Because of the huge size of the common wheat (Triticum aestivum L., 2n ϭ 6x ϭ 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.

Genes detected by wheat expressed sequence tags (ESTs) were mapped into chromosome bins delineated by breakpoints of 159 overlapping deletions. These data were used to assess the organizational and evolutionary aspects of wheat genomes. Relative gene density and recombination rate increased with the relative distance of a bin from the centromere. Single-gene loci present once in the wheat genomes were found predominantly in the proximal, low-recombination regions, while multigene loci tended to be more frequent in distal, high-recombination regions. One-quarter of all gene motifs within wheat genomes were represented by two or more duplicated loci (paralogous sets). For 40 such sets, ancestral loci and loci derived from them by duplication were identified. Loci derived by duplication were most frequently located in distal, high-recombination chromosome regions whereas ancestral loci were most frequently located proximal to them. It is suggested that recombination has played a central role in the evolution of wheat genome structure and that gradients of recombination rates along chromosome arms promote more rapid rates of genome evolution in distal, high-recombination regions than in proximal, low-recombination regions.

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere-telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomeretelomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae. tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere-telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.dysploidy ͉ linkage map ͉ rice ͉ sorghum ͉ wheat

BackgroundA genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.ResultsNucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.ConclusionsIn a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

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.

An understanding of the relationship between N assimilation and grain yield and protein, and the measurement of genetic variation in preanthesis and postanthesis N assimilation in wheat (Triticum aestivum L.) are necessary to achieve additional gains in selecting for both high grain yield and high grain protein. Thus, total N assimilation in the spring wheat cultivars ‘Anza’ and ‘Cajeme 71’ and 96 F5‐lines from the cross of these cultivars was studied in field experiments. Freanthesis N assimilation was similar for the two cultivars, but by maturity Anza had assimilated 9% (P < 0.01) more N than Cajeme 71 in both high and low N fertility levels. This difference was mainly due to greater postanthesis assimilation by Anza (22% of total) than Cajeme 71 (10%). Significant genetic variation among F5 lines in N assimilation prior to anthesis occurred in two of three experiments, but no relationships were found between this trait and grain yield, grain protein concentration, or grain protein yield. Significant genetic variability in N assimilation after anthesis was detected, although estimates of heritabilities were low. Nitrogen assimilation after anthesis strongly influenced grain and grain protein yields, explaining 27 to 39% of the variation, but no relationship was found with grain protein concentration. The residuals from the regression of N assimilation after anthesis on biomass at anthesis were also strongly related to grain and grain N yield in a stagewise regression analysis, indicating variation other than random error was involved. Grain protein concentration was also positively associated with these residuals in one experiment. Possible sources of this variation, particularly with relation to roots are discussed. Total N assimilation showed broad‐sense heritabilities of 21 to 27% and was correlated (r = 0.68 to 0.86; P < 0.01) with grain and grain protein yields. Thus genetic variation in N assimilation has a role in determining grain yield and protein concentration in wheat. Further work to determine the genetic and physiological basis of factors influencing N assimilation is needed, especially with regard to roots.

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.

Translocation and assimilation of N during grain filling are involved in determining grain protein content in wheat (Trificum aestivum L.). Considerable controversy on the physiological basis for high grain protein concentration exists. These aspects of N movement within the plant were studied in field experiments with the spring wheat cultivars Anza and Cajeme 71 and 96 F5 lines from the cross of these cultivars. Cajeme 71 had higher grain protein concentration, higher translocation, translocation efficiency, and a higher proportion of N in the grain than Anza, but no relationship between any of these three parameters and grain protein concentnation was found in the F5 lines. The ratio of N harvest index to grain harvest index, which gives a rough estimate of the relative proportioning of N and carbohydrate in the grain, was positively related to grain protein concentration (r=0.39 to 0.45, P < 0.01), emphasizing the need to consider both N and carbohydrate partitioning while studying the genetic basis of high grain protein concentration. A relatively simple genetic basis was postulated for the observed variation. A two‐gene additive model fit the F5 frequency distribution observed in both low and high N experiments. The F5 lines that assimilated more N after anthesis than required for their yield level, identitied by regression of N assimilation after anthesis on grain yield (Le., high positive residuals), and that had high N translocation were found to be high in grain protein concentration. Excess assimilated N, the sum of translocation and these residuals (positive or negative), was closely related to grain protein concentration (r=0.8 to 0.9, P < 0.01). Further, these data for excess N conform closely to theoretical calculations of the additional N requirement for a 1% increase in grain protein concentration.