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The presence of genotype-by-environment interaction (GEI) complicates selection of superior genotypes and an understanding of environmental and genotypic causes of significant GEI is important in all stages of plant breeding. We present a systematic approach for understanding GEI of complex interrelated traits by combining chromosome substitution lines that allowed us to study the effects of genes on a single chromosome with a structural equation model that approximated the complex processes involving genes, environmental conditions, and traits. We applied the approach to recombinant inbred chromosome wheat lines grown in multiple environments. The final model explained 74% of the yield GEI variation and we found that spikes per square meter (SPSM) GEI had the highest direct effect on yield GEI and that the genetic markers were mostly sensitive to temperature and precipitation during the vegetative and reproductive periods. In addition, we identified a number of direct and indirect causal relationships that described how genes interacted with environmental factors to affect GEI of several important agronomic traits which would not have been possible with previously used methods.

Abstract: The US Wheat Genome Project, funded by the National Science Foundation, developed the first large public Triticeae expressed sequence tag (EST) resource. Altogether, 116 272 ESTs were produced, comprising [...]

A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus snap of group 1 chromosomes were constructed to show EST distribution, EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively, The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E [less than or equal to] [e.sup.-10]), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome I and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant snatches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses.

We constructed high-density deletion bin maps of wheat chromosomes 5A, 5B, and 5D, including 2338 loci mapped with 1052 EST probes and 217 previously mapped loci (total 2555 loci). This information was combined to construct a consensus chromosome bin map of group 5 including 24 bins. A relatively higher number of loci were mapped on chromosome 5B (38%) compared to 5A (34%) and 5D (28%). Differences in the levels of polymorphism among the three chromosomes were partially responsible forthese differences. A higher number of duplicated loci was found on chromosome 5B (42%). Three times more loci were mapped on the long arms than on the short arms, and a significantly higher number of probes, loci. and duplicated loci were mapped on the distal halves than on the proximal halves of the chromosome arms. food overall colinearity was observed among the three homoeologous group 5 chromosomes, except for the previously known 5AL/4AL translocation and a putative small pericentric inversion in chromosome 5A. Statistically significant colinearity was observed between low-copy-number ESTs from wheat homoeologous group 5 and rice chromosomes 12 (88 ESTs), 9 (72 ESTs), and 3 (84 ESTs).

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17.300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general. EST density increased relative to the physical distance from the centromere. The majority of EST--dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes. and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases file numbers of loci were significantly lower in tile centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat (Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the king arms of homoeologous group 4 chromosomes, While 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two consensus previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology (only 26 of the 119 consensus ESTs) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases.

The focus of tiffs 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 die group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- mad small-scale differences in gene order. Of the group 3 mapped EST unigenes ~21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.

To localize wheat (Trilicum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid mad deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs. 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. Tile physical distribution of ESTs was uneven on chromosomes with a tendency toward higher deusities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on lice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate die analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs. construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were die first extensive public wheal EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data lot all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation fear future developments in wheat genomics.

A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L. ), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101.107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 'unigenes.' Analysis of the distribution of these unigenes among the liberties led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.

Genotype x environment interactions (GEI) and quantitative trait loci x environment interactions (QEI) are known to influence the expression of agronomic performance traits in wheat. The aim of this study was to provide biological and environmental explanations for large GEI and QEI known to affect the expression of genes on chromosome 3A of wheat (Triticum aestivum L.), Agronomic performance and molecular marker data available for a population of chromosome 3A recombinant inbred chromosome lines (RICLs-3A) in seven environments was used along with environmental covariate data to construct individual factorial regressions to explain GEI and QEI. Precipitation and temperature before anthesis had the greatest influence on agronomic performance traits for the RICLs-3A, and explained a sizeable portion of the total GEI for those traits. Individual molecular marker x environmental covariate interactions explained a large portion of the total marker x environment interactions for several agronomic traits. Seventy-six percent of the QEI for a major grain yield quantitative trait locus (QTL) was explained by the effect of temperature during preanthesis growth on dissimilar QTL genotype differentials across testing environments. Environmental covariates provided a strong basis for explaining QEI using marker x environmental covariate interactions., OUR CURRENT understanding of QTLs associated with agronomic performance in wheat and other crop plants is limited. The majority of studies investigating QTLs for agronomic traits indicate inconsistent QTL detection [...]

Most experiments on 1RS translocations in wheat (Triticum aestirum L.) cannot separate the effects of introgressions of rye (Secale cereale L.) chromosome arm from the absence of corresponding wheat chromosome arms. The objective of this research was to determine the contribution of individual wheat and rye group 1 chromosome arms. Five group 1 ditelosomics, six substitutions, and 16 translocations of IR in wheat were compared with appropriate controls. All ditelosomics were significantly different from controls for 100-kernel weight (100-KW), flour protein content (FP), Mixograph peak time (MT) and tolerance (MTO), and sodium dodecyl sulfate sedimentation (SDSS) volume. Among the long arms, 1DL was the most important for end-use quality and 1AL the least important, ranking even below the 1RL tested. The contribution of all short arms was low. Substitutions of 1R negatively impacted agronomic performance with the long arm being entirely responsible for this effect. Among translocation lines, those with 1RS.IBL had the highest yield and those with 1RS.1DL the lowest. Negative impact of all translocations of IRS on the end-use quality was far greater than the absence of the corresponding 1S arms of wheat. Translocation 1RS.1AL was the least detrimental to quality and 1RS.1DL the most detrimental. Both the source of the rye chromatin and its position in the wheat genome affected agronomic performance and quality. These results suggest that it may be possible to create new translocations of 1RS in wheat with improved performance. Translocation of 1RS to 1AL is preferred from a quality point of view; that to IBL appears more beneficial for agronomic performance., INTROGRESSIONS OF RYE chromatin into wheat through wheat-rye chromosomal substitutions and translocations have increased the genetic diversity of bread wheat cultivars for various characters (Zeller and Hsam, 1984). The chromosomal [...]

Genetic analyses of complex traits in wheat (Triticum aestivum L.) are facilitated by the availability of unique genetic tools such as chromosome substitution lines and recombinant inbred chromosome lines (RICLs) which allow the effects of genes on single chromosomes to be studied individually. Chromosome 3A of 'Wichita' is known to contain alleles at quantitative trait loci (QTLs) that influence variation in grain yield and agronomic performance traits relative to alleles of 'Cheyenne'. To determine the number, location, and environmental interactions of genes related to agronomic performance on chromosome 3A, QTL and QTL x environment analyses of 98 RICLs-3A were conducted in seven locations across Nebraska from 1999 through 2001. QTLs were detected for seven of eight agronomic traits measured and generally localized to three regions of chromosome 3A. QTL x environment interactions were detected for some QTLs and these interactions were caused by changes in magnitude and crossover interactions. Major QTLs for kernels per square meter and grain yield were associated within a 5-centimorgan (cM) interval and appeared to represent a single QTL with pleiotropic effects. This particular QTL displayed environmental interactions caused by changes in magnitude, wherein the positive effect of the Wichita QTL allele was larger in higher yielding environments., GRAIN YIELD AND AGRONOMIC PERFORMANCE are the most commonly measured, but poorly understood crop traits. Modern strategies for investigating the genetic basis of grain yield and agronomic performance were first [...]

Wheat streak mosaic is a damaging disease of cultivated bread wheat, Triticum aestivum L. em Thell., in many parts of the world. No wheat cultivar has a high level of resistance to WSMV or its vector, the wheat curl mite, Eriophyes tulipae Keifer. Genes conferring resistance to wheat curl mite colonization have been transferred from Aegilops tauschii Coss., Cmc1, and from Agropyron elongatum (Host) Beauv., Cmc2. A gene conditioning resistance to WSMV, Wsm1, was transferred from Agropyron intermedium (Host) Beauv. into common wheat. To broaden the genetic base of wheat, new sources of WSMV resistance are continuously sought. This study reports a new source of WSMV resistance derived from A. intermedium and its transfer into hexaploid wheat. C-banding analysis was used to cytogenetically identify the A. intermedium chromosomes and chromosome arms in three WSMV resistant wheat-A. intermedium derivatives, designated as 6957, 6961, and 6962. All lines were identified as disomic chromosome addition lines with an A. intermedium chromosome arm in common. Restriction fragment length polymorphism analysis was used to establish homoeology of the A. intermedium chromosome arm carrying the gene or gene complex conditioning resistance to WSMV. The arm belonged to the long arm of the wheat Group 4 chromosomes, and was designated as 4Ai#3L. The added A. intermedium chromosomes present in Lines 6957 and 6961 probably originated from centric-fusion. The WSMV resistance of these lines is different from that conditioned by Wsm1 and may have significance in breeding WSMV resistant wheat cultivars.