Agronomy & Plant Genetics

Stem rust is a major disease of wheat (Triticum aestivum L.) worldwide and new Puccinia graminis f. sp. tritici (Pgt) races including TTKSK (Ug99) pose a serious threat to wheat production. The protection of new varieties against Pgt races can be increased by identifying and combining several types of stem rust resistance genes (Sr). We screened a set of 707 wheat lines and cultivars against 11 Pgt races under glass house conditions. Of the tested lines, groups of 99, 513, 289, and 515 exhibited low infection type (IT < 3) to races TTKSK, TRTTF, TTTTF, and RRTTF, respectively. Screening against Pgt races (QFCSC, QTHJC, MCCFC, RCRSC, RKRQC, TPMKC, and QCCSM) showed that most of the tested lines were resistant. These lines were screened with eight DNA markers for the presence of Sr2,

Molecular markers are developed to accelerate deployment of genes for desirable traits segregated in a bi-parental population of recombinant inbred lines (RILs) or doubled haplotype (DH) lines for mapping. However, it would be the most effective if such markers for multiple traits could be identified in an F2 population. In this study, single nucleotide polymorphisms (SNP) chips were used to identify major genes for heading date and awn in an F2 population without developing RILs or DH lines. The population was generated from a cross between a locally adapted spring wheat cultivar “Ningmaizi119” and a winter wheat cultivar “Tabasco” with a diverse genetic background. It was found that the dominant Vrn-D1 allele could make Ningmaizi119 flowered a few months earlier than Tabasco in the greenhouse and without vernalization. The observed effects of the allele were validated in F3 populations. It was also found that the dominant Ali-A1 allele for awnless trait in Tabasco or the recessive...

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. C OMMON wheat (Triticum aestivum L.) is an allo-important cereals, the wheat genome with 16,000 Mb is hexaploid (2n ϭ 6x ϭ 42, AABBDD) containing the largest and rice (Oryza sativa L.) with 415 Mb is the three homoeologous genomes (Sears 1954). Among smallest (Arumuganathan and Earle 1991). The wheat genome is ‫001ف‬ times larger than the model plant Arabidopsis. Even in Arabidopsis only ‫%54ف‬ of the genome 1 These authors contributed equally to this work. represents the gene-containing fraction that is inter-2 Present address: Department of Agronomy, Iowa State University, spersed with noncoding DNA primarily composed of ret-Ames, IA 50014-8122. rotransposon-like repetitive sequences (Barakat et al.

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. G ENOME analysis has been used to establish the hexaploid wheat (Triticum aestivum L.). Each of the 21 evolutionary and homoeologous relationships of chromosomes has been identified and characterized by the three genomes (AA, BB, and DD) that make up with respect to genomic and homoeologous relationships. There is a high degree of colin-1 Present address: Plant Breeding and Acclimatization Institute,

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 map 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 Յ e Ϫ10 ), 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 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses. 2003). The hexaploid wheat genome is also much larger than any of the current plant model species, ‫53ف‬ times 2 Present address:

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n ϭ 6x ϭ 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 5Ј and 3Ј 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. adapted of the major crops, thus offering potential for H EXAPLOID wheat (2n ϭ 6x ϭ 42, Triticum aestiincreased food production. Hexaploid wheat is comvum L.) is one of the world's cornerstone crops, posed of three genomes (A, B, and D), each of which feeds more people than any other crop ‫006ف(‬ million tons is produced annually), and is the most widely contains seven pairs of chromosomes, which have been identified and characterized by Sears (1966), who established that there is a strong homoeologous relationship among chromosomes belonging to the three ge-1

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 the numbers of loci were significantly lower in the 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. C OMMON wheat (Triticum aestivum L., 2n ϭ 6x ϭ that of rice (Oryza sativa L.) and ‫011ف‬ times that of Arabidopsis (Bennett and Smith 1976). It is composed 42, AABBDD) has a genome of ‫61ف‬ million kilobases per haploid cell, which is 35 times larger than of three genomes, contributed by T. uratu Tum. ex Gand. (A genome), Aegilops speltoides Tausch or an extinct close relative (B genome), and Ae. tauschii Coss. (D genome; McFadden and Sears 1946; Kihara 1954; 1 Present address: USDA-ARS Biosciences Research Laboratory, Fargo, ND 58105-5674. Nishikawa 1983; Dvořák and Zhang 1990). The order 2 Present address: Plant Breeding and Acclimatization Institute, Radzi-of loci in these three genomes is thought to be colinear kow 05-870 Blonie, Poland. except for a 4A-5A-7B translocation, a putative 2B-6B 3 Present address: Department of Plant Sciences, North Dakota State translocation, and two inversions on chromosome 4A University, Fargo, ND 58105-5051. (Devos et al. 1995;.

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the 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 highdensity 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.

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 for these 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. Good 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).

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.

The development of wheat varieties with resistance to Fusarium head blight is a major breeding goal for the University of Minnesota's spring wheat breeding program. Currently, the program selects for FHB resistance using a combination of targeted molecular markers associated with major QTL, and phenotypic evaluation in misted, inoculated disease nurseries over several years and environments. Phenotypic selection for FHB resistance is a resource intensive activity, and adds time to the breeding cycle. Genome-wide predictive modeling of line performance has the potential to reduce time and resources allocated to phenotypic selection. Program and trait-specific models need to be evaluated to empirically assess their efficacy in predicting the performance of lines for FHB associated traits. Here we present genome-wide prediction model accuracies for FHB-related traits, expressed as the correlation between the phenotype predicted by the model, and the BLUP of the observed phenotype.

The use of haplotypes may improve the accuracy of genomic prediction over single SNPs because haplotypes can better capture linkage disequilibrium and genomic similarity in different lines and may capture local high-order allelic interactions. Additionally, prediction accuracy could be improved by portraying population structure in the calibration set. A set of 383 advanced lines and cultivars that represent the diversity of the University of Minnesota wheat breeding program was phenotyped for yield, test weight, and protein content and genotyped using the Illumina 90K SNP Assay. Population structure was confirmed using single SNPs. Haplotype blocks of 5, 10, 15, and 20 adjacent markers were constructed for all chromosomes. A multi-allelic haplotype prediction algorithm was implemented and compared with single SNPs using both k-fold cross validation and stratified sampling optimization. After confirming population structure, the stratified sampling improved the predictive ability co...

Genomic selection combines phenotypic and molecular marker data from a training population to predict the genotypic values of untested lines. It can improve breeding efficiency as large pools of untested lines can be evaluated for selection. Training population (TP) composition is one of the most important factors affecting the accuracy of genomic prediction. The University of Minnesota wheat breeding program implements genomic selection at the F5 stage for Fusarium head blight (FHB) resistance. This study used field data for FHB resistance in wheat (Triticum aestivum L.) to investigate the use of small-size TPs designed with and without stratified sampling for three FHB traits in three different F5 populations (TP17, TP18, and TP19). We also compared the accuracies of these two TP design methods with the accuracy obtained from a large size TP. Lastly, we evaluated the impact on trait predictions when the parents of F5 lines were included in the TP. We found that the small size TP s...

Background A 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. Results Nucleotide 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 ...

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 characteri...

Develop a marker-assisted selection protocol for an FHB resistance gene in wheat Screening for Fusarium head blight (FHB) resistance using greenhouse and field-based screening are made difficult by quantitative inheritance, laborious screening methods, and environmental effects. Selection for molecular markers linked to resistance genes may be a more effective means of screening. We have identified quantitative trait loci (QTL) for

2 Interrelationships between ontogeny, allometric mass, and carbon (C): nitrogen (N): phosphorus (P) ratios were quantified in Cuphea, a semi-domesticated indeterminate and phenotypically plastic potential oilseed crop. Relative growth rate and net assimilation rate were estimated as functions of growth stages, phenotypic traits and C:N:P ratios. Ontogenically, N:P ratios in reproductive and metabolic tissues were least variable and were mainly affected by allometric leaf mass and relative growth rate. Reproductive mass is best predicted by allometric stem mass and C:N ratio in structural and metabolic tissues; whereas, net assimilation rate is best predicted by allometric total branch length and relative growth rate. The conservative N:P ratios found in reproductive and metabolic tissues are important in determining reproductive allocation in Cuphea. Large antagonistic effects of C:N on N:P ratios found in different plant tissues suggest that maximum reproductive allocation can be attained by manipulating N:P ratio during ontogeny. A greater investment of resources in reproduction may be possible for this semi-domesticated crop if nutrient and mass allocation to supporting stems and roots can be altered for the benefit of reproductive biomass.

We modeled the Xowering and capsule set dynamics, quantiWed the level of variation in seed characteristics, elucidated the inter-relationships between seed and capsule physical dimensions, and quantiWed their impact on single seed weight in the cuphea germplasm line PSR23. Temporal patterns of Xowering and capsule set were largely time-dependent and highly auto-correlated, with signiWcant autoregressive parameters of number of Xowers (0.76) and number of capsules (0.74). Large numbers of seeds per capsule were associated with large coeYcient of variation in single seed weight. Seed number and seed weight per capsule, when log-transformed, exhibited a slope of ¡0.65 indicating that cuphea plants have only a limited capacity to maintain seed weight by adjusting seed number if resources vary. Capsule tissue/seed weight ratio and number of seeds per capsule have the largest potential impact on single seed weight. Sensitivity analyses indicated that capsule perimeter (>76 mm), capsule major (>23 mm) and minor axes (>7.0 mm), capsule circularity (between 0.350 and 0.375), capsule area (<85 mm 2 ), capsule tissue/seed weight ratio (<0.40), and number of seeds per capsule (»9.0) would optimize single seed weight. This information would help plant breeders exploit genotypic variability in seed and capsule characteristics and agronomists identify optimum trait combinations to produce high yields of this potential oilseed crop.