Hot off the presses! Mar 01 The Plant Genome

The Mar 01 issue of the The Plant Genome is now up on Pubget (About The Plant Genome): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• "The What if Challenge"
  - The Plant Genome 2(1):1-1 (2009)
  
• The Potential of Ultrahigh Throughput Genomic Technologies in Crop Improvement
  - The Plant Genome 2(1):2-2 (2009)
  
• "What if" Challenge of the Rice Biology in the "Next-Generation" Sequencing Era
  - The Plant Genome 2(1):3-4 (2009)
  
• A Genome May Reduce Your Carbon Footprint
  - The Plant Genome 2(1):5-8 (2009)
  
• Marker Imputation in Barley Association Studies
  - The Plant Genome 2(1):11-22 (2009)
  Association mapping requires high marker density, potentially leading to many missing marker data and to high genotyping costs. In human genetics, methods exist to impute missing marker data and whole markers typed in a reference panel but not in the experimental dataset. We sought to determine if an imputation method developed for human data would function effectively in a barley ( L.) panel. The panel contained 98 lines, 2517 single nucleotide polymorphism (SNP) markers, and 716 Diversity Arrays Technology (DArT) markers. Averaged over markers, masked scores were correctly imputed 97.1% of the time. We chose 610 and 273 tag markers in two- and six-row barley subpopulations, respectively. Despite this low number of tags, imputation accuracy was such that for about 80% of non-tag markers, the prediction between imputed and true scores was 0.8 or higher. When DArT markers were used as tags, SNP markers were imputed with similar accuracy, suggesting that the method can ! convert association information from one marker system (e.g., DArT) to another marker system (e.g., SNP). We believe marker imputation methods will have an important future in association studies as a component of tagging methods and in reducing problems due to missing data.
• Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple
  - The Plant Genome 2(1):23-38 (2009)
  A total of 34 apple ( × Borkh.) cDNA libraries were constructed from root, leaf, bud, shoot, flower, and fruit tissues, at various developmental stages and/or under biotic or abiotic stress conditions, and of several genotypes. From these libraries, 190,425 clones were partially sequenced from the 5′ end and 42,619 clones were sequenced from the 3′ end, and a total of 182,241 high-quality expressed sequence tags (ESTs) were obtained. These coalesced into 23,442 tentative contigs and 9843 singletons, for a total of 33,825 apple unigenes. Functional annotation of this unigene set revealed an even distribution of apple sequences among the three main gene ontology categories. Of ∼33,000 apple unigenes, 8437 (25%) had no detectable homologs ( >0.1) in the genome. When the entire apple unigene set was compared with the entire citrus [ (L.) Osbeck] unigene set and the poplar ( Torr. & Gray) predicted proteome, both members of the core eudicot and rosids clade, 13,521! of apple unigenes matched one or more sequences in citrus, while 25,817 had counterparts in the poplar protein database. Apple––citrus–poplar comparisons revealed closer evolutionary relationships between apple and poplar than with the other two species. Genes involved in basic metabolic pathways appear to be largely conserved among apple, citrus, poplar, and .
• A Modified TILLING Method for Wheat Breeding
  - The Plant Genome 2(1):39-47 (2009)
  The large genome and polyploidy of wheat ( L.) makes it difficult to identify desirable genetic changes based on phenotypic screening due to gene redundancy. Forward genetics is, therefore, more difficult in wheat than in diploid plants. A modified TILLING (Targeting Induced Local Lesions IN Genomes) method including the harvest of five heads per M plant, storage of M seeds, using unlabeled primers and agarose gels for mutation detection, and crossing of useful mutants for desired grain quality was explored in this report. A soft wheat cultivar, QAL2000, and a hard wheat cultivar, Ventura, were mutagenized with ethyl methanesulfonate (EMS). Screening of the genes and in 2348 EMS-treated M plants allowed identification of 121 mutants, including silent, missense, and knockout (truncation) mutations. A complete waxy wheat was successfully bred in 18 mo by crossing two truncation mutants ( and ; is naturally null in both mutants). Screening of two genes ( and ) in QAL! 2000 identified 19 mutants. A hard grain variant of a soft cultivar was identified due to a mutation in caused by a premature stop codon. Background mutations were observed and further self-fertilization or crossing with a wild type was performed to eliminate deleterious mutations. With the rapid accumulation of wheat genomics information, many potential target genes of interest can be screened for mutations in these TILLING populations.
• Sweet Sorghum Genetic Diversity and Association Mapping for Brix and Height
  - The Plant Genome 2(1):48-62 (2009)
  Sweet sorghum [ (L.) Moench], like its close relative, sugarcane ( spp.), has been selected to accumulate high levels of edible sugars in the stem. Sweet sorghums are tall and produce high biomass in addition to sugar. Little has been documented about the genetic relationships and diversity within sweet sorghums and how sweet sorghums relate to grain sorghum racial types. In this study, a diverse panel of 125 sorghums (mostly sweet) was successfully genotyped with 47 simple sequence repeats (SSRs) and 322 single nucleotide polymorphisms (SNPs). Using both distance-based and model-based methods, we identified three main genetic groupings of sweet sorghums. Based on observed phenotypes and known origins we classified the three groups as historical and modern syrup, modern sugar/energy types, and amber types. Using SSR markers also scored in an available large grain sorghum germplasm panel, we found that these three sweet groupings clustered with kafir/bicolor, caudatum, ! and bicolor types, respectively. Using the information on population structure and relatedness, association mapping was performed for height and stem sugar (brix) traits. Three significant associations for height were detected. Two of these, on chromosomes 9 and 6, support published QTL studies. One significant association for brix, on chromosome 1, 12kb from a glucose-6-phosphate isomerase homolog, was detected.
• Simulation Appraisal of the Adequacy of Number of Background Markers for Relationship Estimation in Association Mapping
  - The Plant Genome 2(1):63-77 (2009)
  Complex trait dissection through association mapping provides a powerful complement to traditional linkage analysis. The genetic structure of an association mapping panel can be estimated by genomewide background markers and subsequently accounted for in association analysis. Deciding the number of background markers is a common issue that needs to be addressed in many association mapping studies. We first showed that the adequacy of markers in relationship estimation influences the maximum likelihood of the model explaining phenotypic variation and demonstrated this influence with a series of computer simulations with different trait architectures. Analyses and computer simulations were then conducted using two different data sets: one from a diverse set of maize ( L.) inbred lines with a complex population structure and familial relatedness, and the other from a group of crossbred dogs. Our results showed that the likelihood-based model-fitting approach can be used t! o quantify the robustness of genetic relationships derived from molecular marker data. We also found that kinship estimation was more sensitive to the number of markers used than population structure estimation in terms of model fitting, and a robust estimate of kinship for association mapping with diverse germplasm requires a certain amount of background markers (e.g., 300–600 biallelic markers for the simulated pedigree materials, >1000 single nucleotide polymorphisms or 100 simple sequence repeats [SSRs] for the diverse maize panel, and about 100 SSRs for the canine panel). Kinship construction with subsets of the whole marker panel and subsequent model testing with multiple phenotypic traits could provide ad hoc information on whether the number of markers is sufficient to quantify genetic relationships among individuals.
• A Snapshot of the Emerging Tomato Genome Sequence
  - The Plant Genome 2(1):78-92 (2009)
  The genome of tomato ( L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger "International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation" initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11! % of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.
• Gene Content and Distribution in the Nuclear Genome of Fragaria vesca
  - The Plant Genome 2(1):93-101 (2009)
  Thirty fosmids were randomly selected from a library of subsp. (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed wi! th transposable elements (TEs). The most abundant TEs in were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of is predicted to be at least 16%.