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Gowda RSR, Sharma S, Gill RS, Mangat GS, Bhatia D. Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions. FRONTIERS IN PLANT SCIENCE 2023; 14:1174266. [PMID: 37324704 PMCID: PMC10266271 DOI: 10.3389/fpls.2023.1174266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023]
Abstract
Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%-54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.
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Affiliation(s)
- Rakshith S. R. Gowda
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Ludhiana, India
| | - Ranvir Singh Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Gurjit Singh Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
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Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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Li S, Zou J, Fan J, Guo D, Tan L. Identification of quantitative trait loci for important agronomic traits using chromosome segment substitution lines from a japonica × indica cross in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:73. [PMID: 37313327 PMCID: PMC10248660 DOI: 10.1007/s11032-022-01343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 06/15/2023]
Abstract
Asian cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica, which display clear differences in yield-related traits and environmental adaptation. Here, we developed a set of chromosome segment substitution lines (CSSLs) from an advanced backcross between japonica variety C418, as the recipient, and indica variety IR24, as the donor. Through evaluating the genotypes and phenotypes of 181 CSSLs, a total of 85 quantitative trait loci (QTLs) for 14 yield-related traits were detected, with individual QTLs explaining from 6.2 to 42.9% of the phenotypic variation. Moreover, twenty-six of these QTLs could be detected in the two trial sites (Beijing and Hainan). Among these loci, the QTLs for flag leaf width and effective tiller number, qFLW4.2 and qETN4.2, were delimited to an approximately 256-kb interval on chromosome 4. Through a comparison of nucleotide sequences and expression levels in "C418" and the CSSL CR31 containing qFLW4.2 and qETN4.2, we found that the NAL1 (LOC_Os04g52479) gene was the candidate gene for qFLW4.2 and qETN4.2. Our results show that CSSLs are powerful tools for identifying and fine-mapping QTLs, while the novel QTLs identified in this study will also provide new genetic resources for rice improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01343-3.
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Affiliation(s)
- Shuangzhe Li
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Jun Zou
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Jinjian Fan
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Daokuan Guo
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Lubin Tan
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
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Mun BG, Shahid M, Lee GS, Hussain A, Yun BW. A Novel RHS1 Locus in Rice Attributes Seed-Pod Shattering by the Regulation of Endogenous S-Nitrosothiols. Int J Mol Sci 2022; 23:13225. [PMID: 36362013 PMCID: PMC9655508 DOI: 10.3390/ijms232113225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 01/12/2024] Open
Abstract
Seed or pod shattering in rice (Oryza sativa) is considered to be one of the major factors involved in the domestication of rice as a crop. High seed shattering results in significant yield losses. In this study, we characterize the RICEHIGHSHATTERING 1 (RHS1) that corresponds to the locus LOC_Os04g41250 from a greenhouse screen, involving 145 Ac/Ds transposon mutant rice lines. The knockout mutant line rhs1 exhibited a significantly high shattering of grains in comparison to the wild-type plants. The exogenous application of nitric oxide (NO) resulted in a significant reduction in the expression of RHS1 in wild-type rice plants. The absence of RHS1, which encodes a putative armadillo/beta-catenin repeat family protein, resulted in high sensitivity of the rhs1 plants to nitrosative stress. Interestingly, the basal expression levels of QSH1 and SHAT1 genes (transcription factors that regulate seed-pod shattering in rice) were significantly lower in these plants than in wild-type plants; however, nitrosative stress negatively regulated the expression of QSH1 and SHAT1 in both WT and rhs1 plants, but positively regulated QSH4 expression in rhs1 plants alone. The expression levels of genes responsible for NO production (OsNIA1, OsNIA2, and OsNOA1) were lower in rhs1 plants than in WT plants under normal conditions. However, under nitrosative stress, the expression of OsNIA2 significantly increased in rhs1 plants. The expression of CPL1 (a negative regulator of seed shattering in rice) was significantly lower in rhs1 plants, and we found that CPL1 expression was correlated with S-nitrosothiol (SNO) alteration in rhs1. Interestingly noe1, a rice mutant with high SNO levels, exhibited low seed shattering, whereas rhs1 resulted in low SNO levels with high seed shattering. Therefore, RHS1 is a novel gene that negatively regulates the shattering trait in rice via regulation of endogenous SNO levels. However, the molecular mechanisms involved in the control of RHS1-mediated regulation of seed shattering and its interaction with nitric oxide and involvement in plant defense need to be investigated further.
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Affiliation(s)
- Bong-Gyu Mun
- School of Applied Bioscience, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea
| | - Muhammad Shahid
- School of Applied Bioscience, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea
- Agriculture Research Institute, Khyber Pakhtunkhwa, Mingora 19130, Pakistan
| | - Gang Sub Lee
- Biosafety Division, National Institute of Agricultural Science, Jeonju, 54875, Korea
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Byung-Wook Yun
- School of Applied Bioscience, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea
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Malik P, Huang M, Neelam K, Bhatia D, Kaur R, Yadav B, Singh J, Sneller C, Singh K. Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions. RICE (NEW YORK, N.Y.) 2022; 15:37. [PMID: 35819660 PMCID: PMC9276952 DOI: 10.1186/s12284-022-00582-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder's pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.
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Affiliation(s)
- Palvi Malik
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Mao Huang
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ramanjeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Bharat Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- Crop Pathology and Genetics Lab, University of British Columbia, Vancouver, Canada
| | - Jasdeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Clay Sneller
- Department of Horticulture and Crop Science, OARDC, The Ohio State University, Wooster, USA
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
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Eizenga GC, Kim H, Jung JKH, Greenberg AJ, Edwards JD, Naredo MEB, Banaticla-Hilario MCN, Harrington SE, Shi Y, Kimball JA, Harper LA, McNally KL, McCouch SR. Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex ( ORSC). FRONTIERS IN PLANT SCIENCE 2022; 13:787703. [PMID: 35769295 PMCID: PMC9235872 DOI: 10.3389/fpls.2022.787703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as characterization data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions characterized as annual and largely inbreeding. From these groups, 42 "core" O. rufipogon and 25 "core" O. nivara accessions were identified for domestication studies. The third group, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a "pre-breeding" pool for breeders attempting to incorporate novel variation into elite breeding lines.
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Affiliation(s)
- Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Janelle K. H. Jung
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | | | | | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Jennifer A. Kimball
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Lisa A. Harper
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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Novel QTL Associated with Aerenchyma-Mediated Radial Oxygen Loss (ROL) in Rice (Oryza sativa L.) under Iron (II) Sulfide. PLANTS 2022; 11:plants11060788. [PMID: 35336670 PMCID: PMC8948734 DOI: 10.3390/plants11060788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 01/04/2023]
Abstract
In rice, high radial oxygen loss (ROL) has been associated with the reduction in the activity of methanogens, therefore reducing the formation of methane (CH4) due to the abundance in application of nitrogen (N)-rich fertilizers. In this study, we evaluated the root growth behavior and ROL rate of a doubled haploid (DH) population (n = 117) and parental lines 93-11 (P1, indica) and Milyang352 (P2, japonica) in response to iron (II) sulfide (FeS). In addition, we performed a linkage mapping and quantitative trait locus (QTL) analysis on the same population for the target traits. The results of the phenotypic evaluation revealed that parental lines had distinctive root growth and ROL patterns, with 93-11 (indica) and Milyang352 (japonica) showing low and high ROL rates, respectively. This was also reflected in their derived population, indicating that 93.2% of the DH lines exhibited a high ROL rate and about 6.8% had a low ROL pattern. Furthermore, the QTL and linkage map analysis detected two QTLs associated with the control of ROL and root area on chromosomes 2 (qROL-2-1, 127 cM, logarithm of the odds (LOD) 3.04, phenotypic variation explained (PVE) 11.61%) and 8 (qRA-8-1, 97 cM, LOD 4.394, PVE 15.95%), respectively. The positive additive effect (2.532) of qROL-2-1 indicates that the allele from 93-11 contributed to the observed phenotypic variation for ROL. The breakthrough is that the qROL-2-1 harbors genes proposed to be involved in stress signaling, defense response mechanisms, and transcriptional regulation, among others. The qPCR results revealed that the majority of genes harbored by the qROL-2-1 recorded a higher transcript accumulation level in Milyang352 over time compared to 93-11. Another set of genes exhibited a high transcript abundance in P1 compared to P2, while a few were differentially regulated between both parents. Therefore, OsTCP7 and OsMYB21, OsARF8 genes encoding transcription factors (TFs), coupled with OsTRX, OsWBC8, and OsLRR2 are suggested to play important roles in the positive regulation of ROL in rice. However, the recorded differential expression of OsDEF7 and OsEXPA, and the decrease in OsNIP2, Oscb5, and OsPLIM2a TF expression between parental lines proposes them as being involved in the control of oxygen flux level in rice roots.
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Lu Y, Xu Y, Li N. Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies. RICE (NEW YORK, N.Y.) 2022; 15:11. [PMID: 35166949 PMCID: PMC8847465 DOI: 10.1186/s12284-022-00556-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/22/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. RESULTS Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5' regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. CONCLUSIONS Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5' regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.
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Affiliation(s)
- Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Present Address: College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016 China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Ahmadi N, Ramanantsoanirina A, Santos JD, Frouin J, Radanielina T. Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar. RICE (NEW YORK, N.Y.) 2021; 14:44. [PMID: 34014423 PMCID: PMC8137759 DOI: 10.1186/s12284-021-00479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Understanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10-25% reduction of diversity among the Malagasy representatives of indica and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and "Bulu" type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the high plateaux and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands. We proposed the name Rojo for this new rice group.
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Affiliation(s)
- Nourollah Ahmadi
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | | | - João D Santos
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Julien Frouin
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Tendro Radanielina
- Université de Antananarivo, département de biologie et écologie végétale, Antananarivo, Madagascar
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Li J, Zhou J, Zhang Y, Yang Y, Pu Q, Tao D. New Insights Into the Nature of Interspecific Hybrid Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:555572. [PMID: 33072142 PMCID: PMC7538986 DOI: 10.3389/fpls.2020.555572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/01/2020] [Indexed: 06/01/2023]
Abstract
Interspecific and intraspecific hybrid sterility is a typical and common phenomenon of postzygotic reproductive barrier in rice. This is an indicator of speciation involved in the formation of new species or subspecies, and it significantly hampers the utilization of favorable genes from distant parents for rice improvement. The Oryza genus includes eight species with the same AA genome and is a model plant for studying the nature of hybrid sterility and its relationship with speciation. Hybrid sterility in rice is mostly controlled by nuclear genes, with more than 50 sterility loci genetically identified to date, of which 10 hybrid sterility loci or pairs were cloned and characterized at the molecular level. Comparing the mapping results for all sterility loci reported indicated that some of these loci from different species should be allelic to each other. Further research revealed that interactions between the multiple alleles at the hybrid sterility locus caused various genetic effect. One hypothesis for this important phenomenon is that the hybrid sterility loci are orthologous loci, which existed in ancient ancestors of rice. When one or more ancestors drifted to different continents, genetic divergence occurred because of adaptation, selection, and isolation among them such that various alleles from orthologous loci emerged over evolutionary time; hence, interspecific hybrid sterility would be mainly controlled by a few orthologous loci with different alleles. This hypothesis was tested and supported by the molecular characterization of hybrid sterility loci from S1, S5, Sa, qHMS7, and S27. From this, we may further deduce that both allelic and non-allelic interactions among different loci are the major genetic basis for the interspecific hybrid sterility between O. sativa and its AA genome relatives, and the same is true for intraspecific hybrid sterility in O. sativa. Therefore, it is necessary to raise the near-isogenic lines with various alleles/haplotypes and pyramided different alleles/haplotypes from sterile loci in the same genetic background aiming to study allelic and non-allelic interaction among different hybrid sterility loci in the AA genome species. Furthermore, the pyramiding lines ought to be used as bridge parents to overcome hybrid sterility for rice breeding purposes.
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11
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Guo N, Hu J, Yan M, Qu H, Luo L, Tegeder M, Xu G. Oryza sativa Lysine-Histidine-type Transporter 1 functions in root uptake and root-to-shoot allocation of amino acids in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:395-411. [PMID: 32159895 DOI: 10.1111/tpj.14742] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 02/02/2020] [Accepted: 02/11/2020] [Indexed: 05/03/2023]
Abstract
In agricultural soils, amino acids can represent vital nitrogen (N) sources for crop growth and yield. However, the molecular mechanisms underlying amino acid uptake and allocation are poorly understood in crop plants. This study shows that rice (Oryza sativa L.) roots can acquire aspartate at soil concentration, and that japonica subspecies take up this acidic amino acid 1.5-fold more efficiently than indica subspecies. Genetic association analyses with 68 representative japonica or indica germplasms identified rice Lysine-Histidine-type Transporter 1 (OsLHT1) as a candidate gene associated with the aspartate uptake trait. When expressed in yeast, OsLHT1 supported cell growth on a broad spectrum of amino acids, and effectively transported aspartate, asparagine and glutamate. OsLHT1 is localized throughout the rice root, including root hairs, epidermis, cortex and stele, and to the leaf vasculature. Knockout of OsLHT1 in japonica resulted in reduced root uptake of amino acids. Furthermore, in 15 N-amino acid-fed mutants versus wild-type, a higher percentage of 15 N remained in roots instead of being allocated to the shoot. 15 N-ammonium uptake and subsequently the delivery of root-synthesized amino acids to Oslht1 shoots were also significantly decreased, which was accompanied by reduced shoot growth. These results together provide evidence that OsLHT1 functions in both root uptake and root to shoot allocation of a broad spectrum of amino acids in rice.
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Affiliation(s)
- Nan Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jinqi Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Hongye Qu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Le Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mechthild Tegeder
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
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12
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Li W, Zhang Q, Zhu T, Tong Y, Li K, Shi C, Zhang Y, Liu Y, Jiang J, Liu Y, Xia E, Huang H, Zhang L, Zhang D, Shi C, Jiang W, Zhao Y, Mao S, Jiao J, Xu P, Yang L, Gao L. Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating-system evolution. PLANT DIRECT 2020; 4:e00232. [PMID: 32537559 PMCID: PMC7287411 DOI: 10.1002/pld3.232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 05/04/2023]
Abstract
Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.
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Affiliation(s)
- Wei Li
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Qun‐Jie Zhang
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Ting Zhu
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- College of Life ScienceLiaoning Normal UniversityDalianChina
| | - Yan Tong
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Kui Li
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Cong Shi
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yun Zhang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Yun‐Long Liu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Jian‐Jun Jiang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Yuan Liu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - En‐Hua Xia
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Hui Huang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Ping Zhang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Dan Zhang
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Chao Shi
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Wen‐Kai Jiang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - You‐Jie Zhao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Shu‐Yan Mao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Jun‐ying Jiao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Ping‐Zhen Xu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Li Yang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Zhi Gao
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
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13
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Nan H, Li W, Lin YL, Gao LZ. Genome-Wide Analysis of WRKY Genes and Their Response to Salt Stress in the Wild Progenitor of Asian Cultivated Rice, Oryza rufipogon. Front Genet 2020. [DOI: 10.3389/fgene.2020.00359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Li W, Li K, Huang Y, Shi C, Hu WS, Zhang Y, Zhang QJ, Xia EH, Hutang GR, Zhu XG, Liu YL, Liu Y, Tong Y, Zhu T, Huang H, Dan Zhang, Zhao Y, Jiang WK, Yuan J, Niu YC, Gao CW, Gao LZ. SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation. Commun Biol 2020; 3:167. [PMID: 32265482 PMCID: PMC7138787 DOI: 10.1038/s42003-020-0890-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 03/13/2020] [Indexed: 01/22/2023] Open
Abstract
Asian cultivated rice is believed to have been domesticated from a wild progenitor, Oryza rufipogon, offering promising sources of alleles for world rice improvement. Here we first present a high-quality chromosome-scale genome of the typical O. rufipogon. Comparative genomic analyses of O. sativa and its two wild progenitors, O. nivara and O. rufipogon, identified many dispensable genes functionally enriched in the reproductive process. We detected millions of genomic variants, of which large-effect mutations could affect agronomically relevant traits. We demonstrate how lineage-specific expansion of gene families may have contributed to the formation of reproduction isolation. We document thousands of genes with signatures of positive selection that are mainly involved in the reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as forces to govern substantial genomic alterations that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. Li et al. provide a chromosome-based genome of the ancestral rice relative Oryza rufipogon using SMRT, 10x and Hi-C. Using comparative genomics analysis, they identify genes important for agronomical traits and provide insights for the evolution of reproductive systems which can facilitate rice breeding programs.
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Affiliation(s)
- Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642, Guangzhou, China
| | - Kui Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | | | - Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China.,University of the Chinese Academy of Sciences, 100039, Beijing, China
| | | | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Qun-Jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642, Guangzhou, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Ge-Ran Hutang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China.,University of the Chinese Academy of Sciences, 100039, Beijing, China
| | - Xun-Ge Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China.,University of the Chinese Academy of Sciences, 100039, Beijing, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Yuan Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China.,College of Life Science, Liaoning Normal University, 116081, Dalian, China
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642, Guangzhou, China
| | - Yuan Zhao
- Yunnan Agricultural University, 650201, Kunming, China
| | - Wen-Kai Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Jie Yuan
- TGS Inc, 518000, Shenzhen, China
| | | | - Cheng-Wen Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642, Guangzhou, China. .,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern, Kunming Institute of Botany, Chinese Academy of Sciences, 650204, Kunming, China.
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15
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Novel cis-acting regulatory elements in wild Oryza species impart improved rice bran quality by lowering the expression of phospholipase D alpha1 enzyme (OsPLDα1). Mol Biol Rep 2019; 47:401-422. [PMID: 31642040 DOI: 10.1007/s11033-019-05144-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Rice bran oil is good quality edible oil, rich in antioxidants and comprised typically of oleic-linoleic type fatty acids. However, presence of a highly lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) increases free fatty acid content in the oil which further leads to stale flavor and rancidity of the oil, making it unfit for human consumption. In this study, we compared the upstream regions of OsPLDα1 orthologs across 34 accessions representing 5 wild Oryza species and 8 cultivars, to uncover sequence variations and identify cis-elements involved in differential transcription of orthologs. Alignment of the upstream sequences to the Nipponbare OsPLDα1 reference sequence revealed the presence of 39 SNPs. Phylogenetic analysis showed that all the selected cultivars and wild species accessions are closely related to the reference except for three accessions of O. rufipogon (IRGC89224, IRGC104425, and IRGC105902). Furthermore, using exon-specific qRT-PCR, OsPLDα1 expression patterns in immature grains indicated significant differences in transcript abundance between the wild species accessions. In comparison to the control, lowest gene expression was observed in IRGC89224 accession (0.20-fold) followed by IRGC105902 (0.26-fold) and IRGC104425 (0.41-fold) accessions. In-silico analysis of the OsPLDα1 promoter revealed that the copy number variations of CGCGBOXAT, GT1CONSENSUS, IBOXCORE, NODCON2GM, OSE2ROOTNODULE, SURECOREATSULTR11, and SORLIP1AT cis-elements play an important role in the transcriptional activities of orthologous genes. Owing to the presence of ARFAT and SEBF elements only in the IRGC89224 accession, which had the lowest gene expression as well, these putative upstream regulatory sequences have been identified as novel cis-elements which may act as repressors in regulating the OsPLDα1 gene expression. The accessions identified with low OsPLDα1 expressions could be further deployed as potential donors of ideal OsPLDα1 allele for transfer of the desired trait into elite rice cultivars.
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Cheng L, Nam J, Chu SH, Rungnapa P, Min MH, Cao Y, Yoo JM, Kang JS, Kim KW, Park YJ. Signatures of differential selection in chloroplast genome between japonica and indica. RICE (NEW YORK, N.Y.) 2019; 12:65. [PMID: 31414311 PMCID: PMC6692809 DOI: 10.1186/s12284-019-0322-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/02/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND The domestication process of Asian rice (Oryza sativa L.) is complicated. It's well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. RESULTS A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (FST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima's D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. CONCLUSIONS Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.
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Affiliation(s)
- Lin Cheng
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Jungrye Nam
- Center for Crop Breeding on Omics and Artifical Intelligence, Kongju National University, Yesan, 32439, Republic of Korea
| | - Sang-Ho Chu
- Center for Crop Breeding on Omics and Artifical Intelligence, Kongju National University, Yesan, 32439, Republic of Korea
| | - Phitaktansakul Rungnapa
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Yuan Cao
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Ji-Min Yoo
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Jee-Su Kang
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artifical Intelligence, Kongju National University, Yesan, 32439, Republic of Korea.
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.
- Center for Crop Breeding on Omics and Artifical Intelligence, Kongju National University, Yesan, 32439, Republic of Korea.
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17
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Qi H, Yang J, Yin C, Zhao J, Ren X, Jia S, Zhang G. Analysis of Pyricularia oryzae and P. grisea from Different Hosts Based on Multilocus Phylogeny and Pathogenicity Associated with Host Preference in China. PHYTOPATHOLOGY 2019; 109:1433-1440. [PMID: 30973308 DOI: 10.1094/phyto-10-18-0383-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pyricularia oryzae and P. grisea are important agents of major diseases on a wide range of gramineous hosts. Whereas P. oryzae is the most important pathogen causing outbreaks of rice blast, P. grisea is mainly a pathogen of crabgrass. In this study, 103 P. oryzae and 20 P. grisea isolates were collected from seven species of plants, and we analyzed their phylogeny, pathogenicity, and relationship with host preferences to investigate the differences among them from different hosts. Based on phylogenetic analysis of multilocus sequences, 16 isolates from crabgrass and four isolates from green bristlegrass were identified as P. grisea and another 103 isolates from crabgrass, green bristlegrass, goose grass, foxtail millet, wild millet, rice, and sedge belonged to P. oryzae. Results of pathogenicity tests by artificial inoculation demonstrated that six of 10 P. oryzae isolates from rice and three of 44 P. oryzae isolates from green bristlegrass showed cross-infectivity on green bristlegrass and rice, respectively. Taken together, our results demonstrated that isolates from green bristlegrass and crabgrass consist of both P. oryzae and P. grisea and that P. oryzae isolates showed cross-infectivity between rice and green bristlegrass, suggesting that host shifts may occur for P. oryzae and P. grisea.
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Affiliation(s)
- Hexing Qi
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Changfa Yin
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jian Zhao
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xianxian Ren
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shishuang Jia
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Guozhen Zhang
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
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18
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Cheng L, Kim KW, Park YJ. Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice. Sci Rep 2019; 9:10846. [PMID: 31350452 PMCID: PMC6659709 DOI: 10.1038/s41598-019-47318-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/09/2019] [Indexed: 01/15/2023] Open
Abstract
The history of the domestication of rice is controversial, as it remains unknown whether domestication processes occurred once or multiple times. To date, genetic architecture and phylogenetic studies based on the rice nuclear genome have been extensively studied, but the results are quite different. Here, we found interesting results for different selections in Oryza sativa based on comprehensive studies of the rice mitochondrial (mt) genome. In detail, 412 rice germplasms were collected from around the world for variant architecture studies. A total of 10632 variants were detected in the mt genome, including 7277 SNPs and 3355 InDels. Selection signal (πw/πc) indicated that the selection sites in Oryza sativa L. ssp. japonica were different from those of Oryza sativa L. indica rice. The fixation index (FST) was higher between indica and japonica than between indica and wild rice. Moreover, haplotype and phylogenetic analyses also revealed indica clusters and japonica clusters that were well separated from wild rice. As mentioned above, our studies indicate that the selection sites of the indica type were different from those of the japonica type. This means that indica and japonica have experienced different domestication processes. We also found that japonica may have experienced a bottleneck event during domestication.
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Affiliation(s)
- Lin Cheng
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Kyu-Won Kim
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, 32439, Republic of Korea.
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea.
- Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, 32439, Republic of Korea.
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19
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E Y, Meng J, Hu H, Cheng D, Zhu C, Chen W. Effects of organic molecules from biochar-extracted liquor on the growth of rice seedlings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:338-345. [PMID: 30544094 DOI: 10.1016/j.ecoenv.2018.11.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 05/04/2023]
Abstract
There are many reports indicating that biochar can promote growth; however, its mechanism of action remains unclear. The aim of this study was to show that organic molecules from biochar-extracted liquor affect the growth of rice seedlings. In this study, rice seedlings were cultured under water. Agronomic traits and growth-related genes and proteins were used as markers to describe more precisely the effects of biochar on specific growth parameters of rice seedlings. Our results demonstrated that the 3% biochar-extracted liquor amendment clearly promoted growth. The growth-related gene auxin binding protein 1 and its encoded protein were up-regulated. Molecular simulations revealed that 2-acetyl-5-methylfuran from biochar-extracted liquor could interact with auxin binding protein 1 in a similar way to indoleacetic acid binding. The growth of rice seedlings was therefore affected by biochar-extracted liquor, which acted on the ABP1 signalling pathway.
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Affiliation(s)
- Yang E
- Liaoning Biochar Engineering & Technology Research Center, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Jun Meng
- Liaoning Biochar Engineering & Technology Research Center, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Haijun Hu
- Zunyi Normal College, Zunyi 863002, PR China
| | - Dengmiao Cheng
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing 100081, PR China
| | - Changfu Zhu
- Ultrasonography Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, PR China
| | - Wenfu Chen
- Liaoning Biochar Engineering & Technology Research Center, Shenyang Agricultural University, Shenyang 110866, PR China.
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20
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Nadir S, Khan S, Zhu Q, Henry D, Wei L, Lee DS, Chen L. An overview on reproductive isolation in Oryza sativa complex. AOB PLANTS 2018; 10:ply060. [PMID: 30538811 PMCID: PMC6280023 DOI: 10.1093/aobpla/ply060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/21/2018] [Indexed: 05/27/2023]
Abstract
Reproductive isolation is generally regarded as the essence of the speciation process. Studying closely related species is convenient for understanding the genetic basis of reproductive isolation. Therefore, the present review is restricted to the species and subspecies of the Oryza sativa complex, which includes the two domestic rice cultivars and six wild species. Although closely related, these rice species are separated from each other by a range reproductive barriers. This review presents a comprehensive understanding of the forces that shaped the formation of reproductive barriers among and between the species of the O. sativa complex. We suggest the possibility that domestication and artificial breeding in these rice species can lead to the early stages of speciation. Understanding the evolutionary and molecular mechanisms underlying reproductive isolation in rice will increase our knowledge in speciation and would also offer practical significance for the implementation of crop improvement strategies.
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Affiliation(s)
- Sadia Nadir
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- Department of Chemistry, University of Science and Technology, Bannu, Khyber Pakhtunkhwa, Pakistan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Sehroon Khan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qian Zhu
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Doku Henry
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- Biotechnology Lab Complex, CSIR-Crops Research Institute, Ghana
| | - Li Wei
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Dong Sun Lee
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - LiJuan Chen
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
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21
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Kappara S, Neelamraju S, Ramanan R. Down regulation of a heavy metal transporter gene influences several domestication traits and grain Fe-Zn content in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:208-219. [PMID: 30348320 DOI: 10.1016/j.plantsci.2018.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/02/2018] [Accepted: 09/04/2018] [Indexed: 05/07/2023]
Abstract
Biofortification of rice (Oryza sativa L.) would alleviate iron and zinc deficiencies in the target populations. We identified two alleles 261 and 284 of a Gramineae-specific heavy metal transporter gene OsHMA7 by analyzing expression patterns and sequences of genes within QTLs for high Fe & Zn, in Madhukar x Swarna recombinant inbred lines (RILs) with high (HL) or low (LL) grain Fe & Zn. Overexpression of 261 allele increased grain Fe and Zn but most of the transgenic plants either did not survive or did not yield enough seeds and could not be further characterized. Knocking down expression of OsHMA7 by RNAi silencing of endogenous gene resulted in plants with altered domestication traits such as plant height, tiller number, panicle size and architecture, grain color, shape, size, grain shattering, heading date and increased sensitivity to Fe and Zn deficiency. However, overexpression of 284 allele resulted in transgenic lines with either high grain Fe & Zn content (HL-ox) and tolerance to Fe and Zn deficiency or low grain Fe & Zn content (LL-ox) and phenotype similar to RNAi-lines. OsHMA7 transcript levels were five-fold higher in the HL-ox plants whereas LL-ox and RNAi plants showed 2-3 fold reduced levels compared to Kitaake control. Spraying LL-ox and RNAi lines with Fe & Zn at grain filling stage resulted in increased grain yield, significant increase in Fe & Zn content and brown pericarp. Altered expression of OsHMA7 influenced transcript levels of iron-responsive genes indicating cellular Fe-Zn homeostasis and also several domestication-related genes in rice. Our study shows that a novel heavy metal transporter gene influences yield and grain Fe & Zn content and has potential to improve rice production and biofortification.
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Affiliation(s)
| | - Sarla Neelamraju
- Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030, India.
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22
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Wang M, Li W, Fang C, Xu F, Liu Y, Wang Z, Yang R, Zhang M, Liu S, Lu S, Lin T, Tang J, Wang Y, Wang H, Lin H, Zhu B, Chen M, Kong F, Liu B, Zeng D, Jackson SA, Chu C, Tian Z. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet 2018; 50:1435-1441. [PMID: 30250128 DOI: 10.1038/s41588-018-0229-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/07/2018] [Indexed: 12/27/2022]
Abstract
Domesticated species often exhibit convergent phenotypic evolution, termed the domestication syndrome, of which loss of seed dormancy is a component. To date, dormancy genes that contribute to parallel domestication across different families have not been reported. Here, we cloned the classical stay-green G gene from soybean and found that it controls seed dormancy and showed evidence of selection during soybean domestication. Moreover, orthologs in rice and tomato also showed evidence of selection during domestication. Analysis of transgenic plants confirmed that orthologs of G had conserved functions in controlling seed dormancy in soybean, rice, and Arabidopsis. Functional investigation demonstrated that G affected seed dormancy through interactions with NCED3 and PSY and in turn modulated abscisic acid synthesis. Therefore, we identified a gene responsible for seed dormancy that has been subject to parallel selection in multiple crop families. This may help facilitate the domestication of new crops.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhen Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Xu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rui Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Lu
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Tao Lin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongru Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingsheng Chen
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
| | - Chengcai Chu
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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23
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Singh B, Singh N, Mishra S, Tripathi K, Singh BP, Rai V, Singh AK, Singh NK. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex. FRONTIERS IN PLANT SCIENCE 2018; 9:123. [PMID: 29467785 PMCID: PMC5808308 DOI: 10.3389/fpls.2018.00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 01/23/2018] [Indexed: 05/17/2023]
Abstract
Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more fundamental grouping based on the ancestry closely related to 'Indica' and 'Aus' groups of rice cultivars. The Pro-Indica population has substantial presence in the Eastern Himalayan Region and Lower Gangetic Plains, whereas 'Pro-Aus' sub-population was predominant in the Upper Gangetic Plains, Western Himalayan Region, Gujarat Plains and Hills, and Western Coastal Plains. In contrast 'Mid-Gangetic' population was largely concentrated in the Mid Gangetic Plains. The information presented here will be useful in the utilization of wild rice resources for varietal improvement.
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Affiliation(s)
- Balwant Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Nisha Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Shefali Mishra
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Kabita Tripathi
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Bikram P. Singh
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ashok K. Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
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24
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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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25
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Simpson KJ, Wade RN, Rees M, Osborne CP, Hartley SE. Still armed after domestication? Impacts of domestication and agronomic selection on silicon defences in cereals. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12935] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Mark Rees
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield UK
| | - Colin P. Osborne
- Department of Animal and Plant SciencesUniversity of Sheffield Sheffield UK
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26
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Wada H, Masumoto-Kubo C, Tsutsumi K, Nonami H, Tanaka F, Okada H, Erra-Balsells R, Hiraoka K, Nakashima T, Hakata M, Morita S. Turgor-responsive starch phosphorylation in Oryza sativa stems: A primary event of starch degradation associated with grain-filling ability. PLoS One 2017; 12:e0181272. [PMID: 28727805 PMCID: PMC5519062 DOI: 10.1371/journal.pone.0181272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/28/2017] [Indexed: 11/19/2022] Open
Abstract
Grain filling ability is mainly affected by the translocation of carbohydrates generated from temporarily stored stem starch in most field crops including rice (Oryza sativa L.). The partitioning of non-structural stem carbohydrates has been recognized as an important trait for raising the yield ceiling, yet we still do not fully understand how carbohydrate partitioning occurs in the stems. In this study, two rice subspecies that exhibit different patterns of non-structural stem carbohydrates partitioning, a japonica-dominant cultivar, Momiroman, and an indica-dominant cultivar, Hokuriku 193, were used as the model system to study the relationship between turgor pressure and metabolic regulation of non-structural stem carbohydrates, by combining the water status measurement with gene expression analysis and a dynamic prefixed 13C tracer analysis using a mass spectrometer. Here, we report a clear varietal difference in turgor-associated starch phosphorylation occurred at the initiation of non-structural carbohydrate partitioning. The data indicated that starch degradation in Hokuriku 193 stems occurred at full-heading, 5 days earlier than in Momiroman, contributing to greater sink filling. Gene expression analysis revealed that expression pattern of the gene encoding α-glucan, water dikinase (GWD1) was similar between two varieties, and the maximum expression level in Hokuriku 193, reached at full heading (4 DAH), was greater than in Momiroman, leading to an earlier increase in a series of amylase-related gene expression in Hokuriku 193. In both varieties, peaks in turgor pressure preceded the increases in GWD1 expression, and changes in GWD1 expression was correlated with turgor pressure. Additionally, a threshold is likely to exist for GWD1 expression to facilitate starch degradation. Taken together, these results raise the possibility that turgor-associated starch phosphorylation in cells is responsible for the metabolism that leads to starch degradation. Because the two cultivars exhibited remarkable varietal differences in the pattern of non-structural carbohydrate partitioning, our findings propose that the observed difference in grain-filling ability originated from turgor-associated regulation of starch phosphorylation in stem parenchyma cells. Further understanding of the molecular mechanism of turgor-regulation may provide a new selection criterion for breaking the yield barriers in crop production.
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Affiliation(s)
- Hiroshi Wada
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Chisato Masumoto-Kubo
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Koichi Tsutsumi
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Hiroshi Nonami
- Department of Biomechanical Systems, Faculty of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - Fukuyo Tanaka
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Haruka Okada
- Department of Biomechanical Systems, Faculty of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - Rosa Erra-Balsells
- Department of Organic Chemistry-CIHIDECAR, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Kenzo Hiraoka
- Clean Energy Research Center, The University of Yamanashi, Kofu, Yamanashi, Japan
| | - Taiken Nakashima
- Department of Biomechanical Systems, Faculty of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - Makoto Hakata
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
| | - Satoshi Morita
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Chikugo, Fukuoka, Japan
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27
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Wang H, Vieira FG, Crawford JE, Chu C, Nielsen R. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice. Genome Res 2017; 27:1029-1038. [PMID: 28385712 PMCID: PMC5453317 DOI: 10.1101/gr.204800.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/21/2017] [Indexed: 12/30/2022]
Abstract
The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus, indica, and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica, possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow.
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Affiliation(s)
- Hongru Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Filipe G Vieira
- Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Jacob E Crawford
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
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28
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Rashid MAR, Zhao Y, Zhang H, Li J, Li Z. Nucleotide diversity, natural variation, and evolution of Flexible culm-1 and Strong culm-2 lodging resistance genes in rice. Genome 2017; 59:473-83. [PMID: 27373308 DOI: 10.1139/gen-2016-0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lodging resistance is one of the vital traits in yield improvement and sustainability. Culm wall thickness, diameter, and strength are different traits that can govern the lodging resistance in rice. The genes SCM2 and FC1 have been isolated for culm thickness, strength, and flexibility, but their functional nucleotide variations were still unknown. We used a 13× deep sequence of 795 diverse genotypes to present the functional variation and SNP diversity in SCM2 and FC1. The major functional variant for the SCM2 gene was at position 27480181 and for the FC1 gene at position 31072992. Haplotype analysis of both genes provided their various allelic differences among haplotypes. SCM2 alleles further presented the evolution of Oryza sativa L. subsp. indica and subsp. japonica genomes from common parent in different geographical zones, while the haplotypes of FC1 suggested their evolution from different strains of the common parent Oryza rufipogon. SCM2 showed purifying selection and functional associations with rare alleles, while FC1 displayed balanced selection favored by multiple heterozygous alleles. Genotypes with an allelic combination of SCM2-3 and FC1-2 in japonica background exhibited striking resistance against lodging, which can be used in further breeding programs.
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Affiliation(s)
- Muhammad Abdul Rehman Rashid
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yan Zhao
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.,Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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29
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Choi JY, Platts AE, Fuller DQ, Hsing (邢禹依) YI, Wing RA, Purugganan MD. The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice. Mol Biol Evol 2017; 34:969-979. [PMID: 28087768 PMCID: PMC5400379 DOI: 10.1093/molbev/msx049] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Adrian E. Platts
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Dorian Q. Fuller
- Institute of Archaeology, University College London, London, United Kingdom
| | - Yue-Ie Hsing (邢禹依)
- Institute of Plant and Microbial Biology, Academica Sinica, Nankang, Taipei, Taiwan, Republic of China
| | - Rod A. Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ
| | - Michael D. Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice. Sci Rep 2017; 7:43327. [PMID: 28256554 PMCID: PMC5335689 DOI: 10.1038/srep43327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/24/2017] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.
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Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice. G3-GENES GENOMES GENETICS 2016; 6:4105-4114. [PMID: 27729434 PMCID: PMC5144979 DOI: 10.1534/g3.116.035881] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.
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Kim H, Jung J, Singh N, Greenberg A, Doyle JJ, Tyagi W, Chung JW, Kimball J, Hamilton RS, McCouch SR. Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice. RICE (NEW YORK, N.Y.) 2016; 9:56. [PMID: 27730519 PMCID: PMC5059230 DOI: 10.1186/s12284-016-0119-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 09/08/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). RESULTS Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. CONCLUSIONS Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.
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Affiliation(s)
- HyunJung Kim
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Janelle Jung
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Namrata Singh
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Anthony Greenberg
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Wricha Tyagi
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: School of Crop Improvement, College of PG Studies, Central Agricultural University, Umroi Road, Umiam, Meghalaya, India
| | - Jong-Wook Chung
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Chungubk, 28644, Republic of Korea
| | - Jennifer Kimball
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-762, USA
| | - Ruaraidh Sackville Hamilton
- TT Chang Genetics Resource Center and International Rice Genebank, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA.
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Tong W, Kim TS, Park YJ. Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing. RICE (NEW YORK, N.Y.) 2016; 9:57. [PMID: 27757948 PMCID: PMC5069220 DOI: 10.1186/s12284-016-0129-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/07/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic. RESULTS A total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. CONCLUSIONS The chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.
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Affiliation(s)
- Wei Tong
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439 Republic of Korea
| | - Tae-Sung Kim
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439 Republic of Korea
- Department of Agricultural Sciences, College of Natural Sciences, Korea National Open University, Seoul, 03087 Republic of Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 32439 Republic of Korea
- Center for Crop Genetic Resource and Breeding (CCGRB), Kongju National University, Cheonan, 31080 Republic of Korea
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Magwa RA, Zhao H, Yao W, Xie W, Yang L, Xing Y, Bai X. Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice. J Genet 2016; 95:639-46. [PMID: 27659335 DOI: 10.1007/s12041-016-0679-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Awn is one of the most important domesticated traits in rice (Oryza sativa). Understanding the genetic basis of awn length is important for grain harvest and production, because long awn length is disadvantageous for both grain harvest and milling. We investigated the awn length of 529 rice cultivars and performed a Genomewide association studies (GWAS) in the indica and japonica subpopulations, and the whole population. In total, we found 17 loci associated with awn length. Of these loci, seven were linked to previously reported quantitative trait loci, and one was linked to the awn gene An-1. Nine novel loci were repeatedly identified in different environments. One of the nine associations was identified in both the whole and japonica populations. Special interest was the detection of the most significant association SNP, sf0136352825, which was less than 95 kb from the seed shattering gene qSH1. These results may provide potentially favourable haplotypes for molecular breeding in rice.
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Affiliation(s)
- Risper Auma Magwa
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, People's Republic of
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Roy PS, Rao GJN, Jena S, Samal R, Patnaik A, Patnaik SSC, Jambhulkar NN, Sharma S, Mohapatra T. Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India. PLoS One 2016; 11:e0162268. [PMID: 27598392 PMCID: PMC5012674 DOI: 10.1371/journal.pone.0162268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 08/20/2016] [Indexed: 11/23/2022] Open
Abstract
A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei’s genetic diversity value (He) was in the range of 0.034–0.880 revealing two sub-populations SP 1 (membership percentage-27.1%) and SP 2 (72.9%). At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare) subtype (6C7A) was detected in 100 genotypes followed by O. rufipogon (KF428978) subtype (6C6A) in 13 genotypes while indica (93–11) sub type (8C8A) was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha.
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Affiliation(s)
- Pritesh Sundar Roy
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | | | - Sudipta Jena
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Rashmita Samal
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Ashok Patnaik
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | | | | | - Srigopal Sharma
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Trilochan Mohapatra
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
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Kumagai M, Kanehara M, Shoda S, Fujita S, Onuki S, Ueda S, Wang L. Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times. Mol Biol Evol 2016; 33:2496-505. [PMID: 27461246 DOI: 10.1093/molbev/msw142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice.
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Affiliation(s)
- Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masaaki Kanehara
- Department of Teacher Training and School Education, Nara University of Education, Nara, Japan
| | - Shin'ya Shoda
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | | | - Shizuo Onuki
- Department of Archaeology, Graduate School of Humanities and Sociology, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Li Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
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37
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Ru D, Mao K, Zhang L, Wang X, Lu Z, Sun Y. Genomic evidence for polyphyletic origins and interlineage gene flow within complex taxa: a case study ofPicea brachytylain the Qinghai-Tibet Plateau. Mol Ecol 2016; 25:2373-86. [DOI: 10.1111/mec.13656] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/09/2016] [Accepted: 04/14/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Dafu Ru
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Kangshan Mao
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Lei Zhang
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Xiaojuan Wang
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-ecosystem; College of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Yongshuai Sun
- Key Laboratory for Bio-resources and Eco-environment; College of Life Sciences; Sichuan University; Chengdu 610065 China
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Mengla 666303 China
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38
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Wang Y, Gu Y, Gao H, Qiu L, Chang R, Chen S, He C. Molecular and geographic evolutionary support for the essential role of GIGANTEAa in soybean domestication of flowering time. BMC Evol Biol 2016; 16:79. [PMID: 27072125 PMCID: PMC4830004 DOI: 10.1186/s12862-016-0653-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/06/2016] [Indexed: 12/16/2023] Open
Abstract
BACKGROUND Flowering time is a domestication trait of Glycine max and varies in soybeans, yet, a gene for flowering time variation has not been associated with soybean domestication. GIGANTEA (GI) is a major gene involved in the control of flowering time in Arabidopsis, although three GI homologs complicate this model in the soybean genome. RESULTS In the present work, we revealed that the geographic evolution of the GIGANTEAa (GIa) haplotypes in G. max (GmGIa) and Glycine soja (GsGIa). Three GIa haplotypes (H1, H2, and H3) were found among cultivated soybeans and their wild relatives, yet an additional 44 diverse haplotypes were observed in wild soybeans. H1 had a premature stop codon in the 10(th) exon, whereas the other haplotypes encoded full-length GIa protein isoforms. In both wild-type and cultivated soybeans, H2 was present in the Southern region of China, and H3 was restricted to areas near the Northeast region of China. H1 was genetically derived from H2, and it was dominant and widely distributed among cultivated soybeans, whereas in wild populations, the ortholog of this domesticated haplotype H1 was only found in Yellow River basin with a low frequency. Moreover, this mutated GIa haplotype significantly correlated with early flowering. We further determined that the differences in gene expression of the three GmGIa haplotypes were not correlated to flowering time variations in cultivated soybeans. However, only the truncated GmGIa H1 could partially rescue gi-2 Arabidopsis from delayed flowering in transgenic plants, whereas both GmGIa H2 and H3 haplotypes could significantly repress flowering in transgenic Arabidopsis with a wild-type background. CONCLUSIONS Thus, GmGIa haplotype diversification may have contributed to flowering time adaptation that facilitated the radiation of domesticated soybeans. In light of the evolution of the GIa gene, soybean domestication history for an early flowering phenotype is discussed.
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Affiliation(s)
- Yan Wang
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
| | - Yongzhe Gu
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
- />Graduate University, Chinese Academy of Sciences, Yuquan Road 19, 100049 Beijing, China
| | - Huihui Gao
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
- />Graduate University, Chinese Academy of Sciences, Yuquan Road 19, 100049 Beijing, China
| | - Lijuan Qiu
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Ruzhen Chang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Shouyi Chen
- />National Key Laboratory of Plant Genomic, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, 100101 Beijing, China
| | - Chaoying He
- />State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan 100093 Beijing, China
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Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci. G3-GENES GENOMES GENETICS 2015; 5:2267-74. [PMID: 26338659 PMCID: PMC4632046 DOI: 10.1534/g3.115.020834] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.
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40
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Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 2015; 15:506. [PMID: 25468217 DOI: 10.1186/preaccept-2784872521277375] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. RESULTS Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the "pan-genome" of three divergent rice varieties and document several megabases of each genome absent in the other two. CONCLUSIONS Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.
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The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm. G3-GENES GENOMES GENETICS 2015; 5:1585-92. [PMID: 26019188 PMCID: PMC4528315 DOI: 10.1534/g3.115.018317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
TRIMs (terminal-repeat retrotransposons in miniature), which are characterized by their small size, have been discovered in all investigated vascular plants and even in animals. Here, we identified a highly conservative TRIM family referred to as Wukong elements in the maize genome. The Wukong family shows a distinct pattern of tandem arrangement in the maize genome suggesting a high rate of unequal crossing over. Estimation of insertion times implies a burst of retrotransposition activity of the Wukong family after the allotetraploidization of maize. Using next-generation sequencing data, we detected 87 new Wukong insertions in parents of the maize NAM population relative to the B73 reference genome and found abundant insertion polymorphism of Wukong elements in 75 re-sequenced maize lines, including teosinte, landraces, and improved lines. These results suggest that Wukong elements possessed a persistent retrotransposition activity throughout maize evolution. Moreover, the phylogenetic relationships among 76 maize inbreds and their relatives based on insertion polymorphisms of Wukong elements should provide us with reliable molecular markers for biodiversity and genetics studies.
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42
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Tong W, He Q, Wang XQ, Yoon MY, Ra WH, Li F, Yu J, Oo WH, Min SK, Choi BW, Heo EB, Yun BK, Kim KW, Kim TS, Lee CY, Park YJ. A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships amongOryza sativasubspecies. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei Tong
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Qiang He
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Xiao-Qiang Wang
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Min-Young Yoon
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Won-Hee Ra
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Fengpeng Li
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Jie Yu
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Win Htet Oo
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Sun-Kyung Min
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Bu-Woong Choi
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Eun-Beom Heo
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Byoung-Kook Yun
- Department of Industrial and Systems Engineering; College of Engineering; Kongju National University; Cheonan 331-717 Korea
| | - Kyu-Won Kim
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Tae-Sung Kim
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering; College of Engineering; Kongju National University; Cheonan 331-717 Korea
| | - Yong-Jin Park
- Department of Plant Resources; College of Industrial Sciences; Kongju National University; Yesan 340-702 Korea
- Legume Bio-Resource Center of Green Manure; Kongju National University; Yesan 340-702 Korea
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Sun X, Jia Q, Guo Y, Zheng X, Liang K. Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice. PLoS One 2015; 10:e0119239. [PMID: 25774680 PMCID: PMC4361536 DOI: 10.1371/journal.pone.0119239] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/11/2015] [Indexed: 11/19/2022] Open
Abstract
To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93–11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I.
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Affiliation(s)
- Xinli Sun
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
- * E-mail:
| | - Qi Jia
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Yuchun Guo
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Xiujuan Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Kangjing Liang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture & Forestry University, Fuzhou, China
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Choudhury BI, Khan ML, Dayanandan S. Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene. BMC Res Notes 2014; 7:953. [PMID: 25547027 PMCID: PMC4320456 DOI: 10.1186/1756-0500-7-953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 12/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes. FINDINGS The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes. CONCLUSION The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.
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Affiliation(s)
- Baharul I Choudhury
- Biology Department, Forest and Evolutionary Genomics Laboratory, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St, West, Montreal, Quebec H4B 1R6, Canada.
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Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 2014. [PMID: 25468217 PMCID: PMC4268812 DOI: 10.1186/s13059-014-0506-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Results Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the ‘pan-genome’ of three divergent rice varieties and document several megabases of each genome absent in the other two. Conclusions Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0506-z) contains supplementary material, which is available to authorized users.
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Nuruzzaman M, Kanno T, Amada R, Habu Y, Kasajima I, Ishikawa T, Kawai-Yamada M, Uchimiya H. Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression? PLoS One 2014; 9:e102742. [PMID: 25259844 PMCID: PMC4178011 DOI: 10.1371/journal.pone.0102742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/22/2014] [Indexed: 11/21/2022] Open
Abstract
The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type.
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Affiliation(s)
- Mohammed Nuruzzaman
- Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Tatsuo Kanno
- Japanese Science and Technology Agency, PRESTO, Saitama, Japan
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Rika Amada
- Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan
| | - Yoshiki Habu
- Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Ibaraki, Japan
| | - Ichiro Kasajima
- National Agriculture and Food Research Organization, Institute of Floricultural Science, Tsukuba, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Maki Kawai-Yamada
- Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan
| | - Hirofumi Uchimiya
- Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan
- * E-mail:
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Mitani-Ueno N, Ogai H, Yamaji N, Ma JF. Physiological and molecular characterization of Si uptake in wild rice species. PHYSIOLOGIA PLANTARUM 2014; 151:200-7. [PMID: 24320720 DOI: 10.1111/ppl.12125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 05/23/2023]
Abstract
Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv. Nipponbare). However, all wild rice species and the cultivated rice showed similar concentration of Si in the shoots when grown in a field. All species with AA genome showed the same amino acid sequence of both Lsi1 and Lsi2 as O. sativa, whereas species with EE and BB genome showed several nucleotide differences in both Lsi1 and Lsi2. However, proteins encoded by these genes also showed transport activity for Si in Xenopus oocyte. The mRNA expression of Lsi1 in all wild rice species was lower than that in the cultivated rice, whereas the expression of Lsi2 was lower in O. rufipogon and O. barthii but similar in other species. Similar cellular localization of Lsi1 and Lsi2 was observed in all wild rice as the cultivated rice. These results indicate that superior Si uptake, the important trait for rice growth, is basically conserved in wild and cultivated rice species.
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Affiliation(s)
- Namiki Mitani-Ueno
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
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Zhu K, Min C, Xia H, Yang Y, Wang B, Chen K. Characterisation of Indica Special Protein (ISP), a marker protein for the differentiation of Oryza sativa subspecies indica and japonica. Int J Mol Sci 2014; 15:7332-43. [PMID: 24786093 PMCID: PMC4057675 DOI: 10.3390/ijms15057332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/10/2014] [Accepted: 04/16/2014] [Indexed: 02/05/2023] Open
Abstract
Based on both morphological and physiological traits, Asian cultivated rice (Oryza sativa L.) can be classified into two distinct subspecies, indica and japonica. To better understand the differences between the two subspecies, a proteomic approach was used to profile proteins present in the yellow seedling stage of 10 indica and 10 japonica rice varieties. We report the discovery of a new protein, Indica Special Protein (ISP), which was only detected in yellow seedlings of indica varieties, and was absent from japonica varieties. Hence, ISP may represent a key gene for the differentiation of indica and japonica subspecies.
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Affiliation(s)
- Keming Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Chao Min
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Hengchuan Xia
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Bin Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.
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Abstract
Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world's population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.
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Saleh D, Milazzo J, Adreit H, Fournier E, Tharreau D. South-East Asia is the center of origin, diversity and dispersion of the rice blast fungus, Magnaporthe oryzae. THE NEW PHYTOLOGIST 2014; 201:1440-1456. [PMID: 24320224 PMCID: PMC4265293 DOI: 10.1111/nph.12627] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/23/2013] [Indexed: 05/11/2023]
Abstract
• Inferring invasion routes and identifying reservoirs of diversity of plant pathogens are essential in proposing new strategies for their control. Magnaporthe oryzae, the fungus responsible for rice blast disease, has invaded all rice growing areas. Virulent genotypes regularly (re)emerge, causing rapid resistance breakdowns. However, the world-wide genetic subdivision of M. oryzae populations on rice and its past history of invasion have never been elucidated. • In order to investigate the centers of diversity, origin and migration of M. oryzae on rice, we analyzed the genetic diversity of 55 populations from 15 countries. • Three genetic clusters were identified world-wide. Asia was the center of diversity and the origin of most migrations to other continents. In Asia, two centers of diversity were revealed in the Himalayan foothills: South China-Laos-North Thailand, and western Nepal. Sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all M. oryzae populations on rice. • Our results suggest a scenario of early evolution of M. oryzae on rice that matches the past history of rice domestication. This study confirms that crop domestication may have considerable influence on the pestification process of natural enemies.
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Affiliation(s)
- Dounia Saleh
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
- INRA, UMR BGPITA A54/K, F 34398, Montpellier, France
| | | | - Henri Adreit
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
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