | - Tianjun He
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, Zhejiang, China
| | - TingTing Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yiming Pan
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, Zhejiang, China
| | - Dayun Zhou
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, Zhejiang, China
| | - Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Quancong Wu
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, Zhejiang, China
| | - Lailiang Wang
- Lishui Institute of Agriculture and Forestry Sciences, Lishui, Zhejiang, China
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2
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Chen Y, Yang W, Gao R, Chen Y, Zhou Y, Xie J, Zhang F. Genome-Wide Analysis of microRNAs and Their Target Genes in Dongxiang Wild Rice ( Oryza rufipogon Griff.) Responding to Salt Stress. Int J Mol Sci 2023; 24:ijms24044069. [PMID: 36835475 PMCID: PMC9960954 DOI: 10.3390/ijms24044069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Rice (Oryza sativa) is a staple food for more than half of the world's population, and its production is critical for global food security. Moreover, rice yield decreases when exposed to abiotic stresses, such as salinity, which is one of the most detrimental factors for rice production. According to recent trends, as global temperatures continue to rise due to climate change, more rice fields may become saltier. Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is a progenitor of cultivated rice and has a high tolerance to salt stress, making it useful for studying the regulatory mechanisms of salt stress tolerance. However, the regulatory mechanism of miRNA-mediated salt stress response in DXWR remains unclear. In this study, miRNA sequencing was performed to identify miRNAs and their putative target genes in response to salt stress in order to better understand the roles of miRNAs in DXWR salt stress tolerance. A total of 874 known and 476 novel miRNAs were identified, and the expression levels of 164 miRNAs were found to be significantly altered under salt stress. The stem-loop quantitative real-time PCR (qRT-PCR) expression levels of randomly selected miRNAs were largely consistent with the miRNA sequencing results, suggesting that the sequencing results were reliable. The gene ontology (GO) analysis indicated that the predicted target genes of salt-responsive miRNAs were involved in diverse biological pathways of stress tolerance. This study contributes to our understanding of DXWR salt tolerance mechanisms regulated by miRNAs and may ultimately improve salt tolerance in cultivated rice breeding using genetic methods in the future.
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Affiliation(s)
- Yong Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Rifang Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yaling Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (J.X.); (F.Z.)
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3
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Cheng X, Huang Y, Tan Y, Tan L, Yin J, Zou G. Potentially Useful Dwarfing or Semi-dwarfing Genes in Rice Breeding in Addition to the sd1 Gene. RICE (NEW YORK, N.Y.) 2022; 15:66. [PMID: 36542176 PMCID: PMC9772376 DOI: 10.1186/s12284-022-00615-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The "Green revolution" gene sd1 has been used widely in the breeding of modern rice varieties for over half a century. The application of this gene has increased rice yields and thereby supported a significant proportion of the global population. The use of a single gene, however, has raised concerns in the scientific community regarding its durability, especially given the bottleneck in genetic background and the need for large input of fertilizer. New dwarfing or semi-dwarfing genes are needed to alleviate our dependence on the sole "Green revolution" gene. In the past few years, several new dwarfing and semi-dwarfing genes as well as their mutants have been reported. Here, we provide an extensive review of the recent discoveries concerning newly identified genes that are potentially useful in rice breeding, including methods employed to create and effectively screen new rice mutants, the phenotypic characteristics of the new dwarfing and semi-dwarfing mutants, potential values of the new dwarfing and semi-dwarfing genes in rice breeding, and potential molecular mechanisms associated with the newly identified genes.
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Affiliation(s)
- Xiaoyan Cheng
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yi Chun, 336000, Jiangxi, People's Republic of China
| | - Yongping Huang
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China
| | - Yong Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yi Chun, 336000, Jiangxi, People's Republic of China
| | - Lin Tan
- Jiangxi Tiandao Liangan Seed Industry Co., Ltd., 568 South Huancheng Rd., Yuanzhou Dist., Yi Chun, 336000, Jiangxi, People's Republic of China
| | - Jianhua Yin
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China
| | - Guoxing Zou
- National Engineering Research Center of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, People's Republic of China.
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Marsh JI, Petereit J, Bayer PE, Batley J, Edwards D. Expanding Gene-Editing Potential in Crop Improvement with Pangenomes. Int J Mol Sci 2022; 23:ijms23042276. [PMID: 35216392 PMCID: PMC8879065 DOI: 10.3390/ijms23042276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.
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Solis CA, Yong MT, Zhou M, Venkataraman G, Shabala L, Holford P, Shabala S, Chen ZH. Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza. Int J Mol Sci 2022; 23:ijms23042092. [PMID: 35216206 PMCID: PMC8879705 DOI: 10.3390/ijms23042092] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Rice (Oryza sativa), a staple crop for a substantial part of the world’s population, is highly sensitive to soil salinity; however, some wild Oryza relatives can survive in highly saline environments. Sodium/hydrogen antiporter (NHX) family members contribute to Na+ homeostasis in plants and play a major role in conferring salinity tolerance. In this study, we analyzed the evolution of NHX family members using phylogeny, conserved domains, tertiary structures, expression patterns, and physiology of cultivated and wild Oryza species to decipher the role of NHXs in salt tolerance in Oryza. Phylogenetic analysis showed that the NHX family can be classified into three subfamilies directly related to their subcellular localization: endomembrane, plasma membrane, and tonoplast (vacuolar subfamily, vNHX1). Phylogenetic and structural analysis showed that vNHX1s have evolved from streptophyte algae (e.g., Klebsormidium nitens) and are abundant and highly conserved in all major land plant lineages, including Oryza. Moreover, we showed that tissue tolerance is a crucial trait conferring tolerance to salinity in wild rice species. Higher Na+ accumulation and reduced Na+ effluxes in leaf mesophyll were observed in the salt-tolerant wild rice species O. alta, O. latifolia, and O. coarctata. Among the key genes affecting tissue tolerance, expression of NHX1 and SOS1/NHX7 exhibited significant correlation with salt tolerance among the rice species and cultivars. This study provides insights into the evolutionary origin of plant NHXs and their role in tissue tolerance of Oryza species and facilitates the inclusion of this trait during the development of salinity-tolerant rice cultivars.
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Affiliation(s)
- Celymar Angela Solis
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
| | - Miing-Tiem Yong
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600113, India;
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- Correspondence: (S.S.); (Z.-H.C.); Tel.: +61-245-701-934 (Z.-H.C.)
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
- Correspondence: (S.S.); (Z.-H.C.); Tel.: +61-245-701-934 (Z.-H.C.)
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Nagy ED, Stevens JL, Yu N, Hubmeier CS, LaFaver N, Gillespie M, Gardunia B, Cheng Q, Johnson S, Vaughn AL, Vega-Sanchez ME, Deng M, Rymarquis L, Lawrence RJ, Garvey GS, Gaeta RT. Novel disease resistance gene paralogs created by CRISPR/Cas9 in soy. PLANT CELL REPORTS 2021; 40:1047-1058. [PMID: 33704523 PMCID: PMC8184530 DOI: 10.1007/s00299-021-02678-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/24/2021] [Indexed: 05/25/2023]
Abstract
KEY MESSAGE Novel disease resistance gene paralogues are generated by targeted chromosome cleavage of tandem duplicated NBS-LRR gene complexes and subsequent DNA repair in soybean. This study demonstrates accelerated diversification of innate immunity of plants using CRISPR. Nucleotide-binding-site-leucine-rich-repeat (NBS-LRR) gene families are key components of effector-triggered immunity. They are often arranged in tandem duplicated arrays in the genome, a configuration that is conducive to recombinations that will lead to new, chimeric genes. These rearrangements have been recognized as major sources of novel disease resistance phenotypes. Targeted chromosome cleavage by CRISPR/Cas9 can conceivably induce rearrangements and thus emergence of new resistance gene paralogues. Two NBS-LRR families of soy have been selected to demonstrate this concept: a four-copy family in the Rpp1 region (Rpp1L) and a large, complex locus, Rps1 with 22 copies. Copy-number variations suggesting large-scale, CRISPR/Cas9-mediated chromosome rearrangements in the Rpp1L and Rps1 complexes were detected in up to 58.8% of progenies of primary transformants using droplet-digital PCR. Sequencing confirmed development of novel, chimeric paralogs with intact open reading frames. These novel paralogs may confer new disease resistance specificities. This method to diversify innate immunity of plants by genome editing is readily applicable to other disease resistance genes or other repetitive loci.
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Affiliation(s)
- Ervin D Nagy
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA.
| | - Julia L Stevens
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Neil Yu
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Chris S Hubmeier
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Nona LaFaver
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Megan Gillespie
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Brian Gardunia
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Qianshun Cheng
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Steven Johnson
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Audrey L Vaughn
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | | | - Mingqui Deng
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Linda Rymarquis
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Richard J Lawrence
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Graeme S Garvey
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Robert T Gaeta
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
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7
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Feng Y, Yuan X, Wang Y, Yang Y, Zhang M, Yu H, Xu Q, Wang S, Niu X, Wei X. Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross between Oryza sativa and Oryza minuta. RICE (NEW YORK, N.Y.) 2021; 14:43. [PMID: 34014427 PMCID: PMC8137761 DOI: 10.1186/s12284-021-00472-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/10/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Grain size and weight are important target traits determining grain yield and quality in rice. Wild rice species possess substantial elite genes that can be served as an important resource for genetic improvement of rice. In this study, we identify and validate a novel QTL on chromosome 7 affecting the grain size and weight using introgression lines from cross of Oryza sativa and Oryza minuta. RESULTS An introgression line 'IL188' has been achieved from a wild species Oryza minuta (2n = 48, BBCC, W303) into O. sativa japonica Nipponbare. The F2 and F2:3 populations derived from a cross between IL188 and Nipponbare were used to map QTLs for five grain size traits, including grain length (GL), grain width (GW), grain length to width ratio (LWR), grain thickness (GT) and thousand grain weight (TGW). A total of 12 QTLs for the five grain traits were identified on chromosomes 1, 2, 3, 6, 7, and 8. The QTL-qGL7 controlling GL on chromosome 7 was detected stably in the F2 and F2:3 populations, and explained 15.09-16.30% of the phenotypic variance. To validate the effect of qGL7, eight residual heterozygous line (RHL) populations were developed through selfing four F2:3 and four F2:4 plants with different heterozygous segments for the target region. By further developing SSR and Indel markers in the target interval, qGL7 was delimited to a ~ 261 kb region between Indel marker Y7-12 and SSR marker Y7-38, which also showed significant effects on grain width and thousand grain weight. Comparing with the reference genome of Nipponbare, stop or frameshift mutations in the exon of the three putative genes LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. Scanning electron microscopy analysis of the glume's epidermal cells showed that the cell length and width of NIL-qGL7IL188 was higher than NIL-qGL7Nip, indicating that qGL7 increases grain size and weight by regulating cell expansion. CONCLUSIONS In this study, we detected 12 QTLs regulating grain size and weight using an introgression line from a cross between Oryza sativa and Oryza minuta. Of these loci, we confirmed and delimited the qGL7 to a ~ 261 kb region. Three putative genes, LOC_Os07g36830, LOC_Os07g36900 and LOC_Os07g36910 encoding F-box domain-containing proteins may be the candidate genes for qGL7. These results provide a basis for map-based cloning of the qGL7 gene and useful information for marker assisted selection in rice grain quality improvement.
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Affiliation(s)
- Yue Feng
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Xiaoping Yuan
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yiping Wang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yaolong Yang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Mengchen Zhang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hanyong Yu
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qun Xu
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shan Wang
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaojun Niu
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xinghua Wei
- Chinese National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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9
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Mao L, Chen M, Chu Q, Jia L, Sultana MH, Wu D, Kong X, Qiu J, Ye CY, Zhu QH, Chen X, Fan L. RiceRelativesGD: a genomic database of rice relatives for rice research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5574892. [PMID: 31560050 PMCID: PMC6764101 DOI: 10.1093/database/baz110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/25/2019] [Accepted: 08/09/2019] [Indexed: 12/02/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice genomic databases have been constructed, a database providing large-scale curated genomic data from rice relatives and offering specific gene resources is still lacking. Here, we present RiceRelativesGD, a user-friendly genomic database of rice relatives. RiceRelativesGD integrates large-scale genomic resources from 2 cultivated rice and 11 rice relatives, including 208 321 specific genes and 13 643 genes related to photosynthesis and responsive to external stimuli. Diverse bioinformatics tools are embedded in the database, which allow users to search, visualize and download the information of interest. To our knowledge, this is the first genomic database providing a centralized genetic resource of rice relatives. RiceRelativesGD will serve as a significant and comprehensive knowledgebase for the rice community.
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Affiliation(s)
- Lingfeng Mao
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Meihong Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qinjie Chu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lei Jia
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xiangdong Kong
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Xi Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
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10
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Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation. Sci Rep 2018; 8:16346. [PMID: 30397229 PMCID: PMC6218501 DOI: 10.1038/s41598-018-34608-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/15/2018] [Indexed: 12/22/2022] Open
Abstract
Oryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica have similar cold tolerance potentials. The possibility that either distinct or similar genetic mechanisms are involved in the low temperature responses of each species was addressed by comparing their transcriptional networks. General similarities were supported by shared transcriptomic signatures indicative of equivalent metabolic, hormonal, and defense status. However, O. officinalis has maintained an elaborate cold-responsive brassinosteroid-regulated BES1-network that appeared to have been fragmented in O. sativa. BES1-network is potentially important for integrating growth-related responses with physiological adjustments and defenses through the protection of photosynthetic machinery and maintenance of stomatal aperture, oxidative defenses, and osmotic adjustment. Equivalent physiological processes are functional in O. sativa but their genetic mechanisms are under the direct control of ABA-dependent, DREB-dependent and/or oxidative-mediated networks uncoupled to BES1. While O. officinalis and O. sativa represent long periods of speciation and domestication, their comparable cold tolerance potentials involve equivalent physiological processes but distinct genetic networks. BES1-network represents a novel attribute of O. officinalis with potential applications in diversifying or complementing other mechanisms in the cultivated germplasm.
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Sharma R, Draicchio F, Bull H, Herzig P, Maurer A, Pillen K, Thomas WTB, Flavell AJ. Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3811-3822. [PMID: 29767798 PMCID: PMC6054221 DOI: 10.1093/jxb/ery178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/08/2018] [Indexed: 05/05/2023]
Abstract
To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ~70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.
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Affiliation(s)
- Rajiv Sharma
- University of Dundee at JHI, Invergowrie, Dundee, UK
| | | | - Hazel Bull
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Paul Herzig
- Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Andreas Maurer
- Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Klaus Pillen
- Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
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Haritha G, Malathi S, Divya B, Swamy BPM, Mangrauthia SK, Sarla N. Oryza nivara Sharma et Shastry. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-71997-9_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Bisoi SS, Mishra SS, Barik J, Panda D. Effects of different treatments of fly ash and mining soil on growth and antioxidant protection of Indian wild rice. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:446-452. [PMID: 27739878 DOI: 10.1080/15226514.2016.1244164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The aim of the present study was investigation of the effects of fly ash and mining soil on growth and antioxidant protection of two cultivars of Indian wild rice (Oryza nivara and Oryza rufipogon) for possible phytoremediation and restoration of metal-contaminated site. In this study, Indian wild rice showed significant changes in germination, growth, and biochemical parameters after exposure to different ratio of fly ash and mining soil with garden soil. There was significant reduction of germination, fresh weight, dry weight, leaf chlorophyll content, leaf area, Special Analysis Device Chlorophyll (SPAD) Index, proteins, and activities of antioxidant enzymes in both cultivars of the wild rice grown in 100% fly ash and mining soil compared to the plants grown in 100% garden soil. Results from this study showed that in both cultivars of wild rice, all growth and antioxidant parameters increased when grown in 50% fly ash and mining soil. Taken together, Indian wild rice has the capacity to tolerate 50% of fly ash and mining soil, and can be considered as a good candidate for possible phytoremediation of contaminated soils.
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Affiliation(s)
- Sidhanta Sekhar Bisoi
- a Department of Biodiversity and Conservation of Natural Resources , Central University of Orissa , Koraput , Odisha , India
| | - Swati S Mishra
- a Department of Biodiversity and Conservation of Natural Resources , Central University of Orissa , Koraput , Odisha , India
| | - Jijnasa Barik
- a Department of Biodiversity and Conservation of Natural Resources , Central University of Orissa , Koraput , Odisha , India
| | - Debabrata Panda
- a Department of Biodiversity and Conservation of Natural Resources , Central University of Orissa , Koraput , Odisha , India
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Menguer PK, Sperotto RA, Ricachenevsky FK. A walk on the wild side: Oryza species as source for rice abiotic stress tolerance. Genet Mol Biol 2017; 40:238-252. [PMID: 28323300 PMCID: PMC5452139 DOI: 10.1590/1678-4685-gmb-2016-0093] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated. Rice domestication was performed with a narrow genetic diversity, and the other Oryza species are a virtually untapped genetic resource for rice stress tolerance improvement. Here we review the origin of domesticated Oryza sativa from wild progenitors, the ecological and genomic diversity of the Oryza genus, and the stress tolerance variation observed for wild Oryza species, including the genetic basis underlying the tolerance mechanisms found. The summary provided here is important to indicate how we should move forward to unlock the full potential of these germplasms for rice improvement.
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Affiliation(s)
- Paloma Koprovski Menguer
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Raul Antonio Sperotto
- Setor de Genética e Biologia Molecular do Museu de Ciências Naturais (MCN), Centro de Ciências Biológicas e da Saúde (CCBS), Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil
| | - Felipe Klein Ricachenevsky
- Programa de Pós-Graduação em Agrobiologia, Departamento de Biologia, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
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Mbuvi DA, Masiga CW, Kuria E, Masanga J, Wamalwa M, Mohamed A, Odeny DA, Hamza N, Timko MP, Runo S. Novel Sources of Witchweed ( Striga) Resistance from Wild Sorghum Accessions. FRONTIERS IN PLANT SCIENCE 2017; 8:116. [PMID: 28220136 PMCID: PMC5292437 DOI: 10.3389/fpls.2017.00116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/19/2017] [Indexed: 05/04/2023]
Abstract
Sorghum is a major food staple in sub-Saharan Africa (SSA), but its production is constrained by the parasitic plant Striga that attaches to the roots of many cereals crops and causes severe stunting and loss of yield. Away from cultivated farmland, wild sorghum accessions grow as weedy plants and have shown remarkable immunity to Striga. We sought to determine the extent of the resistance to Striga in wild sorghum plants. Our screening strategy involved controlled laboratory assays of rhizotrons, where we artificially infected sorghum with Striga, as well as field experiments at three sites, where we grew sorghum with a natural Striga infestation. We tested the resistance response of seven accessions of wild sorghum of the aethiopicum, drummondii, and arundinaceum races against N13, which is a cultivated Striga resistant landrace. The susceptible control was farmer-preferred variety, Ochuti. From the laboratory experiments, we found three wild sorghum accessions (WSA-1, WSE-1, and WSA-2) that had significantly higher resistance than N13. These accessions had the lowest Striga biomass and the fewest and smallest Striga attached to them. Further microscopic and histological analysis of attached Striga haustorium showed that wild sorghum accessions hindered the ingression of Striga haustorium into the host endodermis. In one of the resistant accessions (WSE-1), host and parasite interaction led to the accumulation of large amounts of secondary metabolites that formed a dark coloration at the interphase. Field experiments confirmed the laboratory screening experiments in that these same accessions were found to have resistance against Striga. In the field, wild sorghum had low Area under the Striga Number Progressive curve (AUSNPC), which measures emergence of Striga from a host over time. We concluded that wild sorghum accessions are an important reservoir for Striga resistance that could be used to expand the genetic basis of cultivated sorghum for resistance to the parasite.
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Affiliation(s)
- Dorothy A. Mbuvi
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | - Clet W. Masiga
- Tropical Institute of Development InnovationsKampala, Uganda
- Sudan Academy of SciencesKhartoum, Sudan
| | - Eric Kuria
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | - Joel Masanga
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | - Mark Wamalwa
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
| | | | - Damaris A. Odeny
- International Crops Research Institute for the Semi-Arid TropicsNairobi, Kenya
| | - Nada Hamza
- Sudan Academy of SciencesKhartoum, Sudan
- Commission for Biotechnology and Genetic Engineering, National Centre for ResearchKhartoum, Sudan
| | - Michael P. Timko
- Department of Biology, University of VirginiaCharlottesville, VA, USA
| | - Steven Runo
- Department of Biochemistry and Biotechnology, Kenyatta UniversityNairobi, Kenya
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Huang J, Gao Y, Jia H, Zhang Z. Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication. Mol Ecol Resour 2016; 16:1465-1477. [DOI: 10.1111/1755-0998.12526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Huang
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Youjun Gao
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Haitao Jia
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
- College of Life Science; Huanggang Normal University; Huanggang 438000 China
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Zhang F, Luo X, Zhou Y, Xie J. Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.). Biotechnol Lett 2015; 38:711-21. [PMID: 26667133 DOI: 10.1007/s10529-015-2012-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/02/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress. RESULTS 505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants. CONCLUSION These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.
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Affiliation(s)
- Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiangdong Luo
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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Dolferus R. To grow or not to grow: a stressful decision for plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:247-261. [PMID: 25443851 DOI: 10.1016/j.plantsci.2014.10.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Progress in improving abiotic stress tolerance of crop plants using classic breeding and selection approaches has been slow. This has generally been blamed on the lack of reliable traits and phenotyping methods for stress tolerance. In crops, abiotic stress tolerance is most often measured in terms of yield-capacity under adverse weather conditions. "Yield" is a complex trait and is determined by growth and developmental processes which are controlled by environmental signals throughout the life cycle of the plant. The use of model systems has allowed us to gradually unravel how plants grow and develop, but our understanding of the flexibility and opportunistic nature of plant development and its capacity to adapt growth to environmental cues is still evolving. There is genetic variability for the capacity to maintain yield and productivity under abiotic stress conditions in crop plants such as cereals. Technological progress in various domains has made it increasingly possible to mine that genetic variability and develop a better understanding about the basic mechanism of plant growth and abiotic stress tolerance. The aim of this paper is not to give a detailed account of all current research progress, but instead to highlight some of the current research trends that may ultimately lead to strategies for stress-proofing crop species. The focus will be on abiotic stresses that are most often associated with climate change (drought, heat and cold) and those crops that are most important for human nutrition, the cereals.
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Affiliation(s)
- Rudy Dolferus
- CSIRO, Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia.
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Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci U S A 2014; 111:E4954-62. [PMID: 25368197 DOI: 10.1073/pnas.1418307111] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
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Sakai H, Kanamori H, Arai-Kichise Y, Shibata-Hatta M, Ebana K, Oono Y, Kurita K, Fujisawa H, Katagiri S, Mukai Y, Hamada M, Itoh T, Matsumoto T, Katayose Y, Wakasa K, Yano M, Wu J. Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res 2014; 21:397-405. [PMID: 24578372 PMCID: PMC4131834 DOI: 10.1093/dnares/dsu006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.
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Affiliation(s)
- Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroyuki Kanamori
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yuko Arai-Kichise
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Mari Shibata-Hatta
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Kaworu Ebana
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Youko Oono
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kanako Kurita
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroko Fujisawa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Satoshi Katagiri
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yoshiyuki Mukai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masao Hamada
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yuichi Katayose
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kyo Wakasa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. ACTA ACUST UNITED AC 2013; 6:4. [PMID: 24280374 PMCID: PMC5395016 DOI: 10.1186/1939-8433-6-4] [Citation(s) in RCA: 1275] [Impact Index Per Article: 115.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/30/2013] [Indexed: 02/07/2023]
Abstract
Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Electronic supplementary material The online version of this article (doi:10.1186/1939-8433-6-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. RICE (NEW YORK, N.Y.) 2013; 6:4. [PMID: 24280374 PMCID: PMC5395016 DOI: 10.1186/1939-8433-6-4#citeas] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/30/2013] [Indexed: 06/19/2023]
Abstract
BACKGROUND Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). RESULTS The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. CONCLUSIONS A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
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Affiliation(s)
- Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | | | - John P Hamilton
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
| | - Hiroyuki Kanamori
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | | | - Shu Ouyang
- Perkin Elmer, Room 4096, 8490 Progress Drive, Frederick, MD 21701 USA
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706 USA
| | - Tsuyoshi Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI 53706 USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
| | - Rebecca M Davidson
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
- Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, CO USA
| | - Haining Lin
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
- Dupont Pioneer, 7200 NW 62nd Ave, Johnston, IA 50131 USA
| | - Lina Quesada-Ocampo
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
| | - Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Sung Shin Lee
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Jungsok Kim
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hisataka Numa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI 48824 USA
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
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23
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Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. RICE (NEW YORK, N.Y.) 2013. [PMID: 24280374 DOI: 10.1186/1939-8433-1186-1184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). RESULTS The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. CONCLUSIONS A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.
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Affiliation(s)
- Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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24
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Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PLANT & CELL PHYSIOLOGY 2013; 54:e6. [PMID: 23299411 PMCID: PMC3583025 DOI: 10.1093/pcp/pcs183] [Citation(s) in RCA: 446] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.
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Affiliation(s)
- Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Sung Shin Lee
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Tsuyoshi Tanaka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hisataka Numa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Jungsok Kim
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hironobu Wakimoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
- Application Solution Department, Hitachi Government & Public Corporation System Engineering, Ltd., Koto-ku, Tokyo, 135-8633 Japan
| | - Ching-chia Yang
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
- Present address: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564 Japan
| | - Masao Iwamoto
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takashi Abe
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
- Graduate School of Science and Technology, Niigata University, Niigata, 950-2181 Japan
| | - Yuko Yamada
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
| | - Akira Muto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, 036-8561 Japan
| | - Hachiro Inokuchi
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
| | - Toshimichi Ikemura
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829 Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takuji Sasaki
- Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502 Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan
- *Corresponding author: E-mail, ; Fax, +81-29-838-7065
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25
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Xu F, Park MR, Kitazumi A, Herath V, Mohanty B, Yun SJ, de los Reyes BG. Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. BMC Genomics 2012; 13:497. [PMID: 22992304 PMCID: PMC3522565 DOI: 10.1186/1471-2164-13-497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 09/14/2012] [Indexed: 01/10/2023] Open
Abstract
Background The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. Results The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. Conclusions Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.
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Affiliation(s)
- Fuyu Xu
- School of Biology and Ecology, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA
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26
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Yang CC, Kawahara Y, Mizuno H, Wu J, Matsumoto T, Itoh T. Independent domestication of Asian rice followed by gene flow from japonica to indica. Mol Biol Evol 2011; 29:1471-9. [PMID: 22319137 DOI: 10.1093/molbev/msr315] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.
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Affiliation(s)
- Ching-chia Yang
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
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27
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Genetic Analysis on Characteristics to Measure Drought Resistance Using Dongxiang Wild Rice (Oryza rufupogon Griff.) and Its Derived Backcross Inbred Lines Population at Seedling Stage. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1671-2927(11)60164-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Collier SM, Hamel LP, Moffett P. Cell death mediated by the N-terminal domains of a unique and highly conserved class of NB-LRR protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:918-31. [PMID: 21501087 DOI: 10.1094/mpmi-03-11-0050] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Plant genomes encode large numbers of nucleotide-binding, leucine-rich repeat (NB-LRR) proteins, many of which are active in pathogen detection and defense response induction. NB-LRR proteins fall into two broad classes: those with a Toll and interleukin-1 receptor (TIR) domain at their N-terminus and those with a coiled-coil (CC) domain at the N-terminus. Within CC-NB-LRR-encoding genes, one basal clade is distinguished by having CC domains resembling the Arabidopsis thaliana RPW8 protein, which we refer to as CCR domains. Here, we show that CCR-NB-LRR-encoding genes are present in the genomes of all higher plants surveyed, and that they comprise two distinct subgroups: one typified by the Nicotiana benthamiana N-required gene 1 (NRG1) protein and the other typified by the Arabidopsis activated disease resistance gene 1 (ADR1) protein. We further report that, in contrast to CC-NB-LRR proteins, the CCR domains of both NRG1- and ADR1-like proteins are sufficient for the induction of defense responses, and that this activity appears to be SGT1-independent. Additionally, we report the apparent absence of both NRG1 homologs and TIR-NB-LRR-encoding genes from the dicot Aquilegia coerulea and the dicotyledonous order Lamiales as well as from monocotyledonous species. This strong correlation in occurrence is suggestive of a functional relationship between these two classes of NB-LRR proteins.
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Affiliation(s)
- Sarah M Collier
- Boyce Thompson Institute for Plant Research, Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA
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29
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Sakai H, Ikawa H, Tanaka T, Numa H, Minami H, Fujisawa M, Shibata M, Kurita K, Kikuta A, Hamada M, Kanamori H, Namiki N, Wu J, Itoh T, Matsumoto T, Sasaki T. Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:796-805. [PMID: 21323774 PMCID: PMC3568898 DOI: 10.1111/j.1365-313x.2011.04539.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 02/09/2011] [Indexed: 05/29/2023]
Abstract
Here we present the genomic sequence of the African cultivated rice, Oryza glaberrima, and compare these data with the genome sequence of Asian cultivated rice, Oryza sativa. We obtained gene-enriched sequences of O. glaberrima that correspond to about 25% of the gene regions of the O. sativa (japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. While patterns of amino acid changes did not differ between the two species in terms of the biochemical properties, genes of O. glaberrima generally showed a larger synonymous-nonsynonymous substitution ratio, suggesting that O. glaberrima has undergone a genome-wide relaxation of purifying selection. We further investigated nucleotide substitutions around splice sites and found that eight genes of O. sativa experienced changes at splice sites after the divergence from O. glaberrima. These changes produced novel introns that partially truncated functional domains, suggesting that these newly emerged introns affect gene function. We also identified 2451 simple sequence repeats (SSRs) from the genomes of O. glaberrima and O. sativa. Although tri-nucleotide repeats were most common among the SSRs and were overrepresented in the protein-coding sequences, we found that selection against indels of tri-nucleotide repeats was relatively weak in both African and Asian rice. Our genome-wide sequencing of O. glaberrima and in-depth analyses provide rice researchers not only with useful genomic resources for future breeding but also with new insights into the genomic evolution of the African and Asian rice species.
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Affiliation(s)
- Hiroaki Sakai
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Ikawa
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
- Tsukuba Division, Mitsubishi Space Software Co., Ltd.Tsukuba, Ibaraki 305-0032, Japan
| | - Tsuyoshi Tanaka
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Hisataka Numa
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Minami
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
- Tsukuba Division, Mitsubishi Space Software Co., Ltd.Tsukuba, Ibaraki 305-0032, Japan
| | - Masaki Fujisawa
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Michie Shibata
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
| | - Kanako Kurita
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
| | - Ari Kikuta
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
| | - Masao Hamada
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
| | - Hiroyuki Kanamori
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
| | - Nobukazu Namiki
- Research Division I, Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki 305-0854, Japan
- Tsukuba Division, Mitsubishi Space Software Co., Ltd.Tsukuba, Ibaraki 305-0032, Japan
| | - Jianzhong Wu
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Itoh
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Takashi Matsumoto
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
| | - Takuji Sasaki
- Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki 305-8602, Japan
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30
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Yang CC, Sakai H, Numa H, Itoh T. Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison. Gene 2011; 477:53-60. [PMID: 21277362 DOI: 10.1016/j.gene.2011.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 12/21/2022]
Abstract
Although a large number of genes are expected to correctly solve a phylogenetic relationship, inconsistent gene tree topologies have been observed. This conflicting evidence in gene tree topologies, known as gene tree discordance, becomes increasingly important as advanced sequencing technologies produce an enormous amount of sequence information for phylogenomic studies among closely related species. Here, we aim to characterize the gene tree discordance of the Asian cultivated rice Oryza sativa and its progenitor, O. rufipogon, which will be an ideal case study of gene tree discordance. Using genome and cDNA sequences of O. sativa and O. rufipogon, we have conducted the first in-depth analyses of gene tree discordance in Asian rice. Our comparison of full-length cDNA sequences of O. rufipogon with the genome sequences of the japonica and indica cultivars of O. sativa revealed that 60% of the gene trees showed a topology consistent with the expected one, whereas the remaining genes supported significantly different topologies. Moreover, the proportions of the topologies deviated significantly from expectation, suggesting at least one hybridization event between the two subgroups of O. sativa, japonica and indica. In fact, a genome-wide alignment between japonica and indica indicated that significant portions of the indica genome are derived from japonica. In addition, literature concerning the pedigree of the indica cultivar strongly supported the hybridization hypothesis. Our molecular evolutionary analyses deciphered complicated evolutionary processes in closely related species. They also demonstrated the importance of gene tree discordance in the era of high-speed DNA sequencing.
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Affiliation(s)
- Ching-chia Yang
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan.
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31
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Zhang M, Wu YH, Lee MK, Liu YH, Rong Y, Santos TS, Wu C, Xie F, Nelson RL, Zhang HB. Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors. Nucleic Acids Res 2010; 38:6513-25. [PMID: 20542917 PMCID: PMC2965241 DOI: 10.1093/nar/gkq524] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their ‘surplus’ genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms’ phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism’s morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.
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Affiliation(s)
- Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
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