A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers

We report herein the mapping of 115 PCR-based orthologous markers, including 110 conserved ortholog set or COSII markers, on the reference RFLP map of eggplant. The result permitted inference of a detailed syntenic relationship between the eggplant and tomato genomes. Further, the position of additional 522 COSII markers was inferred in the eggplant map via eggplant-tomato synteny, bringing the total number of markers in the eggplant genome to 869. Since divergence from their last common ancestor approximately 12 million years ago, the eggplant and tomato genomes have become differentiated by a minimum number of 24 inversions and 5 chromosomal translocations, as well as a number of single gene transpositions possibly triggered by transposable elements. Nevertheless, the two genomes share 37 conserved syntenic segments (CSSs) within which gene/marker order is well preserved. The high-resolution COSII synteny map described herein provides a platform for cross-reference of genetic and genomic information (including the tomato genome sequence) between eggplant and tomato and therefore will facilitate both applied and basic research in eggplant. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta crantz)

The ever increasing body of information on genomics and functional genomics from model plants, and new tools of comparative genomics, provide an opportunity to accelerate the development of molecular markers for increasing the efficiency of breeding of lesser studied crops, so-called “orphan crops.” Conserved ortholog set (COS) markers represent orthologous genes in widely divergent plant species, and are currently the principal tool of choice for comparative genomics. EST sequences of 3 drought tolerance related genes—chalcone synthase (CHS), dihydroflavonol-4-reductase (DHRF) and drought responsive element binding factor 1 (DREB-1) fromMusa sp—were used to identify cassava EST homologs that were then scanned against the Arabidopsis genome database to identify them as COS markers. The CHS and DHRF ESTs were demonstrated to be COS markers, while the DREB EST was shown to belong to a gene family. The three genes were evaluated as single strand conformation polymorphism—single nucleotide polymorphism (SSCP-SNP) markers in the parents of an F1 mapping population and subsequently in the progenies. The DHRF COS marker mapped to linkage group R of the female-derived map while the DREB-1 EST mapped at an end of the male-derived linkage group K. The CHS COS marker could not be mapped because it was not polymorphic in the parents of the mapping population. These new marker tools should accelerate the development of markers associated with genes controlling traits of agronomic interest via the candidate gene loci (CGL) QTL-mapping approach.     

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica

The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus‐type B. napus was derived from B. oleracea, while polima‐type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus‐type B. napus was closer to botrytis‐type than capitata‐type B. oleracea. The sub‐stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome.     

Identification,analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants

We have screened a large tomato EST database against the Arabidopsis genomic sequence and report here the identification of a set of 1025 genes (referred to as a conserved ortholog set, or COS markers) that are single or low copy in both genomes (as determined by computational screens and DNA gel blot hybridization) and that have remained relatively stable in sequence since the early radiation of dicotyledonous plants. These genes were annotated, and a large portion could be assigned to putative functional categories associated with basic metabolic processes, such as energy-generating processes and the biosynthesis and degradation of cellular building blocks. We further demonstrate, through computational screens (e.g., against a Medicago truncatula database) and direct hybridization on genomic DNA of diverse plant species, that these COS markers also are conserved in the genomes of other plant families. Finally, we show that this gene set can be used for comparative mapping studies between highly divergent genomes such as those of tomato and Arabidopsis. This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution.     

Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection

Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice–wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.     

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems critically rely on bona fide orthologs as input. While it is usually done using sequence similarity search, we recently proposed a new combinatorial approach that combines sequence similarity and genome rearrangement. This paper continues the development of the approach and unites genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs. Following this approach, we have implemented a high-throughput system for ortholog assignment on a genome scale, called MSOAR, and applied it to human and mouse genomes. As the result will show, MSOAR is able to find 99 more true orthologs than the INPARANOID program did. In comparison to the iterated exemplar algorithm on simulated data, MSOAR performed favorably in terms of assignment accuracy. We also validated our predicted main ortholog pairs between human and mouse using public ortholog assignment datasets, synteny information, and gene function classification. These test results indicate that our approach is very promising for genome-wide ortholog assignment. Supplemental material and MSOAR program are available at http://msoar.cs.ucr.edu.     

Development of conserved ortholog set markers linked to the restorer gene Rfp1 in rye

Restoration of male fertility is a prerequisite for hybrid rye breeding and currently the most straightforward approach to minimize ergot infection in hybrid rye varieties. Molecular markers are important tools for the efficient introgression and management of restorer genes like Rfp1 originating from unadapted genetic resources. Furthermore, closely linked markers flanking Rfp1 are indispensible for identifying and selecting individuals with haplotypes showing recombination between Rfp1 and other gene(s) that reside in close proximity and have a negative influence on yield. We identified orthologous gene sets in rice, Brachypodium, and Sorghum and used these gene models as templates to establish conserved ortholog set (COS) markers for the restorer gene Rfp1 on the long arm of rye chromosome 4R. The novel co-dominant markers delimit Rfp1 within a 0.7-cM interval and allow prediction of Rfp1 genotypes with a precision not feasible before. The COS markers enabled an alignment of the improved genetic map of rye chromosome 4R with wheat and barley maps and allowed identification of regions orthologous to Rfp1 in wheat and barley on the short arms of chromosomes 6D and 6H, respectively. Results obtained in this study revealed that micro-collinearity around the Rfp1 locus in rye is affected by rearrangements relative to other grass genomes. The impact of the novel COS markers for practical hybrid rye breeding is discussed.     

Rosaceae conserved orthologous set (RosCOS) markers as a tool to assess genome synteny between Malus and Fragaria

Intertribal comparisons of genome synteny between phylogenetically distant genera in Rosaceae, such as Malus (apple) and Fragaria (strawberry), have previously been hampered by a lack of transferable markers that can be used as anchor points between genetic maps. The availability of conserved orthologous set (COS) markers recently developed for this family, coupled with the release of the Malus?×?domestica and Fragaria vesca draft genome sequences, provide new tools for comprehensive pairwise comparisons. The genetic mapping of 56 Rosaceae COS (RosCOS) markers revealed 21 regions of genomic synteny between apple and strawberry. Information concerning the location of RosCOS markers on 15 of 17 apple linkage groups (LG) and all seven LG of strawberry was used to assess the ancestral relationships between the two genera. Four differences in orientation of ancestral chromosome fragments on extant LG were identified in comparison with previous studies, as well as two potential insertions, two potential translocations, and two potential inversions. The set of orthologous markers developed for use in genetic mapping in Rosaceae, in combination with high-throughput analysis, will allow the exploration of chromosome evolution and refinement of ancestral relationships within the family, orientation, and anchoring of genome sequences as they become available and provide resources to develop markers for nonsequenced genomes within the family.     

Comparative mitochondrial genome analysis of Neodontobutis hainanensis and Perccottus glenii reveals conserved genome organization and phylogeny

To investigate the molecular evolution of mitochondrial genomes among the family Odontobutidae, the complete mitochondrial genomes of Neodontobutis hainanensis and Perccottus glenii were sequenced and compared with seven odontobutids species. The genome organization, base composition, codon usage, and gene arrangement of N. hainanensis exhibited high similarity to P. glenii compared to those of other Odontobutidae species. Reconstructed phylogenetic analyses of Odontobutidae strongly supported that Neodontobutis and Perccottus formed a unifying group sister to Odontobutis. Our molecular dating time revealed that the two species diverged approximately 21.7 Ma during Miocene, later than that of Odontobutis. Selection analyses showed stronger selective constraints in mitochondrial genes for P. glenii. However, two positively selected sites in NADH4 and NADH6 genes were respectively detected in N. hainanensis and P. glenii, indicating that they might evolve different metabolic performance in response to the contrasting environments.     

Resistance to Leptosphaeria maculans is conserved in a specific region of the Brassica B genome

 Offspring from asymmetric hybrids between Brassica napus and the three B-genome species Brassica nigra, Brassica juncea and Brassica carinata were analysed for the presence of B-genome markers and resistance to the fungus Leptosphaeria maculans, the causal agent of blackleg disease. Twenty five plants from each species combination were analysed in the first backcross (BC₁) generation, 30 plants in BC₂ and 60 plants in BC₃. The plants were analysed by 46 RFLP markers detecting 85 loci dispersed throughout the B. nigra genome. The plants with additional B. carinata DNA had a decrease in the presence of RFLP markers ranging from 59% in BC₁ to 36% in BC₂ and down to 11% in BC₃. Similar results were obtained in the lines with additional DNA from B. juncea where the 60% presence of RFLP markers in BC₁ was reduced to 33% in BC₂ and to 10% in BC₃. However presence of the markers were significantly lower in the B. nigra-derived material where BC₁ had 46%, BC₂ 25% and BC₃ 8%. Since at least two loci could be detected on each end of the eight linkage groups of the B genome, the degree of symmetry was estimated. After one back-cross between 0.5 and 1.25% intact chromosomes were retained, whereas in BC₂ this frequency was 0.21% for all three B-genome donor species. The maintenance of half-chromosomes ranged from 2.63% to 5.38% in BC₁ and between 0.73% and 1.15% in BC₂. No chromosome arms were found in any of the BC₃ plants. In total, four co-segregating markers for cotyledon and adult-leaf resistance to L. maculans were found which detected six loci located on linkage groups 2, 5 and 8. When the results from the three donor species were compared, one triplicate region in the B genome had preserved the resistance loci in all three species. Received: 19 January 1999 / Accepted: 30 January 1999     

Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana

Over 1000 genetically linked RFLP loci in Brassica napus were mapped to homologous positions in the Arabidopsis genome on the basis of sequence similarity. Blocks of genetically linked loci in B. napus frequently corresponded to physically linked markers in Arabidopsis. This comparative analysis allowed the identification of a minimum of 21 conserved genomic units within the Arabidopsis genome, which can be duplicated and rearranged to generate the present-day B. napus genome. The conserved regions extended over lengths as great as 50 cM in the B. napus genetic map, equivalent to approximately 9 Mb of contiguous sequence in the Arabidopsis genome. There was also evidence for conservation of chromosome landmarks, particularly centromeric regions, between the two species. The observed segmental structure of the Brassica genome strongly suggests that the extant Brassica diploid species evolved from a hexaploid ancestor. The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids.     

The use of image analysis to monitor the germination of seeds of broccoli (Brassica oleracea) and radish (Raphanus sativus)

To study broccoli and radish seed germination under different temperature regimes the germination test has been used to assess final germination percentage, start and rate. This method has been integrated with a computer‐aided image analysis test which is more accurate in monitoring the extent of imbibition phases through the assessment of seed area increase and timing of radicle emergence detected on single seeds. In addition, seed area increase has been used also to establish a close relationship with radicle elongation rate in the time range when ‘visible germination’ is scored by a classical germination test. The results suggest that this image analysis parameter may be considered as a reliable seed imbibition marker to integrate the germination parameters obtained by a germination test.     

芸薹属多倍体植物基因组进化的RAPD分析

多倍化是促进高等植物发生进化的重要力量。为了更清楚地了解多倍体在形成之后其基因组是如何进化的,利用38个随机引物对芸薹属Brassica L.禹氏三角（U’Triangle）中的多倍体物种及其祖先二倍体物种进行了研究。根据扩增出的273条带计算了遗传距离,并用UPGMA法进行了聚类分析。结果发现,二倍体物种B.campestris（AA）与B.oleracea（CC）的亲缘关系比与B.nigra（BB）的要近;异源多倍体B.napus（AACC）比起其二倍体祖先之一B.campestris（AA）与另一个     

RAPD analysis on the genome evolution of polyploids in Brassica

Polyploidy has played an important role in the evolution of higher plants.In order to understand how polyploid genomes evolve after their formation,the Brassica triangle was used to study genomic evolution after the formation of polyploids.Random amplifie     

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC₂DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). QTLs were detected as a marker main effect and/or a marker × environment interaction effect (M × E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs the M × E interaction effect, and at 21 QTLs both the effects were significant. The majority of the M × E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m² and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.     

Isolation and expression analysis of a tobacco AINTEGUMENTA ortholog (NtANTL)

The Arabidopsis AINTEGUMENTA (ANT) protein is essential for proper ovule development, but functions in cell proliferation and organ growth throughout the plant. Here we report the isolation of a full-length cDNA clone from tobacco (Nicotiana tabacum L.) that encodes a protein with high similarity to ANT and is preferentially expressed in the pistil. In situ hybridization analysis on the tobacco ovary shows that the expression pattern of the corresponding gene is different from that of ANT in Arabidopsis.     

基于蓝藻全基因组原始数据的转座元件挖掘及组成分析

二代测序技术及全基因组多样性比较是现代生物学及信息科学研究的热点,对基因组中转座元件(Transposable element)的分析已成为基因组比较分析的重要组成部分。目前对于转座元件的种类、数量和组成的挖掘和分析一般是基于完全拼接后的全基因组序列,对在此之前的海量短片段序列后期处理及拼接仍是目前基因组研究的盲点,以转座元件为主的重复序列在拼接过程中也存在着不可避免的拼接误差或丢失,给转座元件系统的分析带来不确定。文章旨在建立一套分析流程,对铜绿微囊藻NIES 843全基因组构建的罗氏(Roche)公司454测序随机模拟原始数据集的转座元件(主要类型为插入序列:Insert sequence,IS)组成进行分析,结果表明,采用对核酸探针扫描后备选序列分成3组,并分设氨基酸检测阈值的方案分析得到的结果较为可靠,结果显示铜绿微囊藻NIES843的蓝藻转座元件占基因组比例的10.38%,归属于14个IS家族,66个IS亚家族。与之前基于完整拼接基因组数据的两套不同分析流程得到的结果相比,在丰度及家族/亚家族组成上无显著差异,在转座元件序列水平上也显示了高比例的相似性序列重叠,证实了本研究流程在基于高通量测序原始数据的转座元件分析方面具可靠性及实用性。