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Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.

Recent increase in the availability of expressed sequence tag (EST) data has facilitated the development of microsatellite or simple sequence repeat (SSR) markers in a number of plant species groups, including cereals. As these SSRs are derived from ESTs/genes (EST-SSRs), they exhibit a higher potential for transfer through cross-amplification in related species than SSR markers generated from genomic DNA libraries. In this study, a sub-set of 165 EST-SSR markers from a total of 185 assigned to the genetic map of barley was examined for transferability to wheat, rye and rice. A higher proportion, i.e., 78.2% of barley markers showed amplification in wheat followed by 75.2% in rye and 42.4% in rice. Furthermore, in silico comparison of SSR-ESTs (ESTs containing SSRs) corresponding to 185 mapped barley EST-SSR loci against 1,369,182 publicly available cereal ESTs showed significant homology with ESTs of wheat (93.5%), rye (37.3%), rice (57.3%), sorghum (51.9%) and maize (51.9%). Sequence similarity of the barley ESTs with 379,944 ESTs of the two model dicot species, Arabidopsis and Medicago suggested theoretical transferability of barley markers into dicot species although at low frequency (9.7% in Arabidopsis and 8.6% in Medicago ). In silico comparative mapping (sequence comparison) of mapped barley SSR-ESTs against the mapping data of rye, wheat and rice indicated the presence of orthologues of the barley SSR-ESTs in the respective species. Furthermore, nine barley EST-SSRs were experimentally mapped to a rye genetic linkage map and all could be located in the expected orthologous region compared to their position in barley.

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 scoreor =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.

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 the first extensive public wheat 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 for 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 for future developments in wheat genomics.

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.

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 long 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 inversions, 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 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 ∼21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.

To localize wheat (Triticum 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 and 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. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities 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 rice 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.

In several crop species within the Triticeae tribe of the grass family Poaceae, single major aluminum (Al) tolerance genes have been identified that effectively mitigate Al toxicity, a major abiotic constraint to crop production on acidic soils. However, the trait is quantitatively inherited in species within other tribes, and the possible ancestral relationships between major Al tolerance genes and QTL in the grasses remain unresolved. To help establish these relationships, we conducted a molecular genetic analysis of Al tolerance in sorghum and integrated our findings with those from previous studies performed in crop species belonging to different grass tribes. A single locus, AltSB, was found to control Al tolerance in two highly Al tolerant sorghum cultivars. Significant macrosynteny between sorghum and the Triticeae was observed for molecular markers closely linked to putatively orthologous Al tolerance loci present in the group 4 chromosomes of wheat, barley, and rye. However, AltSB was not located within the homeologous region of sorghum but rather mapped near the end of sorghum chromosome 3. Thus, AltSB not only is the first major Al tolerance gene mapped in a grass species that does not belong to the Triticeae, but also appears to be different from the major Al tolerance locus in the Triticeae. Intertribe map comparisons suggest that a major Al tolerance QTL on rice chromosome 1 is likely to be orthologous to AltSB, whereas another rice QTL on chromosome 3 is likely to correspond to the Triticeae group 4 Al tolerance locus. Therefore, this study demonstrates a clear evolutionary link between genes and QTL encoding the same trait in distantly related species within a single plant family.

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to related large-genome species has revolutionized molecular genetics and breeding strategies for improving those crops. Comparative sequence analysis methods can be used to cross-reference genes between species maps, enhance the resolution of comparative maps, study patterns of gene evolution, identify conserved regions of the genomes, and facilitate interspecies gene cloning. In this study, 5,780 Triticeae ESTs that have been physically mapped using wheat ( Triticum aestivum L.) deletion lines and segregating populations were compared using NCBI BLASTN to the first draft of the public rice ( Oryza sativa L.) genome sequence data from 3,280 ordered BAC/PAC clones. A rice genome view of the homoeologous wheat genome locations based on sequence analysis shows general similarity to the previously published comparative maps based on Southern analysis of RFLP. For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes. The physical locations of non-conserved regions were not consistent across rice chromosomes. Some wheat ESTs with multiple wheat genome locations are associated with the non-conserved regions of similarity between rice and wheat. The inverse view, showing the relationship between the wheat deletion map and rice genomic sequence, revealed the breakdown of gene content and order at the resolution conferred by the physical chromosome deletions in the wheat genome. An average of 35% of the putative single copy genes that were mapped to the most conserved bins matched rice chromosomes other than the one that was most similar. This suggests that there has been an abundance of rearrangements, insertions, deletions, and duplications eroding the wheat-rice genome relationship that may complicate the use of rice as a model for cross-species transfer of information in non-conserved regions.

Whole grain consumption has been associated with reduced risk of chronic diseases, such as cardiovascular diseases and cancer. These beneficial effects have been attributed to the unique phytochemicals of grains that complement those found in fruits and vegetables. Wheat is one of the major grains in the human diet; however, little is known about the inherent varietal differences in phytochemical profiles, total phenolic and carotenoid contents, or total antioxidant activities of different wheat varieties, which ultimately influence the associated nutritional and health benefits of wheat and wheat products. The objectives of this study were to determine the phytochemical profiles and total antioxidant activity for 11 diverse wheat varieties and experimental lines. The profiles included free, soluble-conjugated, and insoluble-bound forms of total phenolics, flavonoids, and ferulic acids and carotenoid content including lutein, zeaxanthin, and beta-cryptoxanthin. The results showed that total phenolic content (709.8-860.0 micromol of gallic acid equiv/100 g of wheat), total antioxidant activity (37.6-46.4 micromol of vitamin C/g), and total flavonoid content (105.8-141.8 micromol of catechin equiv/100 g of wheat) did not vary greatly among the 11 wheat lines. However, significant differences in total ferulic acid content (p0.05) and carotenoid content (p0.05) among the varieties were observed, with carotenoid content exhibiting the greatest range of values. Carotenoid content among the 11 wheat varieties exhibited 5-fold, 3-fold, and 12-fold differences in lutein, zeaxanthin, and beta-cryptoxanthin, respectively. A synthetic wheat experimental line, W7985, gave the lowest carotenoid concentrations of any of the genotypes in this study. Such large genotypic differences in carotenoid content may open up new opportunities for breeding wheat varieties with higher nutritional value.

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota × Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using χ2tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.Key words: molecular marker, RFLP, linkage map, oat, Avena.

Aluminum toxicity limits wheat (Triticum aestivum L.) production on acidic soils. The wheat cultivar Atlas 66 reportedly may have both more than one Al tolerance gene and more than one Al tolerance mechanism. The purpose of this study was to identify the Al tolerance mechanisms conferred by the individual Atlas 66 Al tolerance genes present in near-isogenic lines (NILs) of the cv. Century and Chisholm ('Century-T' and 'Chisholn-T). Seedling hydroponic culture analysis revealed that the NILs were not as Al tolerant, nor were they able to exclude Al from root apices as effectively as Atlas 66. Al-inducible malate release from root apices was significantly higher in the NILs compared with the recurrent parents, but less than that observed in Atlas 66. In contrast, root phosphate release was significantly lower than previously reported in Atlas 66, with no major differences observed among lines. These results indicate that the Atlas 66 Al tolerance gene present in each NIL acts by increasing Al-inducible malate release from root tips, but confers only a portion of the Al tolerance of Atlas 66 in both instances. Thus, differences in Al tolerance between the NILs and Atlas 66 can be attributed to malate release differences, and not differential phosphate release. Further, these results indicate that genetic variation at more than one locus underlies the malate-mediated Al tolerance differences in Atlas 66, when compared with Century and Chisholm. The Atlas 66 alleles for these loci have not been introgressed into the NILs.

Lipoxygenases constitute a family of enzymes that catalyze the breakdown of lipids, resulting in products that may have undesirable effects. These enzymes can affect pasta color and cause off-flavors. The purpose of this study was to map the loci associated with lipoxygenase activity in seeds of a durum wheat (Triticum turgidum ssp. durum ) population to determine if lipoxygenase activity is associated with flour color. Seed of the parents, Jennah Khetifa and Cham 1, and the recombinant inbred population consisting of 113 progeny lines were used to assay lipoxygenase activity and flour color. A saturated molecular-marker linkage map for this population was previously constructed. Allele specific primers targeting the wheat homolog to barley LoxA were designed, and a fragment length polymorphism resulting from a miniature inverted-repeat transposable element (MITE) insertion in an intron of the durum wheat LoxA homolog allowed mapping of the locus to chromosome 4BS. To measure lipoxygenase activity, spectrophotometric changes were recorded. Cham 1 had a change in absorbance of 0.284 units of absorbance over 1 min compared with 0.752 units for Jennah Khetifa. Quantitative trait locus analysis of these data indicated that most of the lipoxygenase activity was associated with the wheat lipoxygenase gene (Lpx) on chromosome 4BS. A quantitative trait locus for vitreous appearance of seeds also was associated with this locus. Flour color was not correlated with lipoxygenase activity in this population. With this knowledge, marker-assisted selection can be used to select genotypes with lower lipoxygenase activity in durum wheat populations.

Aluminum (Al) toxicity is a major factor limiting barley growth in acid soils, and genotypes with adequate level of tolerance are needed for improving barley adaptation in Brazil. To study the inheritance of Al tolerance in Brazilian barleys, cultivars Antarctica 1, BR 1 and FM 404 were crossed to sensitive Kearney and PFC 8026, and intercrossed. Parental, F1, F2 and F6 generations were grown in nutrient solution containing 0.03, 0.05 and 0.07 mM of Al and classified for tolerance by the root tip hematoxylin staining assay. Tolerant by sensitive F2 progenies segregated three tolerant to one sensitive, fitting the 3:1 ratio expected for a single gene. The F6 populations segregated one tolerant to one sensitive also fitting a monogenic ratio. The F2 seedlings from crosses among tolerant genotypes scored the same as the parents. Since the population size used would allow detection of recombination as low as 7%, the complete absence of Al sensitive recombinants suggests that tolerance in these cultivars is most probably, controlled by the same gene. Thus, the potential for improving Al tolerance through recombination of these genotypes is very low and different gene sources should be evaluated.

Genetic variation present in 64 durum wheat accessions was investigated by using three sources of microsatellite (SSR) markers: EST-derived SSRs (EST-SSRs) and two sources of SSRs isolated from total genomic DNA. Out of 245 SSR primer pairs screened, 22 EST-SSRs and 20 genomic-derived SSRs were polymorphic and used for genotyping. The EST-SSR primers produced high quality markers, but had the lowest level of polymorphism (25%) compared to the other two sources of genomic SSR markers (53%). The 42 SSR markers detected 189 polymorphic alleles with an average number of 4.5 alleles per locus. The coefficient of similarity ranged from 0.28 to 0.70 and the estimates of similarity varied when different sources of SSR markers were used to genotype the accessions. This study showed that EST-derived SSR markers developed in bread wheat are polymorphic in durum wheat when assaying loci of the A and B genomes. A minumum of ten EST-SSRs generated a very low probability of identity (0.36x10(-12)) indicating that these SSRs have a very high discriminatory power. EST-SSR markers directly sample variation in transcribed regions of the genome, which may enhance their value in marker-assisted selection, comparative genetic analysis and for exploiting wheat genetic resources by providing a more-direct estimate of functional diversity.

Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat.

Quantitative adult plant resistance (APR) to stem rust (Puccinia graminis f. sp. tritici) is an important breeding target in wheat (Triticum aestivum L.) and a potential target for genomic selection (GS). To evaluate the relative importance of known APR loci in applying GS, we characterized a set of CIMMYT germplasm at important APR loci and on a genome-wide profile using genotyping-by-sequencing (GBS). Using this germplasm, we describe the genetic architecture and evaluate prediction models for APR using data from the international Ug99 stem rust screening nurseries. Prediction models incorporating markers linked to important APR loci and seedling phenotype scores as fixed effects were evaluated along with the classic prediction models: Multiple linear regression (MLR), Genomic best linear unbiased prediction (G-BLUP), Bayesian Lasso (BL), and Bayes Cp (BCp). We found the Sr2 region to play an important role in APR in this germplasm. A model using Sr2 linked markers as fixed effects in G-BLUP was more accurate than MLR with Sr2 linked markers (p-value = 0.12), and ordinary G-BLUP (p-value = 0.15). Incorporating seedling phenotype information as fixed effects in G-BLUP did not consistently increase accuracy. Overall, levels of prediction accuracy found in this study indicate that GS can be effectively applied to improve stem rust APR in this germplasm, and if genotypes at Sr2 linked markers are available, modeling these genotypes as fixed effects could lead to better predictions.

Stem rust of wheat (Triticum aestivum L.) caused by Puccinia graminis f. sp. tritici Eriks. and E. Henn. is a globally important disease that can cause severe yield loss. Breeding for quantitative stem rust resistance (QSRR) is important for developing cultivars with durable resistance. Genomic selection (GS) could increase rates of genetic gain for quantitative traits, but few experiments comparing GS and phenotypic selection (PS) have been conducted. Our objectives were to (i) compare realized gain from GS based on markers only with that of PS for QSRR in spring wheat using equal selection intensities; (ii) determine if gains agree with theoretical expectations; and (iii) compare the impact of GS and PS on inbreeding, genetic variance, and correlated response for pseudo-black chaff (PBC), a correlated trait. Over 2 yr, two cycles of GS were performed in parallel with one cycle of PS, with each method replicated twice. For GS, markers were generated using genotyping-by-sequencing, the prediction model was initially trained using historical data, and the model was updated before the second GS cycle. Overall, GS and PS led to a 31 ± 11 and 42 ± 12% increase in QSRR and a 138 ± 22 and 180 ± 70% increase in PBC, respectively. Genetic gains were not significant but were in agreement with expectations. Per year, gains from GS and PS were equal, but GS led to significantly lower genetic variance. This shows that while GS and PS can lead to equal rates of short-term gains, GS can reduce genetic variance more rapidly. Further work to develop efficient GS implementation strategies in spring wheat is warranted.

The role of wheat, and particularly of gluten protein, in our diet has recently been scrutinized. This article provides a summary of the main pathologies related to wheat in the human body, including celiac disease, wheat allergy, nonceliac wheat sensitivity, fructose malabsorption, and irritable bowel syndrome. Differences in reactivity are discussed for ancient, heritage, and modern wheats. Due to large variability among species and genotypes, it might be feasible to select wheat varieties with lower amounts and fewer types of reactive prolamins and fructans. Einkorn is promising for producing fewer immunotoxic effects in a number of celiac research studies. Additionally, the impact of wheat processing methods on wheat sensitivity is reviewed. Research indicates that germination and fermentation technologies can effectively alter certain immunoreactive components. For individuals with wheat sensitivity, less-reactive wheat products can slow down disease development and improve quality of life. While research has not proven causation in the increase in wheat sensitivity over the last decades, modern wheat processing may have increased exposure to immunoreactive compounds. More research is necessary to understand the influence of modern wheat cultivars on epidemiological change.

Key message Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. Abstract The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure. Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2418-4) contains supplementary material, which is available to authorized users.

Key message This consensus map of stem rust genes, QTLs, and molecular markers will facilitate the identification of new resistance genes and provide a resource of in formation for development of new markers for breeding wheat varieties resistant to Ug99. Abstract The global effort to identify new sources of resistance to wheat stem rust, caused by Pucciniagraminis f. sp. tritici race group Ug99 has resulted in numerous studies reporting both qualitative genes and quantitative trait loci. The purpose of our study was to assemble all available information on loci associated with stem rust resistance from 21 recent studies on Triticum aestivum L. (bread wheat) and Triticum turgidum subsp. durum desf. (durum wheat). The software LPmerge was used to construct a stem rust resistance loci consensus wheat map with 1,433 markers incorporating Single Nucleotide Polymorphism, Diversity Arrays Technology, Genotyping-by-Sequencing as well as Simple Sequence Repeat marker information. Most of the markers associated with stem rust resistance have been identified in more than one population. Several loci identified in these populations map to the same regions with known Sr genes including Sr2, SrND643, Sr25 and Sr57 (Lr34/Yr18/Pm38), while other significant markers were located in chromosome regions where no Sr genes have been previously reported. This consensus map provides a comprehensive source of information on 141 stem rust resistance loci conferring resistance to stem rust Ug99 as well as linked markers for use in marker-assisted selection. Electronic supplementary material The online version of this article (doi:10.1007/s00122-014-2326-7) contains supplementary material, which is available to authorized users.

Hybridization between soft and hard wheat creates new associations among loci. Advantages include an increase Interclass hybridization between soft and hard wheat (Triticum in genetic diversity, a potential increase in grain yield, aestivum L.) results in new genetic combinations of potential value. and transfer of pest resistance genes. Both May et al. We investigated whether interclass hybridization could improve enduse quality of both classes. Our objectives were to analyze quality (1989) and Carver (1996) indicated that recovery of soft traits in a population of recombinant inbred lines (RILs) derived from or hard wheat quality characteristics was possible in a cross between the good quality soft white wheat NY6432-18 (NY18), interclass single crosses if genetic variation for grain and good quality hard white wheat Clark’s Cream (CC), identify quality was maintained at a high level within the segrequantitative trait loci (QTLs) for those traits, and use linkage analysis gating population. A better understanding of the underto determine which parent was contributing favorable alleles at spe- lying genetic structure influencing wheat quality would cific QTLs for a given trait. The population was assessed for milling, hasten the development of unique wheats possessing protein and dough mixing, hydration, cookie and loaf traits. Traits value-added traits as well as wheats suited to convenwere measured in two to six environments grown over three seasons tional end-uses. Specifically, we wondered if interclass in Ithaca, NY. The molecular map for the population contains 370 hybridization could create new associations among loci molecular markers including restiction fragment length polymorthat would actually improve end-use quality of both phisms (RFLPs), microsatellites, and markers derived from known function genes in wheat. Linkage groups have been located to all the hard and soft wheat. wheat chromosomes except for 7D. Pinb derived from the puroindo- Wheat flour is classified for use in baking on the basis line b gene on chromosome 5DS was the major QTL for milling, of its texture (soft vs. hard) and chemical properties hydration, and cookie baking traits. The major QTL for mixograph (primarily protein). In the USA, the main use of hard peak time was at the Glu-Dy1 marker, derived from Glu-D1-2 gene wheat flour is for bread baking and the main use of on chromosome 1DL. The Glu-Ax1 and Glu-By1 markers were QTLs soft wheat flour is for cookie baking. Cookie flour is for mixograph peak height and tolerance, respectively. QTLs for flour characterized by low water absorption, fine particleprotein quantity were detected on chromosome 2B. With the excep- size, and low protein content as compared with bread tion of the hydration traits, multiple regression models included alleles flour milled from hard wheat (Hoseney, 1988). During from both parents. Interclass hybridization may be an underexploited the initial milling step, soft wheat endosperm fractures wheat breeding strategy for improvement of agronomic and quality through cell walls and hard wheat endosperm fractures traits in wheat. at the cell wall. As a consequence, soft wheat flour particles are finer than those in hard wheat flours. Sub

Durum wheat (Triticum turgidum L. var. durum) is an economically and nutritionally important cereal crop in the Mediterranean region. To further our understanding of durum genome organization we constructed a durum linkage map using restriction fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs) known as Gatersleben wheat microsatellites (GWMs), amplified fragment length polymorphisms (AFLPs), and seed storage proteins (SSPs: gliadins and glutenins). A population of 110 F9 recombinant inbred lines (RILs) was derived from an intraspecific cross between two durum cultivars, Jennah Khetifa and Cham 1. The two parents exhibit contrasting traits for resistance to biotic and abiotic stresses and for grain quality. In total, 306 markers have been placed on the linkage map – 138 RFLPs, 26 SSRs, 134 AFLPs, five SSPs, and three known genes (one pyruvate decarboxylase and two lipoxygenases). The map is 3598 cM long, with an average distance between markers of 11.8 cM, and 12.1% of the markers deviated significantly from the expected Mendelian ratio 1:1. The molecular markers were evenly distributed between the A and B genomes. The chromosome with the most markers is 1B (41 markers), followed by 3B and 7B, with 25 markers each. The chromosomes with the fewest markers are 2A (11 markers), 5A (12 markers), and 4B (15 markers). In general, there is a good agreement between the map obtained and the Triticeae linkage consensus maps. This intraspecific map provides a useful tool for marker-assisted selection and map-based breeding for resistance to biotic and abiotic stresses and for improvement of grain quality. L'articolo è disponibile sul sito dell'editore: http://www.springerlink.com

Physical attributes, including kernel morphology, are used to grade wheat, and indicate wheat milling and baking quality (MBQ). Using a recombinant inbred population derived from a soft by hard wheat cross, this study quantified kernel traits' sources of variation, studied their heritability, and relationships between morphological and MBQ traits. Transgressive segregation occurred for all traits. Thousand-kernel weight (TKW) and kernel texture (NIR-T) were primarily influenced by genotype and test weight (TW) mainly by year. NIR-T had the highest heritability. Low genetic correlation (GCOR) between kernel length (LEN) and width (WID) suggest independent inheritance. NIR-T and LEN, or WID, showed low GCOR. Thus, it is genetically feasible to produce cultivars with any kernel texture and LEN, or WID, combination. No GCOR was found between TW and flour milling yield (FY), TKW, NIR-T or kernel morphology. GCOR showed that harder wheats had greater FY. Traits' low correlations call for studies clarifying the efficacy of using kernel traits in wheat classification or end-use quality prediction.

Stripe (yellow) rust, caused by Puccinia striiformis West., is an important constraint to wheat production in cool environments. With the purpose of identifying genes for resistance to the disease, a RFLP mapping population of recombinant inbred lines developed from a synthetic [Triticum turgidum L. x Aegilops tauschii (Coss.) Schmal.] x T. aestivum L. cv. 'Opata 85' cross was visually evaluated for seedling infection type in three greenhouse inoculation tests and for adult-plant disease severity in four field tests at Celaya and Toluca, Mexico. A previously unidentified gene from Ae. tauschii, designated as Yr28, was located on chromosome arm 4DS. Although Yr28 strongly influenced seedling resistance, it showed a strong effect in adult plants at only the warmer of the two field sites. A second gene showed high environmental sensitivity in seedling tests, with resistance associa0ted with Opata marker alleles near the adult-plant resistance (APR) gene Yr18 on chromosome arm 7DS. Gene Yr18, known to be present in Opata, strongly reduced disease response in field trials and was tightly linked with leaf-rust resistance gene Lr34. Three other regions from Opata on chromosome arms 3BS, 3DS, and 5DS were also associated with APR.

Wheat spindle streak mosaic bymovirus (WSSMV) causes an economically important disease of winter wheat in Europe and North America. Artificial inoculation with this virus to identify resistant wheat genotypes is difficult. This study was conducted to identify restriction fragment length polymorphism (RFLP) markers associated with resistance to this disease. A population, consisting of 104 F5 recombinant inbred lines from a cross between hexaploid Triticum aestivum cultivars 'Geneva' (resistant) and 'Augusta' (susceptible), was evaluated for WSSMV symptoms under field conditions for four years. Two linked markers on the long arm of chromosome 2D, Xbcd1095 and Xcdo373, were determined to be associated with WSSMV resistance by bulked segregant analysis of the 10 most resistant and 10 most susceptible lines. Marker Xcdo373 accounted for 79% and Xbcd1095 for 73% of the phenotypic variation. Our results suggest that resistance to WSSMV in this population is qualitative in nature and is controlled by few genes. These markers should be useful in the development of wheat cultivars resistant to WSSMV and perhaps also to wheat yellow mosaic bymovirus (WYMV).Key words: wheat, wheat spindle streak mosaic virus (WSSMV), RFLP markers, resistance, bymovirus, wheat yellow mosaic virus, barley yellow mosaic virus.

Aluminum (At) toxicity limits crop productivity in acidic soils. As with many crops, natural genetic variation for Al tolerance has been found in barley (Hordeum vulgare L.). Al tolerance can be evaluated by replicated field trials, by soil bioassays in pots, or by solution culture methods. To date, alternative marker-assisted methods of Al tolerance selection in barley have not been developed. The goal of this study was to identify molecular markers for Alp, a gene in the barley cv Dayton that confers a high level of Al tolerance. An F 2 mapping population was generated from a cross between Dayton and the more aluminum-sensitive cv Harlan Hybrid. Al tolerance in this population was scored by hematoxylin staining, and was confirmed to segregate in a monogenic fashion. Restriction fragment length polymorphism (RFLP) mapping of Alp was undertaken, and it was localized to the long arm of chromosome 4H, 2.1 cM proximal to the marker Xbcd1117 and 2.1 cM distal to the markers Xwg464 and Xcdo1395. These markers can be used for marker-assisted selection of Al tolerance in barley without the need for field trials, soil bioassays, or solution culture analysis. Further, the linkage between XcdoI395 and Alp is interesting because this marker is also linked to the wheat (Triticum aestivum L.) Al tolerance gene Alt RH located on the long arm of chromosome 4D. This result is suggestive of the possibility that Al tolerance in barley and wheat may be due to the action of orthologous loci.

Recombinant inbred lines from the oat (Avena sativa L.) population Kanota × Ogle were analyzed in order to detect quantitative trait loci for Barley Yellow Dwarf resistance. Plants were scored for BYD symptoms in three locations (Urbana-Illinois, Ithaca-New York, and a greenhouse), and in four years (1992, 1993, 1994, and 1995). All plants were inoculated with infected aphids at the three-leaf stage, and the scores were recorded at the early flowering stage. Twenty one chromosomal regions distributed over 16 different linkage groups were associated with BYD resistance. Most regions came from Kanota, while only five were contributed by Ogle. A multiple linear model was fitted for each BYDV isolate in order to evaluate the best combination of markers for selection in a backcross breeding program. In IL the best model explained 19%, 5%, and 17% of the genetic variation for 1992, 1993 and 1994, respectively. The best model for NY explained 16% of the genetic variation in 1992 and8% in 1993. The best model for the greenhouse explained 46% and 44% of the genetic variation in 1994 and 1995, respectively. These models will allow genotypic selection for BYD resistance to the extent that the markers are linked to the QTL.

Background Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). Results Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. Conclusion The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.

Many plant species of agriculture importance are polyploid, having more than two copies of each chromosome per cell. In this paper, we describe statistical methods for genetic map construction in autopolyploid species with particular reference to the use of molecular markers. The first step is to determine the dosage of each DNA fragment (electrophoretic band) from its segregation ratio. Fragments present in a single dose can be used to construct framework maps for individual chromosomes. Fragments present in multiple doses can often be used to link the single chromosome maps into homologous groups and provide additional ordering information. Marker phenotype probabilities were calculated for pairs of markers arranged in different configurations among the homologous chromosomes. These probabilities were used to compute a maximum likelihood estimator of the recombination fraction between pairs of markers. A likelihood ratio test for linkage of multidose markers was derived. The information provided by each configuration and power and sample size considerations are also discussed. A set of 294 RFLP markers scored on 90 plants of the species Saccharum spontaneum L. was used to illustrate the construction of an autopolyploid map. Previous studies conducted on the same data revealed that this species of sugar cane is an autooctaploid with 64 chromosomes arranged into eight homologous groups. The methodology described permitted consolidation of 54 linkage groups into ten homologous groups.

Oat groats are unique among cereals for the high level and the embryo-plus-endosperm localization of lipids. Genetic manipulation of groat quality traits such as oil is desired for optimizing the value of oat in human and livestock diets. A locus having a major effect on oil content in oat groats was located on linkage group 11 by single-factor analysis of variance, simple interval mapping and simplified composite interval mapping. A partial oat cDNA clone for plastidic acetyl-CoA carboxylase (ACCase), which catalyzes the first committed step in de novo fatty acid synthesis, identified a polymorphism linked to this major QTL. Similar QTL and ACCase locus placements were obtained with two recombinant inbred populations, ‘Kanota’בOgle’ (KO) and ‘Kanota’בMarion’ (KM), containing 137 and 139 individual lines, respectively. By having a common parent these populations provide biological replication of the results in that significant genomic regions should be evident in analyses of multiple cross combinations. The KO population was mapped with 150 RFLP loci distributed over the genome and was grown in five diverse environments (locations and years) for measurement of groat oil content. The KM population was mapped with 60 RFLP loci and grown in three environments. The QTL linked to AccaseA on linkage group 11 accounted for up to 48% of the phenotypic variance for groat oil content. These results provide strong support for the hypothesis that ACCase has a major role in determining groat oil content. Other QTLs were identified in both populations which accounted for an additional 10–20% of the phenotypic variance.

Starch paste viscosity of wheat (Triticum aestivum L.) flour is predictive of wheat quality in some styles of oriental noodles. We mapped quantitative genetic variation for flour paste viscosity in the recombinant inbred (RI) population of 78 lines derived from the cross NY6432-18/'Clark's Cream'. The population was evaluated for three seasons in Aberdeen, ID, and one season at Moscow, ID, and Ithaca, NY. We identified nine restriction fragment length polymorphism (RFLP) markers (Xbcd1086, Xbcdl307, Xbcd135c, Xbcdl8, Xbcd402, Xbcd98, Xcdo456, Xcdo678, and Xcdo718) that were associated with significant differences (P < 0.01) in starch viscosity among the RI lines at two or more locations. The RFLP markers Xbcd1307, Xbcd135c, and Xbcd18c had the largest effects across all five environments; they were each associated with an approximate 7% increase in flour viscosity averaged across all RI lines and environments. Starch viscosity can be increased by mutations to the granule bound starch synthase (GBSS) gene of wheat. However, this mapping population is not segregating for GBSS mutations. Therefore, the quantitative trait loci (QTL) identified in this research could likely be combined with the qualitative mutations that are known in other genotypes.

The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German × S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 × S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple × S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into “homologous groups” based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.

Advances in understanding the biochemistry and genetics underlying wheat end-use quality require that cereal chemistry research utilize lines grown in the same environments. It also requires that effects of linkage disequilibrium and small ranges in trait variation be avoided. Our objectives were to: 1) ascertain the effects of genotype and environment and their interactions on hard and soft wheat end-use quality traits, and 2) examine relationships between traits and heritability, using recombinant inbred lines derived from a soft by hard wheat cross. All traits showed transgressive segregation. Kernel texture (KT) was not genetically correlated with mixograph traits, indicating the feasibility of producing soft-textured genotypes with stronger mixing properties. KT was highly genetically correlated with alkaline water retention capacity (AWRC) and moderately genetically correlated with flour yield (FY). Protein content (PRO) was not genetically correlated with dough mixing time across lines, bu...

Comparative mapping of cDNA clones provides an important foundation for examining structural conservation among the chromosomes of diverse genera and for establishing hypotheses about the relationship between gene structure and function in a wide range of organisms. In this study, “anchor probes” were selected from cDNA libraries developed from rice, oat, and barley that were informative for comparative mapping in the grass family. One thousand eight hundred probes were screened on garden blots containing DNA of rice, maize, sorghum, sugarcane, wheat, barley, and oat, and 152 of them were selected as “anchors” because (1) they hybridized to the majority of target grass species based on Southern analysis, (2) they appeared to be low or single copy in rice, and (3) they helped provide reasonably good genome coverage in all species. Probes were screened for polymorphism on mapping parents, and polymorphic markers were mapped onto existing species-specific linkage maps of rice, oat, maize, and wheat. In wheat, both polymorphic and monomorphic markers could be assigned to chromosomes or chromosome arms based on hybridization to nullitetrasomic and ditelosomic stocks. Linkage among anchored loci allowed the identification of homoeologous regions of these distantly related genomes. Anchor probes were sequenced from both ends, providing an average of 260 bp in each direction, and sequences were deposited in GenBank. BLAST was used to compare the sequences with each other and with a non-redundant protein sequence database maintained at the European Molecular Biology Laboratory (EMBL). Of the anchor probes identified in this study 78% showed significant similarity to protein sequences for known genes with BLASTX scores exceeding 100.

Chemical control of the disease with fungicides ap- plied near flowering stage is only partially effective ow- Karnal bunt (Tilletia indica Mitra) infestation of wheat (Triticum ing to the varied modes of spore transmission. It is aestivum L.) kernels reduces grain quality. Deployment of genetic resistance would be preferable to chemical applications for control commercially impractical (Fuentes-Davila and Ra- of the disease. Inoculation studies were carried out in a wheat mapping jaram, 1994) because of the zero tolerance level for KB population with the aim of locating genes for resistance. Recombinant spores imposed by importing countries. Development inbred (RI) lines from a cross between a resistant synthetic wheat of resistant cultivars is the preferred control measure. (Triticum turgidum 'Altar 84' 3 T. tauschii ) and the susceptible The main sources of resistance in CIMMYT's breeding common wheat cultivar 'Opata 85' were inoculated with Karnal bunt program have been Chinese, Indian, and Brazilian sporidial suspension and evaluated for symptom development in the wheats (Fuentes-Davila and Rajaram, 1994). field for three seasons and in the greenhouse. Based on restriction Durum wheat (Triticum durum Desf.) cultivars typi- fragment length polymorphism (RFLP) analyses, regions on chromo- cally show higher levels of field resistance to KB than some arms 3BS and 5AL carrying marker alleles from the Altar durum

Leaf rust, caused by Puccinia recondita Roberge ex Desmaz. f. sp. tritici Eriks. & E. Henn., is a serious disease of wheat (Triticum aestivum L.) worldwide. We evaluated leaf rust resistance in a RFLP-mapping population of wheat inbred lines developed from a synthetic [T. turgidum L. × T. touschii (Coss.) Schmal.] × T. aestivum cross, using inoculation trials performed on seedlings and adult plants. Map locations were assigned for seedling resistance genes LrI0 (chromosome arm 1AS), Lr23 (2BS), Lr27 (3BS), and Lr31 (4BL), and the adult-plant resistance gene Lr34 (7DS). The previously reported interaction between Lr27 and Lr31, requiring the presence of both genes for resistance to avirulent rust pathotypes, was confirmed. Lr23, effective in the durum parent (‘Altar 84’) of the synthetic, was suppressed in the synthetic and in one fourth of the inbred lines by a T. tauschii gene on homoeologous chromosome arm 2DS. This suppressor, designated as SuLr23, appears to be specific for Lr23 and may be orthologous to the gene. DNA markers are useful in refining the characterization of resistance genes and their interactions, toward the goal of constructing durably resistant cultivars via marker-controlled accumulation of specific genes.

Aluminum (Al) toxicity is a major limiting factor in acid soils and more adequate genetic tolerance is needed to improve barley adaptation and production in affected regions. To study the inheritance and chromosome location of the Alp gene controlling Al tolerance in 'Dayton' barley the primary trisomics of sensitive 'Shin Ebisu 16' were crossed to 'Dayton'. Parental, F 1 and F 2 seedlings were grown in nutrient solution containing 0.03, 0.06 and 0.09 mM Al, and classified for tolerance by haematoxylin staining of the roots. In diploid F 2 progeny, Alp was inherited as a single gene, dominant at 0.06mM and recessive at 0.09mM concentrations, as indicated by the 3:1 and 1:3 (tolerant: sensitive) segregation ratios, respectively. Segregation of the trisomic F 1 -derived F 2 seedlings at 0.06mM Al deviated significantly from the 3:1 only for the triplo 4/'Dayton' cross. Data for this cross fit the expected trisomic ratios, indicating that the Alp gene is distally located from the centromere on chromosome 4. These results confirm that tolerance is simply inherited, but expression of tolerance is dependent on Al concentration and allele dose.

In “Corn genome pops out of the pack” (News & Comment,[27 June, p. 1960][1]), Jon Cohen summarizes the June 1997 National Academy of Sciences colloquium “Protecting Our Food Supply: The Value of Plant Genome Initiatives.” The National Corn Genome Initiative, proposing a $143-million, 5-year, federally funded research program, appears to emphasize basic biological research, but because corn is known largely as an agricultural crop, it is likely that the U.S. Department of Agriculture (USDA) would finance it. Even with successful legislation, it is unlikely that new money would become available; instead, it would likely be funded by diversions from other USDA programs, such as Hatch formula funds, the National Rice Institute competitive grants program, and the Agricultural Research Service (ARS) budget. We believe that there will be serious long-term consequences should a single-crop genome research initiative be supported at the expense of existing research infrastructure or mission-oriented research on many important U.S. food crops. We support genomic research on important cereal crop plants, especially wheat, corn, and rice, the three main crops on Earth, in that order. We intend no discredit to a strong corn genome program, but without concurrent research on other species, comparative genome structure cannot be resolved. Transfer of research results from corn to other cereals will not be automatic. Each crop has unique gene complexes and characteristics and specific agricultural research needs. We urge that a national multispecies cereal crop genome program be formulated and implemented. We suggest a tripartite program emphasizing basic genomic science in corn and other cereals, development of genetic resources and methodologies specific to each crop, and application of genomics to solve agricultural and consumer-based problems. With broad-based support, the development, financing, management, and implementation of such a program should reach beyond current modes. As genomic research is innovative, so also should be its facilitation. The Human Genome Project provides valuable lessons for a new plant genome effort. # {#article-title-2} *Co-authors: # {#article-title-3} Cohen's 27 June article discusses dissatisfaction about the rate of release of Arabidopsis genome data from Japanese and European sequencing groups. The European Union (EU) Arabidopsis Sequencing Project integrates its work carefully with the U.S. and Japanese groups (for example, by providing clones for sequencing on the short arm of chromosome 4 to U.S. labs and by integrating the sequence efforts of U.S., Japanese, and European labs with respect to the short arm of chromosome 5, with the aim of rapidly generating a contiguous sequence). The third deposit of a European sequence, ten 200-kilobase contiguous units, was made to the European Bioinformatics Institute on 20 June, before Cohen's article appeared. The preparation of this contiguous sequence from individual components took some time, because it was generated from about 60 cosmid and bacterial artificial chromosome (BAC) clones and contained some difficult regions in terms of sequence complexity. Gene modeling revealed potential frameshifts, which were all resequenced. Our goal of obtaining contiguous sequences may result in initial additional complexities, but it serves the important purpose of revealing larger-scale features that are needed for planning a sequencing strategy. We are now sequencing individual BACs that will not form a contiguous sequence until later this year, when another three will have been completed. The sequences of these individual BACs can be retrieved from the Martinsried Institute for Protein Sequences website while annotation is proceeding. This release policy is consistent with that described in a Memorandum of Understanding signed with our U.S. and Japanese partners last year. The agreement was put in place after the EU component of the Arabidopsis Genome Project began, and it has taken a little time to align our release policy more closely to that thought to be required by the Arabidopsis community. The EU sequencing group knows that, although the release of sequences is a central aspect of a successful genome project, many of the more interesting features of plant chromosomes are only revealed by tackling the construction of contiguous sequences and dealing with complex regions as they occur. # {#article-title-4} Response : My article reflected the criticisms of Bevan's U.S. collaborators, who had serious misgivings about what they contend are unnecessary delays in data release. [1]: /lookup/doi/10.1126/science.276.5321.1960

The use of conventional breeding methods has resulted in consistent crop improvement within the cultivated gene pool by producing genotypes with new combinations of alleles that produce better phenotypes than either of the parents (transgressive segregation). Biotechnology has provided new methods to generate, identify, characterize, and manipulate genetic variation. Among these methods, marker assisted selection (MAS) with DNA markers has been applied in plant improvement programs. However, MAS is limited by the effort required to generate information about map location and breeding value of genes controlling important traits. Comparative genetic analysis across the domesticated grasses facilitates the identification and localization of gene sequences controlling specific traits of interest. The emerging databases of gene sequences will allow directed discovery of genes in higher plants and classification of alleles present within breeding germplasm. Identification of the genes controlling a trait and knowledge of their DNA sequence would facilitate classification of variation in the germplasm pool based on gene fingerprinting or characterization of variation in key DNA sequences. Classification of sequence variants at a targeted locus would substantially reduce the amount of work required to determine their relative breeding value and lead to the identification of superior alleles. Combining direct allele selection (DAS) with conventional selection, would allow more rapid and precise improvement of populations and breeding lines. Limitations of current technology can be minimized by transfer of genetic information across species, identification of highly variable genes, and focusing on the most important genes and traits for the species of interest.

Genetic progress through selection is directly related to the amount of variability present in the population and the quality of genes contributed by the parents. Genetic relationships between lines were studied using DNA marker-based estimates of genetic similarity. A statistical methodology using the width of a confidence interval was developed to determine the number of probes to be surveyed and the precision in the estimation of genetic distance between pairs of cultivars. Precision was affected by type of genetic distance used, the number of cultivars, and amount of genetic diversity present in the studied group. The width of a (1-α)% confidence interval decreased as the number of RFLP fragments increased. Oat and wheat diversity studies were used to illustrate the methodology.

Incorporation of genetic diversity into elite wheat (Triticum aestivum L., 2n1⁄4 6x1⁄4 42, AABBDD) cultivars has long been recognized as a means of improving wheat productivity and securing global wheat supply. Synthetic hexaploid wheat (SHW) genotypes recreated from its two progenitor species, the tetraploid, Triticum turgidum (2n1⁄4 4x1⁄4 28, AABB) and its diploid wild relative, Aegilops tauschii (2n1⁄4 2x1⁄4 14, DD) are a useful resource of new genes for hexaploidwheat improvement. These include many productivity traits such as abiotic (drought, heat, salinity/sodicity, andwaterlogging) and biotic (rusts, septoria, barley yellow dwarfvirus (BYDV), crownrot, tan spot, spot blotch, nematodes,powderymildew, and fusarium head blight) stress resistance/tolerances as well as novel grain quality traits. Numerous SHWs have been produced globally by various institutions including CIMMYT-Mexico, ICARDA-Syria, Department of Primary Industries (DPI), Victoria-Australia, IPK-Germany, Kyoto University-Japan, and USDAARS. This review examines the varied aspects in the utilization of synthetics for wheat improvement including the traits and genes identified, mapped, and transferred to common wheat. It has also been demonstrated that synthetic backcross-derived lines (SBLs, i.e., when SHW is crossed to adapted local bread varieties) show significant yield increases and thus, enhanced yield performance across a diverse range of environments, demonstrating their potential for improving wheat productivity worldwide. This is particularly evident in moisturelimited environments. The use of SBLs, advanced backcross QTL analysis, chromosome introgression lines, and whole genome association mapping is contributing to the elucidation of the genetic architecture of some of the traits. The contribution of transgressive segregation to enhanced phenotypes and the mechanisms including its genetic and physiological basis are yet to be elucidated. 36 FRANCIS C. OGBONNAYA ET AL.

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

Genetic relationship can be a useful predictor of the relative performance of hybrid combinations for a hybrid breeding program resulting in reduced time and cost of hybrid testing. Genetic relationships of 112 wheat (Triticum aestivum L. em. Thell.) lines were estimated using 41 DNA clones hybridizing to 273 DNA fragments and by calculating coefficient of parentage (COP). Heterosis was estimated for 722 hybrids grown in multiple locations, with 189 being tested in more than 1 year. The average RFLP (restriction fragment length polymorphism) based genetic distance index (DI) was 0.35. Midparent heterosis for grain yield ranged from −20 to 57% and high-parent heterosis from −22 to 47%. The correlation between RFLP-based estimates of genetic distance and COP was nonsignificant (−0.33). Coefficient of parentage was significantly correlated with heterosis for all traits in 1991 but not in other years. Genetic distance based on RFLPs scored in this study was not correlated with heterosis in any of the years tested. Further refinement of gene pools and new prediction methods will be required to facilitate the exploitation of genetic variability for hybrid wheat improvement. Key words : wheat, heterosis, genetic distance.

Chromosome 3 displayed the two largest yield QTLs in a previous study of 150 doubled haploid lines derived from a cross of Steptoe and Morex barley varieties. Low-copy number RFLP markers, detected using Southern analysis, are excellent tools for generating robust linkage maps as demonstrated by the Steptoe and Morex map produced by the North American Barley Genome Mapping Project (SM NABGMP). However, this technique can be cumbersome when applied to practically oriented plant breeding programs. In the present report, we demonstrate the conversion of RFLPs to more practically useful PCR-based markers that are co-dominant and allelic to the barley chromosome-3 RFLP markers from which they derive. We have used these sequence-tagged-site (STS) PCR markers to evaluate the putative yield QTL components of the Steptoe chromosome 3 in a Morex backcross population. Headshattering, plant lodging, and yield measurements are reported from five replicated field experiments conducted under diverse growing conditions in Montana. Our study detected significant effects for all three traits in a chromosomal region that evidently corresponds to the larger of the two previously reported chromosome-3 QTLs. However, we failed to detect any yield or other effects which might be coincidental to the second largest yield QTL. The genetic effects of the yield QTL identified in our first backcross breeding population show similar magnitude, environmental interactions, and association with lodging and headshattering QTLs observed in the SM NABGMP experiments. Our study elucidates complex environmental conditioning for headshattering and plant lodging which probably underlie the variable yield effects observed under different growing conditions.

Estimation of genetic diversity present in gene pools is an important determination for breeding programs. This study was conducted to determine the level of variation in durum wheat cultivars (Triticum turgidum L. var durum) based on different measures. Genetic diversity in durum wheat was measured in a collection of 113 improved cultivars and landraces of diverse ecogeographical origin by means of restriction fragment length polymorphism (RFLP), morphophysiological traits, and coefficient of parentage (COP). Thirty-nine clones and a single restriction enzyme were used to measure the RFLP-based genetic distance. Average taxonomic distances were calculated for the morphophysiological traits evaluated in four location-years. Lower genetic distances were observed for both RFLP and morphophysiological traits for the improved cultivars and for some landraces from Morocco and Jordan, while genetic distances were larger for the rest of the landraces. Patterns of variation for morphophysiological traits were associated with days to heading, plant height, and harvest index. Landraces contained 99% of the total fragments observed in the pool of improved varieties and showed 13% unique fragments. Coefficient of parentage analysis revealed 15 ancestral lines that contributed 72% of the genetic make up of improved cultivars. Thirty-nine different ancestors contributed to the remaining 28%. Correlation of distances based on different measures was higher for average taxonomic distance and Nei's genetic distance (r = 0.47) while COP relationship with the other two measures was lower. Narrower genetic diversity in breeding lines based on the measures used, suggests the utilization of other sources of variation.