Expressed sequence tags (ESTs) are a valuable source of molecular markers. To enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in hexaploid wheat (Triticum aestivum L.), over 260,000 ESTs from 5 different grass species were analyzed and 5418 SSR-containing sequences were identified. Using sequence similarity analysis, 156 cross-species superclusters and 138 singletons were used to develop primer pairs, which were then tested on the genomic DNA of barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and wheat. Three-hundred sixty-eight primer pairs produced PCR amplicons from at least one species and 227 primer pairs amplified DNA from two or more species. EST-SSR sequences containing dinucleotide motifs were significantly more polymorphic (74%) than those containing trinucleotides (56%), and polymorphism was similar for markers in both coding and 5' untranslated (UTR) regions. Out of 112 EST-SSR markers, 90 identified 149 loci that were integrated into a reference wheat genetic map. These loci were distributed on 19 of the 21 wheat chromosomes and were clustered in the distal chromosomal regions. Multiple-loci were detected by 39% of the primer pairs. Of the 90 mapped ESTs, putative functions for 22 were identified using BLASTX queries. In addition, 80 EST-SSR markers (104 loci) were located to chromosomes using nullisomic-tetrasomic lines. The enhanced map from this study provides a basis for comparative mapping using orthologous and PCR-based markers and for identification of expressed genes possibly affecting important traits in wheat.

The premature germination of seeds before harvest, known as preharvest sprouting (PHS), is a serious problem in all wheat growing regions of the world. In order to determine genetic control of PHS resistance in white wheat from the relatively uncharacterized North American germplasm, a doubled haploid population consisting of 209 lines from a cross between the PHS resistant variety Cayuga and the PHS susceptible variety Caledonia was used for QTL mapping. A total of 16 environments were used to detect 15 different PHS QTL including a major QTL, QPhs.cnl-2B.1, that was significant in all environments tested and explained from 5 to 31% of the trait variation in a given environment. Three other QTL QPhs.cnl-2D.1, QPhs.cnl-3D.1, and QPhs.cnl-6D.1 were detected in six, four, and ten environments, respectively. The potentially related traits of heading date (HD), plant height (HT), seed dormancy (DOR), and rate of germination (ROG) were also recorded in a limited number of environments. HD was found to be significantly negatively correlated with PHS score in most environments, likely due to a major HD QTL, QHd.cnl-2B.1, found to be tightly linked to the PHS QTL QPhs.cnl-2B.1. Using greenhouse grown material no overlap was found between seed dormancy and the four most consistent PHS QTL, suggesting that greenhouse environments are not representative of field environments. This study provides valuable information for marker-assisted breeding for PHS resistance, future haplotyping studies, and research into seed dormancy.

Reference populations are valuable resources in genetics studies for determining marker order, marker selection, trait mapping, construction of large-insert libraries, cross-referencing marker platforms, and genome sequencing. Reference populations can be propagated indefinitely, they are polymorphic and have normal segregation. Described are two new reference populations who share the same parents of the original wheat reference population Synthetic W7984 (Altar84/ Aegilops tauschii (219) CIGM86.940) x Opata M85, an F(1)-derived doubled haploid population (SynOpDH) of 215 inbred lines and a recombinant inbred population (SynOpRIL) of 2039 F(6) lines derived by single-plant self-pollinations. A linkage map was constructed for the SynOpDH population using 1446 markers. In addition, a core set of 42 SSR markers was genotyped on SynOpRIL. A new approach to identifying a core set of markers used a step-wise selection protocol based on polymorphism, uniform chromosome distribution, and reliability to create nested sets starting with one marker per chromosome, followed by two, four, and six. It is suggested that researchers use these markers as anchors for all future mapping projects to facilitate cross-referencing markers and chromosome locations. To enhance this public resource, researchers are strongly urged to validate line identities and deposit their data in GrainGenes so that others can benefit from the accumulated information.

Drought limits cereal yields in several regions of the world and plant water status plays an important role in tolerance to drought. To investigate and understand the genetic and physiological basis of drought tolerance in barley, differentially expressed sequence tags (dESTs) and candidate genes for the drought response were mapped in a population of 167 F8 recombinant inbred lines derived from a cross between "Tadmor" (drought tolerant) and "Er/Apm" (adapted only to specific dry environments). One hundred sequenced probes from two cDNA libraries previously constructed from drought-stressed barley (Hordeum vulgare L., var. Tokak) plants and 12 candidate genes were surveyed for polymorphism, and 33 loci were added to a previously published map. Composite interval mapping was used to identify quantitative trait loci (QTL) associated with drought tolerance including leaf relative water content, leaf osmotic potential, osmotic potential at full turgor, water-soluble carbohydrate concentration, osmotic adjustment, and carbon isotope discrimination. A total of 68 QTLs with a limit of detection score > or =2.5 were detected for the traits evaluated under two water treatments and the two traits calculated from both treatments. The number of QTLs identified for each trait varied from one to 12, indicating that the genome contains multiple genes affecting different traits. Two candidate genes and ten differentially expressed sequences were associated with QTLs for drought tolerance traits.

Association mapping identified quantitative trait loci (QTLs) and the markers linked to pre-harvest sprouting (PHS) resistance in an elite association mapping panel of white winter wheat comprising 198 genotypes. A total of 1,166 marker loci including DArT and SSR markers representing all 21 chromosomes of wheat were used in the analysis. General and mixed linear models were used to analyze PHS data collected over 4 years. Association analysis identified eight QTLs linked with 13 markers mapped on seven chromosomes. A QTL was detected on each arm of chromosome 2B and one each on chromosome arms 1BS, 2DS, 4AL, 6DL, 7BS and 7DS. All except the QTL on 7BS are located in a location similar to previous reports and, if verified, the QTL on 7BS is likely to be novel. Principal components and the kinship matrix were used to account for the presence of population structure but had only a minor effect on the results. Although, none of the QTLs was highly significant across all environments, a QTL on the long arm of chromosome 4A was detected in three different environments and also using the best linear unbiased predictions over years. Although previous reports have identified this as a major QTL, its effects were minor in our biparental mapping populations. The results of this study highlight the benefits of association mapping and the value of using elite material in association mapping for plant breeding programs.

and forms hydroperoxides. These products are thought to be involved in plant defense, wound response, senes-Lipoxygenases constitute a family of enzymes that catalyze the cence, and development (Hildebrand, 1989). Under cerbreakdown of lipids, resulting in products that may have undesirable effects. These enzymes can affect pasta color and cause off-flavors. The tain processing conditions, high levels of lipoxygenase purpose of this study was to map the loci associated with lipoxygenase activity destroy the yellow color in pasta by oxidation activity in seeds of a durum wheat (Triticum turgidum ssp. durum ) (Joppa and Williams, 1988). Some plant lipoxygenase population to determine if lipoxygenase activity is associated with reaction products also are implicated in the production flour color. Seed of the parents, Jennah Khetifa and Cham 1, and the of aroma or undesirable flavors and odors. In barley recombinant inbred population consisting of 113 progeny lines were (Hordeum vulgare L.), this enzyme is thought to be used to assay lipoxygenase activity and flour color. A saturated molecresponsible for staling in beer (Drost et al., 1990; Wu ular-marker linkage map for this population was previously conet al., 1997). Lipoxygenase activity is directly affected structed. Allele specific primers targeting the wheat homolog to barley by storage conditions. Kaukovirta et al. (1998) measured LoxA were designed, and a fragment length polymorphism resulting from a miniature inverted-repeat transposable element (MITE) inser-oxidation of linoleic acid in flour suspensions of barley tion in an intron of the durum wheat LoxA homolog allowed mapping and malt samples. Results showed that there was great of the locus to chromosome 4BS. To measure lipoxygenase activity, variability of lipoxygenase activity profiles from a single spectrophotometric changes were recorded. Cham 1 had a change in malting, depending on the duration of storage before absorbance of 0.284 units of absorbance over 1 min compared with the assays. They concluded that the rate of lipoxygenase 0.752 units for Jennah Khetifa. Quantitative trait locus analysis of reaction should be considered as a quality factor of malt these data indicated that most of the lipoxygenase activity was associbecause of its effect on malting. In soybean [Glycine ated with the wheat lipoxygenase gene (Lpx ) on chromosome 4BS. max (L.) Merr.] seeds, lipoxygenases are responsible for A quantitative trait locus for vitreous appearance of seeds also was production of the unpleasant beany flavors that have associated with this locus. Flour color was not correlated with lipoxygenase activity in this population. With this knowledge, marker-as-Abbreviations: MITE, miniature inverted-repeat transposable element.

No abstract

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags (ESTs) accounting for 2266 restriction fragments (loci) on the homoeologous group 3 chromosomes of hexaploid wheat (Triticum aestivum L.). Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology (GO) classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large-and small-scale differences in gene order. Of the group 3 mapped EST unigenes ‫12ف‬ and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.T HE success of cultivated wheat (Triticum aestivum self-pollinated species composed of three related dip-L.) as a worldwide food crop can be attributed to loid genomes designated AA, BB, and DD, each of which its diverse genetic resources, unusually wide adaptation, has seven chromosomes. These three genomes are deand broad utility to humankind. Hexaploid wheat is a scendants of extant diploid species that have been widely used as germplasm in genetic studies and crop improvement. The polyploid nature of the wheat genome pro-