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Lei Z, Westerband AC, Wright IJ, He Y, Zhang W, Cai X, Zhou Z, Liu F, Zhang Y. Leaf trait covariation and controls on leaf mass per area (LMA) following cotton domestication. ANNALS OF BOTANY 2022; 130:231-243. [PMID: 35849070 PMCID: PMC9445596 DOI: 10.1093/aob/mcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/05/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS The process of domestication has driven dramatic shifts in plant functional traits, including leaf mass per area (LMA). It remains unclear whether domestication has produced concerted shifts in the lower-level anatomical traits that underpin LMA and how these traits in turn affect photosynthesis. METHODS In this study we investigated controls of LMA and leaf gas exchange by leaf anatomical properties at the cellular, tissue and whole-leaf levels, comparing 26 wild and 31 domesticated genotypes of cotton (Gossypium). KEY RESULTS As expected, domesticated plants expressed lower LMA, higher photosynthesis and higher stomatal conductance, suggesting a shift towards the 'faster' end of the leaf economics spectrum. At whole-leaf level, variation in LMA was predominantly determined by leaf density (LD) both in wild and domesticated genotypes. At tissue level, higher leaf volume per area (Vleaf) in domesticated genotypes was driven by a simultaneous increase in the volume of epidermal, mesophyll and vascular bundle tissue and airspace, while lower LD resulted from a lower volume of palisade tissue and vascular bundles (which are of high density), paired with a greater volume of epidermis and airspace, which are of low density. The volume of spongy mesophyll exerted direct control on photosynthesis in domesticated genotypes but only indirect control in wild genotypes. At cellular level, a shift to larger but less numerous cells with thinner cell walls underpinned a lower proportion of cell wall mass, and thus a reduction in LD. CONCLUSIONS Taken together, cotton domestication has triggered synergistic shifts in the underlying determinants of LMA but also photosynthesis, at cell, tissue and whole-leaf levels, resulting in a marked shift in plant ecological strategy.
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Affiliation(s)
- Zhangying Lei
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, P.R. China
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
| | - Andrea C Westerband
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
| | - Ian J Wright
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- ARC Centre for Plant Success in Nature & Agriculture, Western Sydney University, Penrith, NSW 2751, Australia
| | - Yang He
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, P.R. China
| | - Wangfeng Zhang
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, P.R. China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, P.R. China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, P.R. China
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Lam DT, Buu BC, Lang NT, Toriyama K, Nakamura I, Ishikawa R. Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta. Ecol Evol 2019; 9:2964-2977. [PMID: 30891229 PMCID: PMC6405534 DOI: 10.1002/ece3.4978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/02/2022] Open
Abstract
Oryza rufipogon Griff. is a perennial species of wild rice widely distributed along the channels and rivers of the Mekong Delta, Vietnam. This study attempted to find centers of diversity among wild rice populations in this area and their inter-relationships. The highest genetic diversity was found in the Dong Thap population and the lowest in the Can Tho population. Maternal diversity evaluated using chloroplast INDELs detected ten plastid types, five of which were novel relative to other Asian countries. The mitochondrial genome suggested two unique deletions. One 699-bp deletion via short tandem repeats was accompanied by another deletion including orf153. All accessions carrying the mitochondrial type were found in a particular plastid type. This unique maternal lineage was confined to specific channels where it showed vigorous vegetative growth in comparison to upstream areas where various maternal lineages and maximum genetic diversity occurred. This area along the Mekong Delta is a center of not only nuclear but also maternal diversity.
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Affiliation(s)
- Dinh T. Lam
- United Graduate School of Agricultural ScienceIwate UniversityMoriokaJapan
- Institute of Agricultural Science for Southern VietnamHo Chi Minh CityVietnam
| | - Bui C. Buu
- Institute of Agricultural Science for Southern VietnamHo Chi Minh CityVietnam
| | - Nguyen T. Lang
- High Agricultural Technology Research Institute (HATRI)CanthoVietnam
| | - Kinya Toriyama
- Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Ikuo Nakamura
- Graduate School of HorticultureChiba UniversityMatsudoJapan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
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Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. Genetic diversity of the wx flanking region in rice landraces in northern Laos. BREEDING SCIENCE 2016; 66:580-590. [PMID: 27795683 PMCID: PMC5010311 DOI: 10.1270/jsbbs.16032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8602,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8560,
Japan
- Corresponding author (e-mail: )
| | - Kenneth M. Olsen
- Biology Department, Washington University,
St. Louis 63130-4899,
USA
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
Kirishima, Kagoshima 899-4201,
Japan
| | - Chay Bounphanousay
- Agricultural Research Centre, National Agriculture and Forestry Research Institute,
Nongviengkham, Vientiane 7170,
Lao P.D.R
| | - Toru Matoh
- Graduate School of Agriculture, Kyoto University,
Kyoto 606-8502,
Japan
| | - Yo-Ichiro Sato
- National Institutes for the Humanities,
Minato-ku, Tokyo 105-0001,
Japan
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Zheng Y, Crawford GW, Jiang L, Chen X. Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley. Sci Rep 2016; 6:28136. [PMID: 27324699 PMCID: PMC4914946 DOI: 10.1038/srep28136] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/01/2016] [Indexed: 11/09/2022] Open
Abstract
Plant remains dating to between 9000 and 8400 BP from a probable ditch structure at the Huxi site include the oldest rice (Oryza sativa) spikelet bases and associated plant remains recovered in China. The remains document an early stage of rice domestication and the ecological setting in which early cultivation was taking place. The rice spikelet bases from Huxi include wild (shattering), intermediate, and domesticated (non-shattering) forms. The relative frequency of intermediate and non-shattering spikelet bases indicates that selection for, at the very least, non-shattering rice was underway at Huxi. The rice also has characteristics of japonica rice (Oryza sativa subsp. japonica), helping to clarify the emergence of a significant lineage of the crop. Seeds, phytoliths and their context provide evidence of increasing anthropogenesis and cultivation during the occupation. Rice spikelet bases from Kuahuqiao (8000-7700 BP), Tianluoshan (7000-6500 BP), Majiabang (6300-6000 BP), and Liangzhu (5300-4300 BP) sites indicate that rice underwent continuing selection for reduced shattering and japonica rice characteristics, confirming a prolonged domestication process for rice.
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Affiliation(s)
- Yunfei Zheng
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Jiashan Road, Hangzhou, 310014, China
| | - Gary W Crawford
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Leping Jiang
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Jiashan Road, Hangzhou, 310014, China
| | - Xugao Chen
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Jiashan Road, Hangzhou, 310014, China
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Garaycochea S, Speranza P, Alvarez-Valin F. A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500022. [PMID: 26504677 PMCID: PMC4610308 DOI: 10.3732/apps.1500022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. METHODS A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. RESULTS From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. DISCUSSION We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought.
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Affiliation(s)
- Silvia Garaycochea
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria (INIA), Rincón del Colorado, Canelones, Uruguay
| | - Pablo Speranza
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- Sección Biomatemática, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Jiang J, Tan L, Zhu Z, Fu Y, Liu F, Cai H, Sun C. Molecular evolution of the TAC1 gene from rice (Oryza sativa L.). J Genet Genomics 2012; 39:551-60. [PMID: 23089365 DOI: 10.1016/j.jgg.2012.07.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/02/2012] [Accepted: 07/30/2012] [Indexed: 11/28/2022]
Abstract
Tiller angle is a key feature of the architecture of cultivated rice (Oryza sativa), since it determines planting density and influences rice yield. Our previous work identified Tiller Angle Control 1 (TAC1) as a major quantitative trait locus that controls rice tiller angle. To further clarify the evolutionary characterization of the TAC1 gene, we compared a TAC1-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of O. rufipogon and five accessions of O. nivara. Only one single nucleotide polymorphism (SNP), a synonymous substitution, was detected in TAC1 coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions. These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution. Nucleotide diversities in the TAC1 gene regions of O. sativa and O. rufipogon of 0.00116 and 0.00112, respectively, further indicate that TAC1 has been highly conserved during the course of rice domestication. A functional nucleotide polymorphism (FNP) of TAC1 was only found in the japonica rice group. A neutrality test revealed strong selection, especially in the 3'-flanking region of the TAC1 coding region containing the FNP in the japonica rice group. However, no selection occurred in the indica and wild-rice groups. A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.
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Affiliation(s)
- Jiahuan Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, National Centre for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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Reagon M, Thurber CS, Gross BL, Olsen KM, Jia Y, Caicedo AL. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evol Biol 2010; 10:180. [PMID: 20550656 PMCID: PMC2898691 DOI: 10.1186/1471-2148-10-180] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. RESULTS We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. CONCLUSIONS Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.
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Affiliation(s)
- Michael Reagon
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Carrie S Thurber
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Briana L Gross
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Yulin Jia
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
| | - Ana L Caicedo
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
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9
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Abstract
Unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. Here we clone and characterize GS3, an evolutionarily important gene controlling grain size in rice. We show that GS3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to demonstrate that the dominant allele for short grain complements the long-grain phenotype. An association study revealed that a C to A mutation in the second exon of GS3 (A allele) was associated with enhanced grain length in Oryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (theta(pi)) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to a Japonica-like ancestor and demonstrated introgression into the Indica gene pool. This study indicates a critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativa and enhances the potential for genetic manipulation of grain size in rice.
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Kovach MJ, McCouch SR. Leveraging natural diversity: back through the bottleneck. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:193-200. [PMID: 18313975 DOI: 10.1016/j.pbi.2007.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 11/20/2007] [Accepted: 12/13/2007] [Indexed: 05/24/2023]
Abstract
Plant breeders have long recognized the existence of useful genetic variation in the wild ancestors of our domesticated crop species. In cultivated rice (Oryza sativa), crosses between high-yielding elite cultivars and low-yielding wild accessions often give rise to superior offspring, with wild alleles conferring increased performance in the context of the elite cultivar genetic background. Because the breeding value of wild germplasm cannot be determined by examining the performance of wild accessions, a phylogenetic approach is recommended to determine which interspecific combinations are most likely to be useful in a breeding program. As we deepen our understanding of how genetic diversity is partitioned within and between cultivated and wild gene pools of Oryza, breeders will have increased power to make predictions about the most efficient strategies for utilizing wild germplasm for rice improvement.
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Affiliation(s)
- M J Kovach
- Department of Plant Breeding and Genetics, 162 Emerson Hall, Cornell University, Ithaca, NY 14853, USA
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Prathepha P. Genetic variation of wild rice populations from Thailand and the Lao PDR based on molecular markers. Pak J Biol Sci 2008; 11:26-33. [PMID: 18819589 DOI: 10.3923/pjbs.2008.26.33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The two wild rice species, Oryza rufipogon and O. nivara, which inhabit Thailand and the Lao PDR, are threatened with the loss of their natural habitats. The losses are primarily attributable to human intervention. Before this process advances, it is crucial to obtain basic information on the genetic variations of these species, so important knowledge about the current status of genetic variability. In this study, genetic variation within and between fourteen natural populations of the two populations from Thailand and Lao PDR was investigated at the DNA level by analysis of Polymerase Chain Reaction (PCR) mediate molecular markers. The results illustrated that wild rice from Thailand carried deletion (D) type ORF 100, but deletion and non-deletion type (ND) were found in wild rice samples from the Lao PDR. Five different plastid subtypes (7C7A, 6C8A, 7C6A, 6C7A and 9C7A) were found in the collected samples. Both polymorphism and pattern of distribution of p-SINE1-r2 in the two wild rice species were found among the populations. These data indicated that genetic variation existed in these natural populations of wild rice, suggesting that the strategies should be developed that are conducive to the conservation of wild rice in its natural environment.
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Affiliation(s)
- Preecha Prathepha
- Walai Rukhavej Botanical Research Institute (WRBRI), Mahasarakham University, Khamriang District, Maha Sarakham Province, 44150, Thailand
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New insights into the history of rice domestication. Trends Genet 2007; 23:578-87. [DOI: 10.1016/j.tig.2007.08.012] [Citation(s) in RCA: 357] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
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Kawakami SI, Ebana K, Nishikawa T, Sato YI, Vaughan DA, Kadowaki KI. Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.). Genome 2007; 50:180-7. [PMID: 17546083 DOI: 10.1139/g06-139] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A-H) based on insertion-deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon, suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogon - O. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogon - O. nivara complex.
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Affiliation(s)
- Shin-ichi Kawakami
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Kato H, Tezuka K, Feng YY, Kawamoto T, Takahashi H, Mori K, Akagi H. Structural diversity and evolution of the Rf-1 locus in the genus Oryza. Heredity (Edinb) 2007; 99:516-24. [PMID: 17622268 DOI: 10.1038/sj.hdy.6801026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Rf-1 locus in rice is agriculturally important as it restores fertility in plants with BT-type cytoplasmic male sterility (CMS). The Rf-1 locus contains several duplicated copies of the gene responsible for restoration of fertility. We analyzed the genomic structure of the Rf-1 locus in the genus Oryza to clarify the structural diversity and evolution of the locus. We identified six genes (Rf-1A to Rf-1F) with homology to Rf-1 at this locus in Oryza species with an AA genome. The Rf-1 locus structures in the rice accessions examined were very complex and fell into at least six classification types. The nucleotide sequences of the duplicated genes and their flanking regions were highly conserved suggesting that the complex Rf-1 locus structures were produced by homologous recombination between the duplicated genes. The fact that complex Rf-1 locus structures were common to Oryza species that have evolved independently indicates that a duplication of the ancestral Rf-1 gene occurred early in rice evolution and that homologous recombination resulted in the diversification of Rf-1 locus structures. Additionally, the amino acid sequences of each duplicated gene were conserved between species. This suggests that the duplicated genes in the Rf-1 locus may have divergent functions and may act by controlling mitochondrial gene expression in rice as occurs in the restoration of CMS.
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Affiliation(s)
- H Kato
- Laboratory of Plant Breeding and Genetics, Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjyo-Nakano, Akita, Japan
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Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9156-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Shahid Masood M, Nishikawa T, Fukuoka SI, Njenga PK, Tsudzuki T, Kadowaki KI. The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 2004; 340:133-9. [PMID: 15556301 DOI: 10.1016/j.gene.2004.06.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2004] [Revised: 05/15/2004] [Accepted: 06/01/2004] [Indexed: 10/26/2022]
Abstract
We determined the complete nucleotide sequence of the chloroplast genome of wild rice, Oryza nivara and compared it with the corresponding published sequence of relative cultivated rice, Oryza sativa. The genome was 134,494 bp long with a large single-copy region of 80,544 bp, a small single-copy region of 12,346 bp and two inverted repeats of 20,802 bp each. The overall A+T content was 61.0%. The O. nivara chloroplast genome encoded identical functional genes to O. sativa in the same order along the genome. On the other hand, detailed analysis revealed 57 insertion, 61 deletion and 159 base substitution events in the entire chloroplast genome of O. nivara. Among substitutions, transversions were much higher than transitions with the former even more frequent than the latter in the coding region. Most of the insertions/deletions were single-base but a few large length mutations were also detected. The frequency of insertion/deletion events was more in the coding region within inverted repeats. In contrast, a very few substitution events were identified in the coding region. Polymorphism was observed among rice cultivars at loci of large insertion/deletion events. This is the first report describing comparative and genome wide chloroplast analysis between a wild and cultivated crop.
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Affiliation(s)
- M Shahid Masood
- Molecular Biodiversity Laboratory, Genetic Diversity Department, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Ibaraki, Tsukuba 305-8602, Japan
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Akagi H, Yokozeki Y, Inagaki A, Fujimura T. Origin and evolution of twin microsatellites in the genus Oryza. Heredity (Edinb) 1998. [DOI: 10.1046/j.1365-2540.1998.00371.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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