AA Genome Research Articles

Ortholog Alleles at Xa3/Xa26 Locus Confer Conserved Race-Specific Resistance against Xanthomonas oryzae in Rice

The rice disease resistance (R) gene Xa3/Xa26 (having also been named Xa3 and Xa26) against Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight disease, belongs to a multiple gene family clustered in chromosome 11 and is from an AA genome rice cultivar (Oryza sativa L.). This family encodes leucine-rich repeat (LRR) receptor kinase-type proteins. Here, we show that the orthologs (alleles) of Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3, from wild Oryza species O. officinalis (CC genome) and O. minuta (BBCC genome), respectively, were also R genes against Xoo. Xa3/Xa26-2 and Xa3/Xa26-3 conferred resistance to 16 of the 18 Xoo strains examined. Comparative sequence analysis of the Xa3/Xa26 families in the two wild Oryza species showed that Xa3/Xa26-3 appeared to have originated from the CC genome of O. minuta. The predicted proteins encoded by Xa3/Xa26, Xa3/Xa26-2, and Xa3/Xa26-3 share 91–99% sequence identity and 94–99% sequence similarity. Transgenic plants carrying a single copy of Xa3/Xa26, Xa3/Xa26-2, or Xa3/Xa26-3, in the same genetic background, showed a similar resistance spectrum to a set of Xoo strains, although plants carrying Xa3/Xa26-2 or Xa3/Xa26-3 showed lower resistance levels than the plants carrying Xa3/Xa26. These results suggest that the Xa3/Xa26 locus predates the speciation of A and C genome, which is approximately 7.5 million years ago. Thus, the resistance specificity of this locus has been conserved for a long time.

Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.)

We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.

Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

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.

Cloning and molecular characterization of TaAGO1, a member of argonaute gene family in wheat (Triticum aestivum L.)

Argonaute (AGO) proteins play important roles in RNA silencing processes through formation of complexes with the mature microRNAs. In this study, a wheat AGO gene referred to TaAGO1, which shares high similarities to AtAGO1 in Arabidopsis and OsAGO1 in rice, was characterized. As a cDNA full length of 3747 bp, TaAGO1 encodes a 1099-aa polypeptide with a molecular weight of 122 kD and an isoelectric point (pI) of 9.52. Subcellular prediction analysis suggests that TaAGO1 is to target onto the cytoplasm after endoplasmic reticulum (ER) sorted. Similar to AtAGO1 and OsAGO1, TaAGO1 contains PIWI and DDH, two conserved domains in AGOs. Phylogenetic analysis indicated that TaAGO1 was possibly derived from different progenitors with its homologous across diverse plant species. The transcripts of TaAGO1 were significantly regulated by the stresses of phosphorus deprivation and dehydration, and exogenous treatment of abscisic acid (ABA), suggesting that this wheat AGO member also exerts roles on mediating above signaling transductions. Southern blotting analysis revealed that genome AA, SS, and DD, three diploids composing of the hexaploid wheat, all harbored two copies of TaAGO1. Down-regulation of TaAGO1 in wheat led to conspicuously phenotypic alterations of the young plantlets, with a variety of abnormal growth features. Taking the results in this study together, it was implicated that TaAGO1 exists as a subset of copies in wheat and plays critical roles on silencing of appropriate target genes via regulation of TaAGO1-MiRNAs complex formation. Key words : Wheat (Triticum aestivum L.), argonaute (AGO) gene 1, cloning, molecular characterization, antisense expression.

Analysis of ESTs from a Normalized cDNA Library of the Rhizome Tip of Oryza longistaminata

Oryza longistaminata, a perennial wild rice species with an AA genome, is characterized by the presence of rhizomatous stems. The rhizomatous trait in rice was previously shown to be quantitatively controlled by many genes, but the molecular mechanism related to rhizome development is still unknown. In the present study, expressed sequence tags (ESTs) generated from rhizome tips of O. longistaminata were collected and analyzed. A total of 10,283 complimentary deoxyribunucleic acid clones were randomly sequenced, which generated 10,136 raw sequences, and finally, 4,419 unisequences with diverse functional categories were generated. These unisequences were mapped onto the Oryza sativa genome, which revealed that 4,285 (96.97%) and 4,151 (93.94%) of the unisequences were alignable to the japonica and indica genomic sequences, respectively, with >80% sequence identity. Additionally, 41 unisequences showed four typical types of alternative splicing patterns. More than 600 simple sequence repeats were identified in these unisequences. A subset of unisequences were physically colocalized onto rhizome-related quantitative trait locus intervals in rice and sorghum, and one gene, OLRR1, was further confirmed to be enriched in the rhizome tip and young leaf by real-time polymerase chain reaction and in situ hybridization. Unisequences reported in this study provide valuable data for molecular dissection of the rhizomatous growth habit in O. longistaminata.

In vitro induction of tetraploid plants from callus cultures of diploid bananas (Musa acuminata, AA group) ‘Kluai Leb Mu Nang’ and ‘Kluai Sa’

Tetraploid plants were induced successfully from diploid bananas Musa acuminata (AA genome) ‘Kluai Leb Mu Nang’ and ‘Kluai Sa’ (2n = 2x = 22) with in vitro oryzalin treatment. Calluses from in vitro-grown shoot tips of both cultivars were treated with oryzalin at concentrations of 1.5 or 3 mg l−1 for 24, 48 and 72 h, respectively. The oryzalin treatments produced tetraploids at a frequency of 15.6% in ‘Kluai Leb Mu Nang’ and 16.7% in ‘Kluai Sa’ as detected by flow cytometry. Chromosome counting showed that the tetraploid plant chromosome number was (2n = 4x = 44). The selected tetraploid plants were transplanted in the field and variations in the morphological characteristic of leaf shape and fruit bunch compared to normal diploid plants were found under the same growing condition even after 3 years of cultivation.

Genetic Variation and Evolution of the Pi9 Blast Resistance Locus in the AA Genome Oryza Species

The rice nucleotide-binding site–leucine-rich repeat (NBS-LRR)-encoding resistance (R) gene Pi9 confers broad-spectrum resistance to the fungal pathogen Magnaporthe oryzae. The Pi9 locus comprises many NBS-LRR-like genes and is an ancient locus that is highly conserved in cultivated and wild rice species. To understand the genetic variation and molecular evolutionary mechanism of the Pi9 alleles in different rice species, we studied five AA genome Oryza species including two cultivated rice species (Oryza sativa and Oryza glaberrima) and three wild rice species (Oryza nivara, Oryza rufipogon, and Oryza barthii). A 2.9-kb fragment spanning the NBS-LRR core region of the Pi9 gene was amplified and sequenced from 40 accessions. Sequence comparison revealed that the Pi9 alleles had an intermediate-diversified nucleotide polymorphism among the AA genome Oryza species. Sequence variations were more abundant in the LRR region than in the NBS region, indicating that the LRR region has played a more important role for the evolution of the Pi9 alleles. Furthermore, positive selection was found to be the main force promoting the divergence of the Pi9 alleles, especially in the LRR region. Our results reveal the characteristics and evolutionary dynamics of the Pi9 alleles among the two cultivated and three wild rice species.

Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters

Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica 'Nipponbare' promoters with retrotransposons conserved in Oryza sativa subsp. indica '93-11' and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detail, the evolutionary dynamics of five retrotransposons in the promoter regions of 95 rice genotypes. Our data suggest that four of five insertions (Rp2-Rp5) occurred in the ancestor of AA genome, while the other insertion (Rp1) predates the ancestral divergence of Oryza officinalis (CC genome). Four retrotransposons (Rp2-Rp5) were present in 52% (Rp2), 29% (Rp3), 53% (Rp4), and 43% (Rp5) of the rice genotypes with AA genome type, and the fifth retrotransposon (Rp1) was present in 95% of the rice genotypes with AA, BBCC, or CC genome types. Furthermore, most of these retrotransposons were found to evolve slower than flanking promoter regions, suggesting a role in promoter function for regulating downstream genes.

Isolation and characterization of genome-specific markers in Oryza species with the BB genome

Wild species of rice with many valuable agronomic traits are an important genetic resource for improving cultivated rice by wide hybridization. Genome- or chromosome-specific markers are useful for monitoring genome introgression and for identifying genome components. From 47 random amplified polymorphic DNAs (RAPDs) of nine Oryza species, three bands ( Ogla225, Opun225, and Opun246) were found to be genome specific with distinct sizes. Their specificities were further characterized by Southern hybridization, sequence analysis, and fluorescent in situ hybridization (FISH). Ogla225 is specifically amplified from the AA genome but homologous sequences were conserved among Oryza species. Opun225 occurs at a low copy number although is specifically amplified from Oryza punctata. There are estimated 2000–3300 repeats of Opun246 in each haploid genome of Oryza species with the BB or BBCC genome. Clusters of Opun246 repeats were detected at heterochromatic regions on almost all chromosomes of the BB genomes by FISH. Opun246 may be a useful marker for monitoring the introgression of BB genome or for identifying the conserved components of BB genome in genetic resource. The results from this study and our previous study both indicate that numerous unique repeats play role in the differentiation of the BB genome from other Oryza genomes.

Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis

BackgroundExtensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.ResultsWe previously identified a hotspot for genic rearrangement and transposon accumulation in the Orp region of Asian rice (Oryza sativa, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (O. nivara, AA) of Asian rice and African rice (O. glaberrima) using the BB genome Oryza species (O. punctata) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that Orp region was primarily and recently expanded in the Asian rice species O. sativa and O. nivara. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either O. nivara or O. sativa regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.ConclusionsThe LTR-retrotransposon insertion hotspot in the Orp region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of O. sativa germplasm.

Plasticity of Tiller Dynamics in Wild RiceOryza rufipogonGriff.: A Strategy for Resilience in Suboptimal Environments

Rice cultivation in tropical Asia is susceptible to drought and flood and the need is high for stress resistant genes. Wild riceOryza rufipogonGriff., grows in close sympatric association with cultivated rice in various habitats across the globe and possesses traits for survival under challenging environments. The species adapts according to the level of soil moisture available and modifies phenology, biomass production and grain yield. Variation in tiller dynamics of the species between contrasting environments gives an estimate of the adaptation. The species possesses AA genome, which permits genetic compatibility for cross breeding with cultivated rice. Utility of the species as possible repository of stress resistant genes is evaluated in this review by examining variation in assimilate partitioning between different classes of tillers of ecotypes growing across a gradation of habitats against background knowledge available for cultivated rice. Models have been constructed to explain mechanisms of tillering and tiller dynamics, and reveal the genotypic permissibility for resilience in sub-optimal environments. It is concluded that environmentally cued alteration in assimilate production and partitioning mask genetic potential for tiller production and survival. Tiller number in excess of resource capacity is corrected by senescence of late-tillers possibly through an ethylene-mediated signal.

Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing.

BackgroundOryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic and abiotic stress, QTLs with agronomically important traits and high ability to use nitrogen efficiently (NUE). However, only limited genomic or transcriptomic data of O. longistaminata are currently available.ResultsIn this study we present the first comprehensive characterization of the O. longistaminata root transcriptome using 454 pyrosequencing. One sequencing run using a normalized cDNA library from O. longistaminata roots adapted to low N conditions generated 337,830 reads, which assembled into 41,189 contigs and 30,178 singletons. By similarity search against protein databases, putative functions were assigned to over 34,510 uni-ESTs. Comparison with ESTs derived from cultivated rice collections revealed expressed genes across different plant species, however 16.7% of the O. longistaminata ESTs had not been detected as expressed in O. sativa. Additionally, 15.7% had no significant similarity to known sequences. RT-PCR and Southern blot analyses confirmed the expression of selected novel transcripts in O. longistaminata.ConclusionOur results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates sufficient genomic information for adequate de novo assembly of a large number of transcripts in a wild rice species, O. longistaminata. The generated sequence data are publicly available and will facilitate gene discovery in O. longistaminata and rice functional genomic studies. The large number of abundant of novel ESTs suggests different metabolic activity in O. longistaminata roots in comparison to O. sativa roots.

ANALYSIS OF GENETIC DIVERSITY AND RELATIONSHIPS IN EAST AFRICAN 'APPLE BANANA' (AAB GENOME) AND 'MURARU' (AA GENOME) DESSERT BANANAS USING MICROSATELLITE MARKERS

ISHS IV International Symposium on Banana: International Conference on Banana and Plantain in Africa: Harnessing International Partnerships to Increase Research Impact ANALYSIS OF GENETIC DIVERSITY AND RELATIONSHIPS IN EAST AFRICAN 'APPLE BANANA' (AAB GENOME) AND 'MURARU' (AA GENOME) DESSERT BANANAS USING MICROSATELLITE MARKERS

EFFECT OF RIPENING ON TOTAL POLYPHENOL CONTENTS OF MUSA HYBRIDS AND CULTIVARS GROWN IN CAMEROON

Bananas and plantains (#Musa# spp.) are staple food in the southern provinces of Cameroon and surrounding countries and play a significant role in the population's diet. To enhance the use of some cultivars as food, and the creation and selection of new Musa hybrids in the Centre Africain de Recherche sur Bananiers et Plantains (CARBAP), the total polyphenol contents were determined at three ripening stages in 32 Musa cultivars and hybrids from the CARBAP germplasm collection. Total polyphenol compounds of dried pulverized Musa pulp were determined at 760 nm using an optimized Folin-Ciocalteu method. Significant differences among Musa cultivars were found. During the ripening process, the concentrations of phenolic compounds vary significantly (P=0.05). High total polyphenol contents (>75 ?g gallic acid equivalents/100 g dry matter) of the unripe pulp were detected in 'CRBP755' (AAAB genome), 'Kelong Mekintu' (AAB genome), 'Red Yade' (AAB genome), 'Popoulou CMR' (AAB genome), 'Topala' (AAB genome), 'Foconah' (AAB genome), 'Gros Michel' (AAA genome), 'IDN110' (AA genome), 'Pisang Jari Buaya' (AA genome), 'Pisang Mas' (AA genome) and 'Yangambi Km5' (AAA genome). These cultivars could be used more in Cameroon and even in the subregion. Their use could also be enhanced in #Musa# breeding programs in CARBAP and other research institutes. (Resume d'auteur)

MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF MUSA GERMPLASM IN SRI LANKA AND SELECTION OF SUPERIOR GENOTYPES

ISHS IV International Symposium on Banana: International Conference on Banana and Plantain in Africa: Harnessing International Partnerships to Increase Research Impact MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF MUSA GERMPLASM IN SRI LANKA AND SELECTION OF SUPERIOR GENOTYPES

EFFECT OF MODE OF RIPENING ON ETHYLENE BIOSYNTHESIS DURING RIPENING OF DIPLOID BANANA (MUSA SPP.) FRUIT

Ripening is the main physiological process affecting banana (Musa spp.) fruit quality traits. The progress of banana ripening process differs for fruit ripened on the plant versus green harvested bunches and depends on the treatment of the fruit after harvest. We investigated the effect of the mode of ripening on ethylene biosynthesis of 'IDN 110' (Musa acuminata, AA genome) banana fruit ripened (a) in planta (On-Plant); (b) ex planta in air (Air-Fruit); or (c) after acetylene treatment (Ace-Fruit). The levels of ethylene production of the whole fruit and, those of 1-aminocyclopropane-1-carboxylic acid (ACC) in pulp, and ACC oxidase (MA-ACO1 and MA-ACO2) and ACC synthase (MA-ACS1) mRNA in both peel and pulp tissues were examined. From harvesting at mature-green stage, the ripening speed of fruit was not correlated with ethylene production. Ace-Fruit took 10 days to reach overripe stage with a maximum of 22.6 μl kg -1 h -1 of ethylene production, whereas Air-Fruit and On-Plant fruit took 27 and 33 days to reach overripe stage, respectively, and produced 11.5 and 29.6 μl kg -1 h -1 of ethylene, respectively. During ripening, ACC accumulated differentially; except for On-Plant fruit, ACC level increased during ripening and concomitantly with ethylene production and MA-ACS1 mRNA level. Whatever the mode of ripening, the level of MA-ACO1 mRNA was 100-fold higher than that of MA-ACO2. The mRNA level of MA-ACO1 and MA-ACO2 were accumulated sequentially during fruit development and ripening. MA-ACO1 gene was transiently induced between mature green and ripe stages while that of MA-ACO2 increased mainly at the overripe stage. The pattern of MA-AC02 gene expression was correlated with that of ethylene production whatever the mode of ripening while this correlation was observed with MA-ACO1 only On-Plant fruit. These results suggest that: (a) the level of ripening-ethylene production of the whole fruit is not the sole factor controlling the speed of fruit ripening in planta; (b) this level is regulated at the downstream step of ACC biosynthesis mediated by the MA-ACS1 gene; and (c) the product of MA-ACO2 might be involved in this regulation in pulp tissue. These findings are also discussed in regard with improvement of banana quality traits project throughout breeding programs.

Anatomy and morphology character of five Indonesian banana cultivars (Musa spp.) of different ploidy level

Sumardi I, Wulandari M (2011) Anatomy and morphology character of five Indonesian banana cultivars (Musa spp.) of different ploidy level. Biodiversitas 12: 167-175. In Indonesia there are many cultivars of banana, and some of them produce edible fruits. Beside their morphology, the character which necessary as a tool for classification is anatomical character. The aim of this research were to describe the anatomical character and morphology of fives Indonesian banana cultivars based on their level of ploidy. The cultivars were collected from Banana Germplasm Plantation, Yogyakarta District, Indonesia. The samples of roots, rhizome, and leaf were collected from five banana cultivars i.e.: Musa acuminata cv Penjalin, M. balbisiana cv Kluthuk warangan, M. acuminata cv Ambon warangan, M. paradisiaca cv Raja nangka, and M. paradisiaca cv Kluthuk susu. For anatomy observation samples were prepared using paraffin method, stained with 1% safranin in 70% ethanol. To observe the structure of stomata and epidermis surface, slide were prepared using modification of whole mount method. Slides were observed using Olympus BHB microscope completed with Olympus camera BM-10A. Stem and leaf morphology character of diploid level (AA and BB genome) is different with triploid level (AAA, AAB, and ABB genome). Anatomy and morphology character of root and rhizome of banana in diploid level (AA and BB genome) and triploid level (AAA, AAB, and ABB genome) is quite similar. Distribution of stomata is found in leaf and pseudostem. Stomata is found in adaxial and abaxial epidermis layer. The size of guard cells in triploid cultivars was longer than that diploid cultivars. The root composed of epidermis layer, cortex and cylinder vascular of five cultivar’s root show anomalous structure. Rhizome consist of peripheric and centre zone. Anatomically, this was no differences in the rhizome structure among five banana cultivars. The row of vascular bundles acts as demarcation area between peripheric and central zone. In the cultivar with BB genome (diploid) and ABB genome (triploid) the row of vascular bundle was not found. The differences of leaf anatomy were base on: size and number of stomata distribution, number of subsidiary cells, number of hypodermal layers, structure and number of parenchyma palisade, size of airspace in petiole and mesophyll and the vascular bundle structure.Key words: anatomical character, morphology, banana cultivar, ploidy level

Genetical and molecular analysis reveals a cooperating relationship between cytoplasmic male sterility- and fertility restoration-related genes in Oryza species

Although the characterization of genes associated with cytoplasmic male sterility (CMS) and fertility restoration (Rf) has been well documented, the evolutionary relationship between nuclear Rf and CMS factors in mitochondria in Oryza species is still less understood. Here, 41 accessions from 7 Oryza species with AA genome were employed for analyzing the evolutionary relationships between the CMS factors and Rf candidates on chromosome 10. The phylogenetic tree based on restriction fragment length polymorphism patterns of CMS-associated mitochondrial genes showed that these 41 Oryza accessions fell into 3 distinct groups. Another phylogenetic tree based on PCR profiles of the nuclear Rf candidates on chromosome 10 was also established, and three groups were distinctively grouped. The accessions in each subgroup/group of the two phylogenetic trees are well parallel to each other. Furthermore, the 41 investigated accessions were test-crossed with Honglian (gametophytic type) and Wild-abortive (sporophytic type) CMS, and 5 groups were classified according to their restoring ability. The accessions in the same subgroup of the two phylogenetic trees shared similar fertility restoring pattern. Therefore, we conclude that the CMS-associated mitotypes are compatible to the Rf candidate-related nucleotypes, CMS and Rf have a parallel evolutionary relation in the Oryza species.

배추 유전체 염기서열 해독 전략과 현황

Brassica rapa is considered an ideal candidate to act as a reference species for Brassica genomic studies. Among the three basic Brassica species, B. rapa (AA genome) has the smallest genome (529 Mbp), compared to B. nigra (BB genome, 632 Mbp) and B. oleracea (CC genome, 696 Mbp). There is also a large collection of available cultivars of B. rapa, as well as a broad array of B. rapa genomic resources available. Under international consensus, various genomic studies on B. rapa have been conducted, including the construction of a physical map based on 22.5X genome coverage, end sequencing of 146,000 BACs, sequencing of >150,000 expressed sequence tags, and successful phase 2 shotgun sequencing of 589 euchromatic region-tiling BACs based on comparative positioning with the Arabidopsis genome. These sequenced BACs mapped onto the B. rapa genome provide beginning points for genome sequencing of each chromosome. Applying this strategy, all of the 10 chromosomes of B. rapa have been assigned to the sequencing centers in seven countries, Korea, UK, China, India, Canada, Australia, and Japan. The two longest chromosomes, A3 and A9, have been sequenced except for several gaps, by NAAS in Korea. Meanwhile a China group, including IVF and BGI, performed whole genome sequencing with Illumina system. These Sanger and NGS sequence data will be integrated to assemble a draft sequence of B. rapa. The imminent B. rapa genome sequence offers novel insights into the organization and evolution of the Brassica genome. In parallel, the transfer of knowledge from B. rapa to other Brassica crops would be expected.

Ac/Ds 삽입 변이체를 이용한 벼 유전자 기능 연구

Rice is the staple food of more than 50% of the worlds population. Cultivated rice has the AA genome (diploid, 2n=24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos (Hirochika. 1997) have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems has been utilized as main insertional mutagens in rice. A main drawback of a T-DNA scheme is that Agrobacteria-mediated transformation in rice requires extensive facilities, time, and labor. In contrast, the Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. Revertants can be utilized to correlate phenotype with genotype. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertionally mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been launched by collaborative works from 2001 in Korea.