The purpose of this study was to determine whether the rates of tomato seed germination under 
 different stress and nonstress conditions were under common genetic controls by examining 
 quantitative trait loci (QTL) affecting such traits. Seeds 
 of BC1 progeny of a 
 cross between a
 slow-germinating tomato breeding line and a rapid-germinating tomato wild accession were 
 evaluated for germination under nonstress as well as cold, salt, and drought stress conditions. In 
 each treatment, the most rapidly-germinating seeds were selected, grown to maturity, and 
 subjected to molecular marker analysis. A selective genotyping approach detected between 6 and 
 9 QTL affecting germination rate under each of the four conditions, with a total of 14 QTL 
 identified. Ten QTL affected germination rate under 2 or 3 conditions, which were considered 
 germination-related common QTL. Four QTL affected germination rate only in one treatment, 
 which were considered germination-related, condition-specific QTL . The results indicated that 
 mostly the same QTL affected seed germination under different stress and nonstress conditions, 
 supporting a previous suggestion that similar physiological mechanisms contribute to rapid seed 
 germination under different conditions. Marker-assisted selection for the common QTL may 
 result in progeny with rapid seed germinability under different conditions.

Majid R. Foolad

Prakash  Subbiah

Liping  Zhang

Common QTL Affect the Rate of Tomato Seed Germination under Different Stress and Nonstress Conditions

We describe the construction and screening of a large insert genomic library from the diploid potato clone HB171(13) that has been shown to express durable quantitative field resistance to Phytophthora infestans, the causal agent of potato late blight disease. Integrated genetic mapping of the field resistance quantitative trait locus with markers developed from populations segregating for Rpi-blb3, Rpi-abpt, R2, and R2-like resistance, all located on linkage group IV, has positioned the field resistance QTL within the proximity of this R gene cluster. The library has been successfully screened with resistance gene analogues (RGA) potentially linked to the R gene cluster. Over 30 positive BAC clones were identified and confirmed by PCR and Southern hybridisations to harbour RGA-like sequences. In addition, BAC end sequencing of positive clones has corroborated two BAC clones with a very high level of nucleotide similarity to the RGA probes utilised.

Ingo Hein

Karen McLean

Boulos Chalhoub

Glenn J. Bryan

Generation and Screening of a BAC Library from a Diploid Potato Clone to Unravel Durable Late Blight Resistance on Linkage Group IV

In this study, we detail the construction of a custom cDNA spotted microarray containing 7728 wheat ESTs and the use of the array to identify host genes that are differentially expressed upon challenges with leaf rust fungal pathogens. Wheat cultivar RL6003 (Thatcher Lr1) was inoculated with Puccinia triticina virulence phenotypes BBB (incompatible) or TJB (7-2) (compatible) and sampled at four different time points (3, 6, 12, and 24 hours) after inoculation. Transcript expression levels relative to a mock treatment were measured. One hundred ninety two genes were found to have significantly altered expression between the compatible and incompatible reactions. Among those were genes involved in photosynthesis, the production of reactive oxygen species, ubiquitination, signal transduction, as well as in the shikimate/phenylpropanoid pathway. These data indicate that various metabolic pathways are affected, some of which might be used by RL6003 to mount a coordinated defense against an incompatible fungal pathogen.

Bourlaye  Fofana

Travis W. Banks

Brent  McCallum

Stephen E. Strelkov

Sylvie  Cloutier

Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways

The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>&#x00D7;</mml:mo></mml:math>L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1&#8201;cM and an average of 750&#8201;kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes &#x223C;214&#x02009;000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs.

Genome Mapping and Molecular Breeding of Tomato

Laser microdissection (LM) provides a useful method for isolating specific
cells or tissues from biological samples. Here, we adapted microdissection
protocols to allow high-resolution transcript analysis of different tissues
from developing Arabidopsis seed. Sufficient RNA (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>&#x223C;</mml:mo></mml:math>50 ng) was extracted from
endosperm tissue for RT-PCR. However, to obtain enough RNA for microarray
analyses, it was necessary to amplify the RNA. PCR- and IVT-based
amplification methods were investigated and several important technical
aspects of amplification were identified (such as target truncation and
alterations in signal intensity). We found that when starting from only 50 ng of RNA, amplification methods based on PCR and IVT produced sufficient
product for reliable microarray hybridizations, with two-round IVT giving
the best results. Microarray analyses, using endosperm-derived RNA amplified
by two-round IVT, reproducibly identified endosperm enriched marker genes.
Thus, when combined with RNA-amplification protocols, LM is a robust and
reliable technique for high-throughput tissue-specific gene expression
analysis.

Robert C. Day

Les  McNoe

Richard C. Macknight

Evaluation of Global RNA Amplification and Its Use for High-Throughput Transcript Analysis of Laser-Microdissected Endosperm

Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact.

Mariko  Kouduka

Daisuke  Sato

Manabu  Komori

Motohiro  Kikuchi

Kiyoshi  Miyamoto

Akinori  Kosaku

Mohammed  Naimuddin

Atsushi  Matsuoka

Koichi  Nishigaki

A Solution for Universal Classification of Species Based on Genomic DNA

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International Journal of Plant Genomics