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Lam DT, Ichitani K, Henry RJ, Ishikawa R. Molecular and Morphological Divergence of Australian Wild Rice. PLANTS 2020; 9:plants9020224. [PMID: 32050528 PMCID: PMC7076673 DOI: 10.3390/plants9020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/19/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022]
Abstract
Two types of perennial wild rice, Australian Oryza rufipogon and a new taxon Jpn2 have been observed in Australia in addition to the annual species Oryza meridionalis. Jpn2 is distinct owing to its larger spikelet size but shares O. meridionalis-like morphological features including a high density of bristle cells on the awn surface. All the morphological traits resemble O. meridionalis except for the larger spikelet size. Because Jpn2 has distinct cytoplasmic genomes, including the chloroplast (cp), cp insertion/deletion/simple sequence repeats were designed to establish marker systems to distinguish wild rice in Australia in different natural populations. It was shown that the new taxon is distinct from Asian O. rufipogon but instead resembles O. meridionalis. In addition, higher diversity was detected in north-eastern Australia. Reproductive barriers among species and Jpn2 tested by cross-hybridization suggested a unique biological relationship of Jpn2 with other species. Insertions of retrotransposable elements in the Jpn2 genome were extracted from raw reads generated using next-generation sequencing. Jpn2 tended to share insertions with other O. meridionalis accessions and with Australian O. rufipogon accessions in particular cases, but not Asian O. rufipogon except for two insertions. One insertion was restricted to Jpn2 in Australia and shared with some O. rufipogon in Thailand.
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Affiliation(s)
- Dinh Thi Lam
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan;
- Institute of Agricultural Science for Southern Vietnam, District 1, Ho Chi Minh City 121, Vietnam
| | - Katsuyuki Ichitani
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan;
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia;
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
- Correspondence: ; Tel.: +81-172-39-3778
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Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development. PLANTS 2019; 8:plants8100398. [PMID: 31597300 PMCID: PMC6843657 DOI: 10.3390/plants8100398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/28/2019] [Accepted: 10/03/2019] [Indexed: 12/14/2022]
Abstract
Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.
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Li J, Zhou J, Xu P, Deng X, Deng W, Zhang Y, Yang Y, Tao D. Mapping five novel interspecific hybrid sterility loci between Oryza sativa and Oryza meridionalis. BREEDING SCIENCE 2018; 68:516-523. [PMID: 30697112 PMCID: PMC6345236 DOI: 10.1270/jsbbs.18001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/22/2018] [Indexed: 05/27/2023]
Abstract
Oryza meridionalis is a potential source for improving Asian cultivated rice O. sativa via direct hybridization and backcrossing. However, hybrid sterility between O. sativa and O. meridionalis is the main barrier of reproduction hindering the transfer of favorable genes from O. meridionalis to O. sativa. To investigate the nature of hybrid sterility between O. sativa and O. meridionalis, three accessions of O. meridionalis were used as male parents to cross Dianjingyou 1, an O. sativa subsp. japonica cultivar following the backcross with the recurrent parent of Dianjingyou 1. Twenty pollen sterility NILs (BC6F1) were obtained and genotyped by using simple sequence repeat (SSR) markers distributed across the 12 rice chromosomes. The heterozygous markers were employed to genotype the corresponding segregation populations for mapping sterility genes. As a result, five novel loci for pollen sterility between O. sativa and O. meridionalis were identified and designated as S51(t), S52(t), S53(t), S54(t) and S55(t), respectively. The genetic behavior of five novel loci followed one-locus allelic interaction model. The disharmonious interaction between Asian cultivated rice allele and wild relative allele led to the partial or full abortion of male gametes for one parent allele in the heterozygotes. These results will be useful for elucidating the mechanism of interspecific hybrid sterility and further utilizing favorable genes from O. meridionalis for enhancement of rice breeding.
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Niihama M, Mochizuki M, Kurata N, Nonomura KI. PCR-based INDEL markers co-dominant between Oryza sativa, japonica cultivars and closely-related wild Oryza species. BREEDING SCIENCE 2015; 65:357-361. [PMID: 26366120 PMCID: PMC4542938 DOI: 10.1270/jsbbs.65.357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/06/2015] [Indexed: 06/05/2023]
Abstract
Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis. We confirmed that up to 155 of 188 markers developed for detection of japonica-indica INDELs could also detect INDELs between rice cultivars and wild AA-species accessions. Percentages of applicable markers were higher in O. rufipogon accessions (61.7 to 85.6%), and lower in accessions of other four AA species (39.8 to 51.4%). These markers were distributed throughout the rice chromosomes, and will be useful for genotyping of CSSLs and other genetic resources derived from crosses between rice cultivars and closely related wild species.
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Affiliation(s)
- Mitsuru Niihama
- Plant Genetics Laboratory, National Institute of Genetics,
Mishima, Shizuoka 411-8540,
Japan
| | - Misato Mochizuki
- Plant Genetics Laboratory, National Institute of Genetics,
Mishima, Shizuoka 411-8540,
Japan
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics,
Mishima, Shizuoka 411-8540,
Japan
- Department of Life Science, SOKENDAI (Graduate University for Advanced Studies),
Mishima, Shizuoka 411-8540,
Japan
| | - Ken-Ichi Nonomura
- Department of Life Science, SOKENDAI (Graduate University for Advanced Studies),
Mishima, Shizuoka 411-8540,
Japan
- Experimental Farm, National Institute of Genetics,
Mishima, Shizuoka 411-8540,
Japan
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Sotowa M, Ootsuka K, Kobayashi Y, Hao Y, Tanaka K, Ichitani K, Flowers JM, Purugganan MD, Nakamura I, Sato YI, Sato T, Crayn D, Simon B, Waters DLE, Henry RJ, Ishikawa R. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms. RICE (NEW YORK, N.Y.) 2013; 6:26. [PMID: 24280095 PMCID: PMC3874672 DOI: 10.1186/1939-8433-6-26] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/09/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice. RESULTS Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets. CONCLUSION Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon. One lineage is closely related to O. meridionalis and another to Asian O. rufipogon. The first was presumed to have evolved by divergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon, possibly arrived in Australia later.
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Affiliation(s)
- Masahiro Sotowa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kenta Ootsuka
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuu Kobayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yin Hao
- Science of Cryobiosystem, The United Graduate School of Agriculture Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Katsunori Tanaka
- Faculty of Humanities, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Katsuyuki Ichitani
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Jonathan M Flowers
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ikuo Nakamura
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 0271-8510, Japan
| | - Yo-Ichiro Sato
- Research Institute for Humanity and Nature, Kyoto 603-8047, Japan
| | - Tadashi Sato
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland 6811, Australia
| | - Bryan Simon
- Queensland Herbarium, Brisbane Botanic Gardens Mt Coot-tha, Brisbane, Queensland 4066, Australia
| | - Daniel LE Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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Banaticla-Hilario MCN, van den Berg RG, Hamilton NRS, McNally KL. Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon. Ecol Evol 2013; 3:3047-62. [PMID: 24101993 PMCID: PMC3790550 DOI: 10.1002/ece3.689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/17/2013] [Accepted: 06/23/2013] [Indexed: 11/11/2022] Open
Abstract
Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
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Affiliation(s)
- Maria Celeste N Banaticla-Hilario
- T.T. Chang Genetic Resources Center, International Rice Research Institute Los Baños, Laguna, Philippines ; Biosystematics Group, Wageningen University and Research Center Wageningen, The Netherlands
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Waters DLE, Nock CJ, Ishikawa R, Rice N, Henry RJ. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecol Evol 2012; 2:211-7. [PMID: 22408737 PMCID: PMC3297189 DOI: 10.1002/ece3.66] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/30/2011] [Accepted: 10/03/2011] [Indexed: 12/16/2022] Open
Abstract
Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.
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Shu Y, Li Y, Zhu Y, Zhu Z, Lv D, Bai X, Cai H, Ji W, Guo D. Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1-8. [PMID: 20162255 DOI: 10.1007/s00122-010-1285-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 01/24/2010] [Indexed: 05/04/2023]
Abstract
Introns often have a high probability of mutation as a result of DNA insertions and deletions (indels). In this study, 503 introns with exon-derived insertions were identified using a comprehensive search of the soybean genome. Of the 375 pairs of PCR primer sets designed for the loci in question, 161 primer sets amplified length polymorphism among nine soybean varieties and were identified as soybean gene-intron-driven functional sequence characterized amplified region (SCAR) markers. These SCAR markers are distributed among all 20 of the soybean chromosomes, and they developed from numerous genes involved in various physiological and biochemical processes that influence important agronomic traits of the soybean. The development of these novel gene-driven functional SCAR markers was fast and cost effective, and their use will facilitate molecular-assisted breeding of the soybean.
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Affiliation(s)
- Yongjun Shu
- College of Life Science, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
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Tsuchimoto S, Hirao Y, Ohtsubo E, Ohtsubo H. New SINE families from rice, OsSN, with poly(A) at the 3' ends. Genes Genet Syst 2008; 83:227-36. [PMID: 18670134 DOI: 10.1266/ggs.83.227] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A database search of the sequences flanking a member of rice retrotransposon RIRE7 revealed that a 298-bp sequence in the region downstream of the member is a repetitive sequence interspersed in the genome of Oryza sativa cv. Nipponbare. Most of the repetitive sequences were flanked by a direct repeat of a target-site sequence, about 14 bp in length. The consensus sequence, 293 bp in length, had no regions encoding any proteins but had sequence motifs of an internal promoter of RNA polymerase III. These indicate that the sequence is a retroposon SINE, designated OsSN1 (Oryza sativa SINE1). OsSN1 is a new rice SINE, because it has no homology with any of the three p-SINE families previously identified from rice, and because it has a stretch of A at the 3' end, unlike p-SINE and any other Gramineae SINEs which have a stretch of T at the 3' end. The Nipponbare genome was found to have many members related to OsSN1, forming two additional new SINE families (designated OsSN2 and OsSN3). OsSN2 and OsSN3 are highly homologous to the 3' and 5' regions of OsSN1, respectively. This suggests that OsSN1 has a mosaic structure, which is generated by sequence exchange (or shuffling) between ancestral OsSN2 and OsSN3. Despite the absence of homology in the 3' regions between OsSN1 (or OsSN2) and OsSN3, a sequence, 5'-TTCTC-3', is commonly present in the region preceding the A stretch at the 3' end. This sequence together with the A stretch and a stem-loop structure found in the region near the A stretch are assumed to be important for retroposition. OsSN members were present in strains of Oryza species, as were p-SINE members. Some of the members showed insertion polymorphism at the respective loci among the rice strains. p-SINE had such polymorphic members, which are useful for classification and phylogenetic analysis of various strains of Oryza species. The polymorphic members of OsSN were more frequently found than those of p-SINE, and therefore, such members are likely to be useful for extensive taxonomic and phylogenetic studies on various rice strains.
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Affiliation(s)
- Suguru Tsuchimoto
- Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo, Japan.
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Xu JH, Cheng C, Tsuchimoto S, Ohtsubo H, Ohtsubo E. Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs. Genes Genet Syst 2007; 82:217-29. [PMID: 17660692 DOI: 10.1266/ggs.82.217] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Oryza rufipogon, the progenitor of the cultivated rice species Oryza sativa, is known by its wide intraspecific variation. In this study, we performed phylogenetic analyses of O. rufipogon strains and their relationships to O. sativa strains by using 26 newly identified p-SINE1 members from O. rufipogon strains, in addition to 23 members previously identified from O. sativa strains. A total of 103 strains of O. rufipogon and O. sativa were examined for the presence and absence of each of the p-SINE1 members at respective loci by PCR with a pair of primers that hybridize to the regions flanking each p-SINE1 member. A phylogenetic tree constructed on the basis of the insertion polymorphism of p-SINE1 members showed that O. rufipogon and O. sativa strains are classified into three groups. The first group consisted of O. rufipogon perennial strains mostly from China and O. sativa ssp. japonica strains, which included javanica strains forming a distinct subgroup. The second group consisted of almost all the O. rufipogon annual strains, a few O. rufipogon perennial strains and O. sativa ssp. indica strains. These groupings, in addition to other results, support the previous notion that annual O. rufipogon originated in the O. rufipogon perennial population, and that O. sativa originated polyphyletically in the O. rufipogon populations. The third group consisted of the other perennial strains and intermediate-type strains of O. rufipogon, in which the intermediate-type strains are most closely related to a hypothetical ancestor with no p-SINE1 members at the respective loci and to those belonging to the other rice species with the AA genome. This suggests that O. rufipogon perennial strains are likely to have originated from the O. rufipogon intermediate-ecotype population.
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Affiliation(s)
- Jian-Hong Xu
- Institute of Molecular and Cellular Biosciences, the University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Deragon JM, Zhang X. Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol 2007; 55:949-56. [PMID: 17345676 DOI: 10.1080/10635150601047843] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Short interspersed elements (SINEs) are a class of dispersed mobile sequences that use RNA as an intermediate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their use as molecular makers to retrace phylogenetic relations among wild and cultivated Oryza and Brassica species. In Brassicaceae, further use of SINE markers is limited by our partial knowledge of endogenous SINE families (their origin and evolution histories) and by the absence of a clear classification. To solve this problem, phylogenetic relations among all known Brassicaceae SINEs were analyzed and a new classification, grouping SINEs in 15 different families, is proposed. The relative age and size of each Brassicaceae SINE family was evaluated and new phylogenetically supported subfamilies were described. We also present evidence suggesting that new potentially active SINEs recently emerged in Brassica oleracea from the shuffling of preexisting SINE portions. Finally, the comparative evolution history of SINE families present in Arabidopsis thaliana and Brassica oleracea revealed that SINEs were in general more active in the Brassica lineage. The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed.
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Affiliation(s)
- Jean-Marc Deragon
- CNRS UMR6547, GDR2157 Biomove, Université Blaise Pascal, 24 Avenue des Landais, 63177, Aubière, France.
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Miyabayashi T, Nonomura KI, Morishima H, Kurata N. Genome Size of Twenty Wild Species of Oryza Determined by Flow Cytometric and Chromosome Analyses. BREEDING SCIENCE 2007; 57:73-78. [PMID: 0 DOI: 10.1270/jsbbs.57.73] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
| | - Ken-Ichi Nonomura
- National Institute of Genetics
- Graduate University for Advanced Studies/Sokendai
| | | | - Nori Kurata
- National Institute of Genetics
- Graduate University for Advanced Studies/Sokendai
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Abstract
Mobile elements represent a unique and under-utilized set of tools for molecular ecologists. They are essentially homoplasy-free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.
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Affiliation(s)
- David A Ray
- Department of Biology, West Virginia University, 53 Campus Dr, Morgantown, WV 26506, USA.
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