Analysis of the Structural Organization and Expression of the Vrn-D1 Gene Controlling Growth Habit (Spring vs. Winter) in Aegilops tauschii Coss

The duration of the vegetative period is an important agronomic characteristic of cereal crops. It is mainly influenced by the Vrn (response to vernalization) and Ppd (response to photoperiod) genes. In this work, we searched for alleles of several known genes of these two systems of response to external conditions in 15 accessions of Aegilops tauschii Coss. (syn. Ae. squarrosa L.), with the aim of studying the impact these alleles have on the vegetative period duration and growth habit. As a result, three allelic variants have been found for the Vrn-D1 gene: (i) one intact (winter type), (ii) one with a 5437 bp deletion in the first intron and (iii) one previously undescribed allele with a 3273 bp deletion in the first intron. It has been shown that the spring growth habit of Ae. tauschii can be developed due to the presence of a new allele of the Vrn-D1 gene. Significant differences in expression levels between the new allelic variant of the Vrn-D1 gene and the intact allele vrn-D1 were confirmed by qPCR. The new allele can be introgressed into common wheat to enhance the biodiversity of the spring growth habit and vegetative period duration of plants.

Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat

Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.

Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes

The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii.

Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Background

One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping.

Results

The DArTseq GBS approach generated 10 K SNPs and 40 K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsp. durum, turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin.

Conclusions

The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties, and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

Using intervarietal substitution lines for the identification of wheat chromosomes involved in early responses to water-deficit stress

Water deficit induces reactive oxygen species (ROS) overproduction, which in turn inhibits plant growth and development. High concentrations of ROS disrupt the osmotic balance in plant cells and alter membrane integrity. Chromosomes carrying structural or regulatory genes must be detected to better understand plant response mechanisms to stress. The aim of our study was to identify Triticum aestivum L. chromosomes involved in early responses to short-term water-deficit stress (1, 3 and 6 h). In the present study, intervarietal substitution lines of drought-tolerant 'Saratovskaya 29' and sensitive 'Janetzkis Probat' wheat cultivars were examined. We studied the biochemical plant response system and conducted an analysis of catalase, ascorbate peroxidase and guaiacol peroxidase activities, levels of lipid peroxidation and changes in relative water content. Our results determined that the first reaction was a significant increase in guaiacol peroxidase (GPX) activity. However, the strongest impact on plant responses was found for catalase (CAT), which caused a significant decrease in lipid peroxidation (LPO) levels. Our findings indicate that chromosomes 5A, 4B, 6B and 7D are associated with early responses to short-term osmotic stress in wheat.

Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii

Aegilops tauschii, the D-genome donor of bread wheat, Triticum aestivum, is a storehouse of genetic diversity, and an important resource for future wheat improvement. Genomic and population analysis of 549 Ae. tauschii and 103 wheat accessions was performed by using 13,135 high quality SNPs. Population structure, principal component, and cluster analysis confirmed the differentiation of Ae. tauschii into two lineages; lineage 1 (L1) and lineage 2 (L2), the latter being the wheat D-genome donor. Lineage L1 contributes only 2.7% of the total introgression from Ae. tauschii for a set of United States winter wheat lines, confirming the great amount of untapped genetic diversity in L1. Lineage L2 accessions had overall greater allelic diversity and wheat accessions had the least allelic diversity. Both lineages also showed intra-lineage differentiation with L1 being driven by longitudinal gradient and L2 differentiated by altitude. There has previously been little reported on natural hybridization between L1 and L2. We found nine putative inter-lineage hybrids in the population structure analysis, each containing numerous lineage-specific private alleles from both lineages. One hybrid was confirmed as a recombinant inbred between the two lineages, likely artificially post collection. Of the remaining eight putative hybrids, a group of seven from Georgia carry 713 SNPs with private alleles, which points to the possibility of a novel L1-L2 hybrid lineage. To facilitate the use of Ae. tauschii in wheat improvement, a MiniCore consisting of 29 L1 and 11 L2 accessions, has been developed based on genotypic, phenotypic and geographical data. MiniCore reduces the collection size by over 10-fold and captures 84% of the total allelic diversity in the whole collection.

Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions

Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.

Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions

Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.

BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust

Crop diseases reduce wheat yields by ~25% globally and thus pose a major threat to global food security¹. Genetic resistance can reduce crop losses in the field and can be selected through the use of molecular markers. However, genetic resistance often breaks down following changes in pathogen virulence, as experienced with the wheat yellow (stripe) rust fungus Puccinia striiformis f. sp. tritici (Pst)². This highlights the need to (1) identify genes that, alone or in combination, provide broad-spectrum resistance, and (2) increase our understanding of the underlying molecular modes of action. Here we report the isolation and characterization of three major yellow rust resistance genes (Yr7, Yr5 and YrSP) from hexaploid wheat (Triticum aestivum), each having a distinct recognition specificity. We show that Yr5, which remains effective to a broad range of Pst isolates worldwide, is closely related yet distinct from Yr7, whereas YrSP is a truncated version of Yr5 with 99.8% sequence identity. All three Yr genes belong to a complex resistance gene cluster on chromosome 2B encoding nucleotide-binding and leucine-rich repeat proteins (NLRs) with a non-canonical N-terminal zinc-finger BED domain³ that is distinct from those found in non-NLR wheat proteins. We developed diagnostic markers to accelerate haplotype analysis and for marker-assisted selection to expedite the stacking of the non-allelic Yr genes. Our results provide evidence that the BED-NLR gene architecture can provide effective field-based resistance to important fungal diseases such as wheat yellow rust.

Interspecific and intergeneric hybridization as a source of variation for wheat grain quality improvement

The hybridization events with wild relatives and old varieties are an alternative source for enlarging the wheat quality variability. This review describes these process and their effects on the technological and nutritional quality. Wheat quality and its end-uses are mainly based on variation in three traits: grain hardness, gluten quality and starch. In recent times, the importance of nutritional quality and health-related aspects has increased the range of these traits with the inclusion of other grain components such as vitamins, fibre and micronutrients. One option to enlarge the genetic variability in wheat for all these components has been the use of wild relatives, together with underutilised or neglected wheat varieties or species. In the current review, we summarise the role of each grain component in relation to grain quality, their variation in modern wheat and the alternative sources in which wheat breeders have found novel variation.

The use of SNP hybridisation arrays and cytogenetics to characterise deletions of chromosome 4B in hexaploid wheat (Triticum aestivum L.)

Many deletions of the wheat Della ( Rht - B1 ) gene and its flanking regions were isolated in a simple phenotypic screen, and characterised by modified analysis of SNP hybridisation data and cytogenetics. In a dwarf wheat suppressor screen, many tall 'revertants' were isolated following mutagenesis of a severely dwarfed (Rht-B1c) hexaploid wheat. About 150 lines were identified as putative deletions of Rht-B1c, based on the PCR analysis. Southern blot hybridisation established that most of them lacked the Rht-B1 gene, but retained the homoeologues Rht-A1 and Rht-D1. PCR assays were developed for orthologues of two genes that flank Rht-1/Della in the genomes of the model species Brachypodium and rice. Deletion of the B-genome-specific homoeologues of these two genes was confirmed in the Rht-B1 deletion lines, indicating loss of more than a single gene. SNP chip hybridisation analysis established the extents of deletion in these lines. Based on the synteny with Brachypodium chromosomes 1 and 4 g, and rice chromosomes 3g and 11g, notional deletion maps were established. The deletions ranged from interstitial deletions of 4BS through to loss of all 4BS markers. There were also instances, where all 4BS and 4BL markers were lost, and these lines had poor fertility and narrow stems and leaves. Cytogenetic studies on selected lines confirmed the loss of portions of 4BS in lines that lacked most or all 4BS markers. They also confirmed that lines lacking both 4BS and 4BL markers were nullisomics for 4B. These nested deletion lines share a common genetic background and will have applications in assigning markers to regions of 4BS as well as to 4BL. The potential for this type of analysis in other regions of the wheat genome is discussed.

Seedling Resistance to Stem Rust and Molecular Marker Analysis of Resistance Genes in Wheat Cultivars of Yunnan, China

Stem rust is one of the most potentially harmful wheat diseases, but has been effectively controlled in China since 1970s. However, the interest in breeding wheat with durable resistance to stem rust has been renewed with the emergence of Ug99 (TTKSK) virulent to the widely used resistance gene Sr31, and by which the wheat stem rust was controlled for 40 years in wheat production area worldwide. Yunnan Province, located on the Southwest border of China, is one of the main wheat growing regions, playing a pivotal role in the wheat stem rust epidemic in China. This study investigated the levels of resistance in key wheat cultivars (lines) of Yunnan Province. In addition, the existence of Sr25, Sr26, Sr28, Sr31, Sr32, and Sr38 genes in 119 wheat cultivars was assessed using specific DNA markers. The results indicated that 77 (64.7%) tested wheat varieties showed different levels of resistance to all the tested races of Puccinia graminis f. sp. tritici. Using molecular markers, we identified the resistance gene Sr31 in 43 samples; Sr38 in 10 samples; Sr28 in 12 samples, and one sample which was resistant against Ug99 (avirulent to Sr32). No Sr25 or Sr26 (effective against Ug99) was identified in any cultivars tested. Furthermore, 5 out of 119 cultivars tested carried both Sr31 and Sr38 and eight contained both Sr31 and Sr28. The results enable the development of appropriate strategies to breed varieties resistant to stem rust.

Identification and genetic mapping of PmAF7DS a powdery mildew resistance gene in bread wheat (Triticum aestivum L.)

Gene PmAF7DS confers resistance to wheat powdery mildew (isolate Bgt#211 ); it was mapped to a 14.6-cM interval ( Xgwm350 a- Xbarc184 ) on chromosome 7DS. The flanking markers could be applied in MAS breeding. Wheat powdery mildew (Pm) is caused by the biotrophic pathogen Blumeria graminis tritici (DC.) (Bgt). An ongoing threat of breakdown of race-specific resistance to Pm requires a continuous effort to discover new alleles in the wheat gene pool. Developing new cultivars with improved disease resistance is an economically and environmentally safe approach to reduce yield losses. To identify and characterize genes for resistance against Pm in bread wheat we used the (Arina × Forno) RILs population. Initially, the two parental lines were screened with a collection of 61 isolates of Bgt from Israel. Three Pm isolates Bgt#210 , Bgt#211 and Bgt#213 showed differential reactions in the parents: Arina was resistant (IT = 0), whereas Forno was moderately susceptible (IT = -3). Isolate Bgt#211 was then used to inoculate the RIL population. The segregation pattern of plant reactions among the RILs indicates that a single dominant gene controls the conferred resistance. A genetic map of the region containing this gene was assembled with DNA markers and assigned to the 7D physical bin map. The gene, temporarily designated PmAF7DS, was located in the distal region of chromosome arm 7DS. The RILs were also inoculated with Bgt#210 and Bgt#213. The plant reactions to these isolates showed high identity with the reaction to Bgt#211, indicating the involvement of the same gene or closely linked, but distinct single genes. The genomic location of PmAF7DS, in light of other Pm genes on 7DS is discussed.

Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture

Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5-15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution. If several cloned R genes were available, it would be possible to pyramid R genes in a crop, which might provide more durable resistance. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.

A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments

Background

Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat varieties that maintain yield (YD) under moderate or even intense nitrogen (N) deficiency can adapt to low input management systems. A detailed genetic map is necessary for both wheat molecular breeding and genomics research. In this study, an F_6:7 recombinant inbred line population comprising 188 lines was used to construct a novel genetic map and subsequently to detect quantitative trait loci (QTL) for YD and response to N stress.

Results

A genetic map consisting of 591 loci distributed across 21 wheat chromosomes was constructed. The map spanned 3930.7 cM, with one marker per 6.7 cM on average. Genomic simple sequence repeat (g-SSR), expressed sequence tag-derived microsatellite (e-SSR), diversity arrays technology (DArT), sequence-tagged sites (STS), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeat (ISSR) molecular markers were included in the map. The linear relationships between loci found in the present map and in previously compiled physical maps were presented, which were generally in accordance. Information on the genetic and physical positions and allele sizes (when possible) of 17 DArT, 50 e-SSR, 44 SRAP, five ISSR, and two morphological markers is reported here for the first time. Seven segregation distortion regions (SDR) were identified on chromosomes 1B, 3BL, 4AL, 6AS, 6AL, 6BL, and 7B. A total of 22 and 12 QTLs for YD and yield difference between the value (YDDV) under HN and the value under LN were identified, respectively. Of these, QYd-4B-2 and QYddv-4B, two major stable QTL, shared support interval with alleles from KN9204 increasing YD in LN and decreasing YDDV. We probe into the use of these QTLs in wheat breeding programs. Moreover, factors affecting the SDR and total map length are discussed in depth.

Conclusions

This novel map may facilitate the use of novel markers in wheat molecular breeding programs and genomics research. Moreover, QTLs for YD and YDDV provide useful markers for wheat molecular breeding programs designed to increase yield potential under N stress.

A review of the occurrence of Grain softness protein-1 genes in wheat (Triticum aestivum L.)

Grain softness protein-1 (Gsp-1) is a small, 495-bp intronless gene found throughout the Triticeae tribe at the distal end of group 5 chromosomes. With the Puroindolines, it constitutes a key component of the Hardness locus. Gsp-1 likely plays little role in grain hardness, but has direct interest due to its utility in phylogeny and its role in arabinogalactan peptides. Further role(s) remain to be identified. In the polyploid wheats, Triticum aestivum and T. turgidum, the gene is present in a homoeologous series. Since its discovery, there have been conflicting reports and data as to the number of Gsp-1 genes and the level of sequence polymorphism. Little is known about allelic variation within a species. In the simplest model, a single Gsp-1 gene is present in each wheat and Aegilops tauschii genome. The present review critically re-examines the published and some unpublished data (sequence available in the NCBI nucleotide and MIPS Wheat Genome Databases). A number of testable hypotheses are identified, and include the level of polymorphism that may represent (and define) different Gsp-1 alleles, the existence of a fourth Gsp-1 gene, and the apparent, at times, high level of naturally-occurring or artifactual gene chimeras. In summary, the present data provide firm evidence for at most, three Gsp-1 genes in wheat, although there are numerous data that suggest a more complex model.

Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat

Group 1 chromosomes of the Triticeae tribe have been studied extensively because many important genes have been assigned to them. In this paper, chromosome 1 linkage maps of Triticum aestivum, T. tauschii, and T. monococcum are compared with existing barley and rye maps to develop a consensus map for Triticeae species and thus facilitate the mapping of agronomic genes in this tribe. The consensus map that was developed consists of 14 agronomically important genes, 17 DNA markers that were derived from known-function clones, and 76 DNA markers derived from anonymous clones. There are 12 inconsistencies in the order of markers among seven wheat, four barley, and two rye maps. A comparison of the Triticeae group 1 chromosome consensus map with linkage maps of homoeologous chromosomes in rice indicates that the linkage maps for the long arm and the proximal portion of the short arm of group 1 chromosomes are conserved among these species. Similarly, gene order is conserved between Triticeae chromosome 1 and its homoeologous chromosome in oat. The location of the centromere in rice and oat chromosomes is estimated from its position in homoeologous group 1 chromosomes of Triticeae.

Molecular cytogenetic analysis of Agropyron chromatin specifying resistance to barley yellow dwarf virus in wheat

Nine families of bread wheat (TC5, TC6, TC7, TC8, TC9, TC10, TC14, 5395-(243AA), and 5395) with resistance to barley yellow dwarf virus and containing putative translocations between wheat and a group 7 chromosome of Agropyron intermedium (L1 disomic addition line, 7Ai#1 chromosome) induced by homoeologous pairing or tissue culture were analyzed. C-banding, genomic in situ hybridization (GISH), and restriction fragment length polymorphism (RFLP) in combination with repetitive Agropyron-specific sequences and deletion mapping in wheat were used to determine the relative locations of the translocation breakpoints and the size of the transferred alien chromatin segments in hexaploid wheat-Agropyron translocation lines. All homoeologous compensating lines had complete 7Ai#1 or translocated 7Ai#1-7D chromosomes that substitute for chromosome 7D. Two complete 7Ai#1 (7D) substitution lines (5395-(243AA) and 5395), one T1BS-7Ai#1S∙7Ai#1L addition line (TC7), and two different translocation types, T7DS-7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and T7DS∙7DL-7Ai#1L (TC14), substituting for chromosome 7D were identified. The substitution line 5395-(243AA) had a reciprocal T1BS∙1BL-4BS/T1BL-4BS∙4BL translocation. TC14 has a 6G (6B) substitution. The RFLP data from deletion mapping studies in wheat using 37 group 7 clones provided 10 molecular tagged chromosome regions for homoeologous and syntenic group 7 wheat or Agropyron chromosomes. Together with GISH we identified three different sizes of the transferred Agropyron chromosome segments with approximate breakpoints at fraction length (FL) 0.33 in the short arm of chromosome T7DS-7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and another at FL 0.37 of the nonhomoeologous translocated chromosome T1BS-7Ai#1S∙7Ai#1L (TC7). One breakpoint was identified in the long arm of chromosome T7DS∙7DL-7Ai#1L (TC14) at FL 0.56. We detected some nonreciprocal translocations for the most proximal region of the chromosome arm of 7DL, which resulted in small duplications. Key words : C-banding, genomic in situ hybridization (GISH), physical mapping, translocation mapping, RFLP analysis.

The use of cell culture for subchromosomal introgressions of barley yellow dwarf virus resistance from Thinopyrum intermedium to wheat

Barley yellow dwarf virus (BYDV) resistance has been transferred to wheat from a group 7 chromosome of Thinopyrum (Agropyron) intermedium. The source of the resistance gene was the L1 disomic addition line, which carries the 7Ai-1 chromosome. The resistance locus is on the long arm of this chromosome. BYDV resistant recombinant lines were identified after three or more generations of selection against a group 7 Th. intermedium short arm marker (red coleoptile) and selection for the presence of BYDV resistance. One recombinant line produced by ph. mutant induced homoeologous pairing and 14 recombinant lines induced by cell culture have been identified. Resistance in seven of the cell culture induced recombinants has been inherited via pollen according to Mendelian segregation ratios for up to eight generations. Meiotic analysis of heterozygotes indicates that the alien chromatin in the cell culture induced recombinants is small enough to allow regular meiotic behaviour. The ph-induced recombinant was less regular in meiosis. A probe, pEleAcc2, originally isolated from Th. elongatum and that hybridizes to dispersed repeated DNA sequences, was utilised to detect Th. intermedium chromatin, which confers resistance to BYDV, in wheat backgrounds. Quantification of these hybridization signals indicated that the translocations involved a portion of alien chromatin that was smaller than the complete long arm of 7Ai-1. Restriction fragment length polymorphism analysis confirmed the loss of the short arm of 7Ai-1 and indicated the retention of segments of the long arm of 7Ai-1. Two 7Ai-1L DNA markers always assorted with the BYDV resistance. A third 7Ai-IL DNA marker was also present in seven of eight recombinants. In all recombinants except TC7, the 7Ai-1L markers replaced the 7DL markers. None of the wheat group 7 markers was missing from TC7. It is concluded that all the resistant lines are the result of recombination with wheat chromosome 7D, except line TC7, which is the result of recombination with an unidentified nongroup 7 chromosome.

Molecular genetic maps of the group 6 chromosomes of hexaploid wheat (Triticum aestivum L. em. Thell.)

Restriction fragment length polymorphism (RFLP) maps of chromosomes 6A, 6B, and 6D of hexaploid wheat (Triticum aestivum L. em. Thell.) have been produced. They were constructed using a population of F7-8 recombinant inbred lines derived from a synthetic wheat x bread wheat cross. The maps consist of 74 markers assigned to map positions at a LOD >= 3 (29 markers assigned to 6A, 24 to 6B, and 21 to 6D) and 2 markers assigned to 6D ordered at a LOD of 2.7. Another 78 markers were assigned to intervals on the maps. The maps of 6A, 6B, and 6D span 178, 132, and 206 cM, respectively. Twenty-one clones detected orthologous loci in two homoeologues and 3 detected an orthologous locus in each chromosome. Orthologous loci are located at intervals of from 1.5 to 26 cM throughout 70% of the length of the linkage maps. Within this portion of the maps, colinearity (homosequentiality) among the three homoeologues is strongly indicated. The remainder of the linkage maps consists of three segments ranging in length from 47 to 60 cM. Colinearity among these chromosomes and other Triticeae homoeologous group 6 chromosomes is indicated and a consensus RFLP map derived from maps of the homoeologous group 6 chromosomes of hexaploid wheat, tetraploid wheat, Triticum tauschii, and barley is presented. Key words : RFLP, wheat, linkage maps, molecular markers.

New slow-rusting leaf rust and stripe rust resistance genes Lr67 and Yr46 in wheat are pleiotropic or closely linked

The common wheat genotype 'RL6077' was believed to carry the gene Lr34/Yr18 that confers slow-rusting adult plant resistance (APR) to leaf rust and stripe rust but located to a different chromosome through inter-chromosomal reciprocal translocation. However, haplotyping using the cloned Lr34/Yr18 diagnostic marker and the complete sequencing of the gene indicated Lr34/Yr18 is absent in RL6077. We crossed RL6077 with the susceptible parent 'Avocet' and developed F(3), F(4) and F(6) populations from photoperiod-insensitive F(3) lines that were segregating for resistance to leaf rust and stripe rust. The populations were characterized for leaf rust resistance at two Mexican sites, Cd. Obregon during the 2008-2009 and 2009-2010 crop seasons, and El Batan during 2009, and for stripe rust resistance at Toluca, a third Mexican site, during 2009. The F(3) population was also evaluated for stripe rust resistance at Cobbitty, Australia, during 2009. Most lines had correlated responses to leaf rust and stripe rust, indicating that either the same gene, or closely linked genes, confers resistance to both diseases. Molecular mapping using microsatellites led to the identification of five markers (Xgwm165, Xgwm192, Xcfd71, Xbarc98 and Xcfd23) on chromosome 4DL that are associated with this gene(s), with the closest markers being located at 0.4 cM. In a parallel study in Canada using a Thatcher × RL6077 F(3) population, the same leaf rust resistance gene was designated as Lr67 and mapped to the same chromosomal region. The pleiotropic, or closely linked, gene derived from RL6077 that conferred stripe rust resistance in this study was designated as Yr46. The slow-rusting gene(s) Lr67/Yr46 can be utilized in combination with other slow-rusting genes to develop high levels of durable APR to leaf rust and stripe rust in wheat.

A robust molecular marker for the detection of shortened introgressed segment carrying the stem rust resistance gene Sr22 in common wheat

Stem rust resistance gene Sr22 transferred to common wheat from Triticum boeoticum and T. monococcum remains effective against commercially prevalent pathotypes of Puccinia graminis f. sp. tritici, including Ug99 and its derivatives. Sr22 was previously located on the long arm of chromosome 7A. Several backcross derivatives (hexaploid) possessing variable sized Sr22-carrying segments were used in this study to identify a closely linked DNA marker. Expressed sequenced tags belonging to the deletion bin 7AL-0.74-0.86, corresponding to the genomic location of Sr22 were screened for polymorphism. In addition, RFLP markers that mapped to this region were targeted. Initial screening was performed on the resistant and susceptible DNA bulks obtained from backcross derivatives carrying Sr22 in three genetic backgrounds with short T. boeoticum segments. A cloned wheat genomic fragment, csIH81, that detected RFLPs between the resistant and susceptible bulks, was converted into a sequence tagged site (STS) marker, named cssu22. Validation was performed on Sr22 carrying backcross-derivatives in fourteen genetic backgrounds and other genotypes used for marker development. Marker cssu22 distinguished all backcross-derivatives from their respective recurrent parents and co-segregated with Sr22 in a Schomburgk (+Sr22)/Yarralinka (-Sr22)-derived recombinant inbred line (RIL) population. Sr22 was also validated in a second population, Sr22TB/Lakin-derived F(4) selected families, containing shortened introgressed segments that showed recombination with previously reported flanking microsatellite markers.

Development of wheat lines carrying stem rust resistance gene Sr39 with reduced Aegilops speltoides chromatin and simple PCR markers for marker-assisted selection

The use of major resistance genes is a cost-effective strategy for preventing stem rust epidemics in wheat crops. The stem rust resistance gene Sr39 provides resistance to all currently known pathotypes of Puccinia graminis f. sp. tritici (Pgt) including Ug99 (TTKSK) and was introgressed together with leaf rust resistance gene Lr35 conferring adult plant resistance to P. triticina (Pt), into wheat from Aegilops speltoides. It has not been used extensively in wheat breeding because of the presumed but as yet undocumented negative agronomic effects associated with Ae. speltoides chromatin. This investigation reports the production of a set of recombinants with shortened Ae. speltoides segments through induction of homoeologous recombination between the wheat and the Ae. speltoides chromosome. Simple PCR-based DNA markers were developed for resistant and susceptible genotypes (Sr39#22r and Sr39#50s) and validated across a set of recombinant lines and wheat cultivars. These markers will facilitate the pyramiding of ameliorated sources of Sr39 with other stem rust resistance genes that are effective against the Pgt pathotype TTKSK and its variants.

Fine scale genetic and physical mapping using interstitial deletion mutants of Lr34 /Yr18: a disease resistance locus effective against multiple pathogens in wheat

The Lr34/Yr18 locus has contributed to durable, non-race specific resistance against leaf rust (Puccinia triticina) and stripe rust (P. striiformis f. sp. tritici) in wheat (Triticum aestivum). Lr34/Yr18 also cosegregates with resistance to powdery mildew (Pm38) and a leaf tip necrosis phenotype (Ltn1). Using a high resolution mapping family from a cross between near-isogenic lines in the "Thatcher" background we demonstrated that Lr34/Yr18 also cosegregated with stem rust resistance in the field. Lr34/Yr18 probably interacts with unlinked genes to provide enhanced stem rust resistance in "Thatcher". In view of the relatively low levels of DNA polymorphism reported in the Lr34/Yr18 region, gamma irradiation of the single chromosome substitution line, Lalbahadur(Parula7D) that carries Lr34/Yr18 was used to generate several mutant lines. Characterisation of the mutants revealed a range of highly informative genotypes, which included variable size deletions and an overlapping set of interstitial deletions. The mutants enabled a large number of wheat EST derived markers to be mapped and define a relatively small physical region on chromosome 7DS that carried Lr34/Yr18. Fine scale genetic mapping confirmed the physical mapping and identified a genetic interval of less than 0.5 cM, which contained Lr34/Yr18. Both rice and Brachypodium genome sequences provided useful information for fine mapping of ESTs in wheat. Gene order was more conserved between wheat and Brachypodium than with rice but these smaller grass genomes did not reveal sequence information that could be used to identify a candidate gene for rust resistance in wheat. We predict that Lr34/Yr18 is located within a large insertion in wheat not found at syntenic positions in Brachypodium and rice.

An intervarietal genetic linkage map of Indian bread wheat (Triticum aestivum L.) and QTL maps for some metric traits

Bread wheat (Triticum aestivum L.) exhibits very narrow genetic diversity and hence there is high relatedness among cultivated varieties. However, a population generated from an intervarietal cross, with the parents differing in a large number of traits, could lead to the generation of QTL maps which will be useful in practice. In this report a genetic linkage map of wheat is constructed using a cross between two Indian bread wheat varieties: Sonalika and Kalyansona. The linkage map consisted of 236 markers and spanned a distance of 3639 cM, with 1211.2 cM for the A genome, 1669.2 cM for the B genome, 192.4 cM for the D genome and 566.2 cM for unassigned groups. Linkage analysis defined 37 linkage groups of which 24 were assigned to 17 chromosomes. The genetic map was used to identify QTLs by composite internal mapping (CIM) for three metric traits, viz. culm length (CL), flag leaf length (FLL) and flag leaf breadth (FLB). Of 25 QTLs identified in this study, 15 have not been reported previously. Multitrait CIM (MCIM) analysis was carried out for traits that were significantly correlated such as FLB-FLL and CL-FLB-FLL. Detection of a large number of QTLs for the three traits analysed suggests that in parent cultivars that are not too diverse, the differences at genetic level detected as polymorphisms may be mostly associated with QTLs for the observed differences.

Molecular genetic characterization of the Lr34/Yr18 slow rusting resistance gene region in wheat

Wheat expressed sequence tags (wESTs) were identified in a genomic interval predicted to span the Lr34/Yr18 slow rusting region on chromosome 7DS and that corresponded to genes located in the syntenic region of rice chromosome 6 (between 2.02 and 2.38 Mb). A subset of the wESTs was also used to identify corresponding bacterial artificial chromosome (BAC) clones from the diploid D genome of wheat (Aegilops tauschii). Conservation and deviation of micro-colinearity within blocks of genes were found in the D genome BACs relative to the orthologous sequences in rice. Extensive RFLP analysis using the wEST derived clones as probes on a panel of wheat genetic stocks with or without Lr34/Yr18 revealed monomorphic patterns as the norm in this region of the wheat genome. A similar pattern was observed with single nucleotide polymorphism analysis on a subset of the wEST derived clones and subclones from corresponding D genome BACs. One exception was a wEST derived clone that produced a consistent RFLP pattern that distinguished the Lr34/Yr18 genetic stocks and well-established cultivars known either to possess or lack Lr34/Yr18. Conversion of the RFLP to a codominant sequence tagged site (csLV34) revealed a bi-allelic locus, where a variant size of 79 bp insertion in an intron sequence was associated with lines or cultivars that lacked Lr34/Yr18. This association with Lr34/Yr18 was validated in wheat cultivars from diverse backgrounds. Genetic linkage between csLV34 and Lr34/Yr18 was estimated at 0.4 cM.

Resistance gene analogues of wheat: molecular genetic analysis of ESTs

Using two divergent nucleotide binding site (NBS) regions from wheat sequences of the NBS-LRR (leucine rich repeat) class, we retrieved 211 wheat and barley NBS-containing resistance gene analogue (RGA) expressed sequence tags (ESTs). These ESTs were grouped into 129 gene sequence groups that contained ESTs that were at least 70% identical at the DNA level over at least 200 bp. Probes were obtained for 89 of these RGA families and chromosome locations were determined for 72 of these probes using nullitetrasomic Chinese Spring wheat lines. RFLP analysis of 49 of these RGA probes revealed 65 mappable polymorphic bands in the doubled haploid Cranbrook x Halberd wheat population (C x H). These bands mapped to 49 loci in C x H. RGA loci were detected on all 21 chromosomes using the nullitetrasomic lines and on 18 chromosomes (linkage groups) in the C x H map. This identified a set of potential markers that could be developed further for use in mapping and ultimately cloning NBS-LRR-type disease resistance genes in wheat.

Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population

A genetic linkage mapping study was conducted in 93 doubled-haploid lines derived from a cross between Triticum aestivum L. em. Thell 'Arina' and a Norwegian spring wheat breeding line, NK93604, using diversity arrays technology (DArT), amplified fragment length polymorphism (AFLP), and simple sequence repeat (SSR) markers. The objective of this study was to understand the distribution, redundancy, and segregation distortion of DArT markers in comparison with AFLP and SSR markers. The map contains a total of 624 markers with 189 DArTs, 165 AFLPs and 270 SSRs, and spans 2595.5 cM. All 3 marker types showed significant (p < 0.01) segregation distortion, but it was higher for AFLPs (24.2%) and SSRs (22.6%) than for DArTs (13.8%). The overall segregation distortion was 20.4%. DArTs showed the highest frequency of clustering (27.0%) at < 0.5 cM intervals between consecutive markers, which is 3 and 15 times higher than SSRs (8.9%) and AFLPs (1.8%), respectively. This high proportion of clustering of DArT markers may be indicative of gene-rich regions and (or) the result of inclusion of redundant clones in the genomic representations, which was supported by the presence of very high correlation coefficients (r > 0.98) and multicollinearity among the clustered markers. The present study is the first to compare the utility of DArT with AFLP and SSR markers, and the present map has been successfully used to identify novel QTLs for resistance to Fusarium head blight and powdery mildew and for anther extrusion, leaf segment incubation, and latency.Key words: 'Arina', diversity arrays technology, double haploid, genetic map, marker clustering, microsatellite.

Leaf tip necrosis, molecular markers and beta1-proteasome subunits associated with the slow rusting resistance genes Lr46/Yr29

Resistance based on slow-rusting genes has proven to be a useful strategy to develop wheat cultivars with durable resistance to rust diseases in wheat. However this type of resistance is often difficult to incorporate into a single genetic background due to the polygenic and additive nature of the genes involved. Therefore, markers, both molecular and phenotypic, are useful tools to facilitate the use of this type of resistance in wheat breeding programs. We have used field assays to score for both leaf and yellow rust in an Avocet-YrA x Attila population that segregates for several slow-rusting leaf and yellow rust resistance genes. This population was analyzed with the AFLP technique and the slow-rusting resistance locus Lr46/Yr29 was identified. A common set of AFLP and SSR markers linked to the Lr46/Yr29 locus was identified and validated in other recombinant inbred families developed from single chromosome recombinant populations that segregated for Lr46. These populations segregated for leaf tip necrosis (LTN) in the field, a trait that had previously been associated with Lr34/Yr18. We show that LTN is also pleiotropic or closely linked to the Lr46/Yr29 locus and suggest that a new Ltn gene designation should be given to this locus, in addition to the one that already exists for Lr34/Yr18. Coincidentally, members of a small gene family encoding beta-1 proteasome subunits located on group 1L and 7S chromosomes implicated in plant defense were linked to the Lr34/Yr18 and Lr46/Yr29 loci.

Development of PCR markers for the selection of wheat stem rust resistance genes Sr24 and Sr26 in diverse wheat germplasm

The use of major resistance genes is the most cost-effective strategy for preventing stem rust epidemics in Australian wheat crops. The long-term success of this strategy is dependent on combining resistance genes that are effective against all predominant races of the pathogen, a task greatly assisted by the use of molecular markers linked to individual resistance genes. The wheat stem rust resistance genes Sr24 and Sr26 (derived from Agropyron elongatum) and SrR and Sr31 (derived from rye) are available in wheat as segments of alien chromosome translocated to wheat chromosomes. Each of these genes provides resistance to all races of wheat stem rust currently found in Australia . We have developed robust PCR markers for Sr24 and Sr26 (this study) and SrR and Sr31 (previously reported) that are applicable across a wide selection of Australian wheat germplasm. Wheat lines have recently become available in which the size of the alien segments containing Sr26, SrR and Sr31 has been reduced. Newly developed PCR-markers can be used to identify the presence of the shorter alien segment in all cases. Assuming that these genes have different gene-for-gene specificities and that the wheat industry will discourage the use of varieties carrying single genes only, the newly developed PCR markers will facilitate the incorporation of two or more of the genes Sr24, Sr26, SrR and Sr31 into wheat lines and have the potential to provide durable control to stem rust in Australia and elsewhere.

Radiation hybrid mapping of the species cytoplasm-specific (scsae) gene in wheat

Radiation hybrid (RH) mapping is based on radiation-induced chromosome breakage and analysis of chromosome segment retention or loss using molecular markers. In durum wheat (Triticum turgidum L., AABB), an alloplasmic durum line [(lo) durum] has been identified with chromosome 1D of T. aestivum L. (AABBDD) carrying the species cytoplasm-specific (scsae) gene. The chromosome 1D of this line segregates as a whole without recombination, precluding the use of conventional genome mapping. A radiation hybrid mapping population was developed from a hemizygous (lo) scsae--line using 35 krad gamma rays. The analysis of 87 individuals of this population with 39 molecular markers mapped on chromosome 1D revealed 88 radiation-induced breaks in this chromosome. This number of chromosome 1D breaks is eight times higher than the number of previously identified breaks and should result in a 10-fold increase in mapping resolution compared to what was previously possible. The analysis of molecular marker retention in our radiation hybrid mapping panel allowed the localization of scsae and 8 linked markers on the long arm of chromosome 1D. This constitutes the first report of using RH mapping to localize a gene in wheat and illustrates that this approach is feasible in a species with a large complex genome.

Resistance genes for rye stem rust (SrR) and barley powdery mildew (Mla) are located in syntenic regions on short arm of chromosome

Genetic stocks were developed for the localization and eventual cloning of the stem rust resistance gene SrR that occurs in wheat lines carrying the 1RS translocation from Secale cereale 'Imperial' rye. We have used a mutation-based approach for molecular analysis of the SrR region in rye. Forty-one independent mutants resulting in loss of SrR resistance were isolated: many of these were deletions of various sizes that were used to locate SrR with respect to chromosome group 1S markers. The analysis of the mutants showed that markers about 1 Mb apart flanking the barley Mla locus also flank SrR. Additionally, three of the approximately 20 closely related sequences of Mla in rye are deleted in each of six interstitial deletion mutants of SrR. The results indicate that the SrR region in rye is syntenic to the Mla region in barley or that SrR is possibly orthologous to the Mla locus.

DNA markers in plant improvement: an overview

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

The cre1 and cre3 nematode resistance genes are located at homeologous loci in the wheat genome

Differential responses in host-nematode pathotype interactions occur in wheat lines carrying different cereal cyst nematode resistance (Cre) genes. Cre1, located on chromosome 2B, confers resistance to most European nematodes and the sole Australian pathotype, while Cre3, present on chromosome 2D, is highly resistant to the Australian pathotype and susceptible to a number of European pathotypes. Genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) proteins that cosegregate with the Cre3 locus cross hybridize to homologues whose restriction fragment length polymorphism (RFLP) patterns distinguish near-isogenic Cre1 nematode-resistant wheat lines. Genetic mapping showed that the NBS-LRR gene members that distinguished the Cre1 near-isogenic lines were located on chromosome 2BL at a locus, designated Xcsl107, that cosegregates with the Cre1 locus. A haplotype of NBS-LRR genes from the Xcsl107 locus provides a diagnostic marker for the presence of Cre1 nematode resistance in a wide collection of wheat lines and segregating families. Genetic analysis of NBS-LRR haplotypes that cosegregate with Cre1 and Cre3 resistance, together with flanking cDNA markers and other markers from homoeologous group 2 chromosomes, revealed a conserved gene order that suggests Cre1 and Cre3 are homeoloci.

An integrative genetic linkage map of winter wheat (Triticum aestivum L.)

We constructed a genetic linkage map based on a cross between two Swiss winter wheat ( Triticum aestivum L.) varieties, Arina and Forno. Two-hundred and forty F(5) single-seed descent (SSD)-derived lines were analysed with 112 restriction fragment length polymorphism (RFLP) anonymous probes, 18 wheat cDNA clones coding for putative stress or defence-related proteins and 179 simple-sequence repeat (SSR) primer-pairs. The 309 markers revealed 396 segregating loci. Linkage analysis defined 27 linkage groups that could all be assigned to chromosomes or chromosome arms. The resulting genetic map comprises 380 loci and spans 3,086 cM with 1,131 cM for the A genome, 920 cM for the B genome and 1,036 cM for the D genome. Seventeen percent of the loci showed a significant ( P < 0.05) deviation from a 1:1 ratio, most of them in favour of the Arina alleles. This map enabled the mapping of QTLs for resistance against several fungal diseases such as Stagonospora glume blotch, leaf rust and Fusarium head blight. It will also be very useful for wheat genetic mapping, as it combines RFLP and SSR markers that were previously located on separate maps.

Tandemly duplicated Safener-induced glutathione S-transferase genes from Triticum tauschii contribute to genome- and organ-specific expression in hexaploid wheat

Glutathione S-transferase (GST) gene expression was examined in several Triticum species, differing in genome constitution and ploidy level, to determine genome contribution to GST expression in cultivated, hexaploid bread wheat (Triticum aestivum). Two tandemly duplicated tau class GST genes (TtGSTU1 and TtGSTU2) were isolated from a single bacterial artificial chromosome clone in a library constructed from the diploid wheat and D genome progenitor to cultivated wheat, Triticum tauschii. The genes are very similar in genomic structure and their encoded proteins are 95% identical. Gene-specific reverse transcriptase-polymerase chain reaction analysis revealed differential transcript accumulation of TtGSTU1 and TtGSTU2 in roots and shoots. Expression of both genes was induced by herbicide safeners, 2,4-dichlorophenoxyacetic acid and abscisic acid, in the shoots of T. tauschii; however, expression of TtGSTU1 was always higher than TtGSTU2. In untreated seedlings, TtGSTU1 was expressed in both shoots and roots, whereas TtGSTU2 expression was only detected in roots. RNA gel-blot analysis of ditelosomic, aneuploid lines that are deficient for 6AS, 6BS, or 6DS chromosome arms of cultivated, hexaploid bread wheat showed differential genome contribution to safener-induced GST expression in shoots compared with roots. The GST genes from the D genome of hexaploid wheat contribute most to safener-induced expression in the shoots, whereas GSTs from the B and D genomes contribute to safener-induced expression in the roots.

Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene

The introduction of semidwarf rice (Oryza sativa L.) led to record yield increases throughout Asia in the 1960s. The major semidwarfing allele, sd-1, is still extensively used in modern rice cultivars. The phenotype of sd-1 is consistent with dwarfism that results from a deficiency in gibberellin (GA) plant growth hormones. We propose that the semidwarf (sd-1) phenotype is the result of a deficiency of active GAs in the elongating stem arising from a defective 20-oxidase GA biosynthetic enzyme. Sequence data from the rice genome was combined with previous mapping studies to locate a putative GA 20-oxidase gene (Os20ox2) at the predicted map location of sd-1 on chromosome 1. Two independent sd-1 alleles contained alterations within Os20ox2: a deletion of 280 bp within the coding region of Os20ox2 was predicted to encode a nonfunctional protein in an indica type semidwarf (Doongara), whereas a substitution in an amino acid residue (Leu-266) that is highly conserved among dioxygenases could explain loss of function of Os20ox2 in a japonica semidwarf (Calrose76). The quantification of GAs in elongating stems by GC-MS showed that the initial substrate of GA 20-oxidase activity (GA53) accumulated, whereas the content of the major product (GA20) and of bioactive GA1 was lower in semidwarf compared with tall lines. We propose that the Os20ox2 gene corresponds to the sd-1 locus.

The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the triticeae

The Sh2/A1 orthologous region of maize, rice, and sorghum contains five genes in the order Sh2, X1, X2, and two A1 homologs in tandem duplication. The Sh2 and A1 homologs are separated by approximately 20 kb in rice and sorghum and by approximately 140 kb in maize. We analyzed the fate of the Sh2/A1 region in large-genome species of the Triticeae (wheat, barley, and rye). In the Triticeae, synteny in the Sh2/A1 region was interrupted by a break between the X1 and X2 genes. The A1 and X2 genes remained colinear in homeologous chromosomes as in other grasses. The Sh2 and X1 orthologs also remained colinear but were translocated to a nonhomeologous chromosome. Gene X1 was duplicated on two nonhomeologous chromosomes, and surprisingly, a paralog shared homology much higher than that of the orthologous copy to the X1 gene of other grasses. No tandem duplication of A1 homologs was detected but duplication of A1 on a nonhomeologous barley chromosome 6H was observed. Intergenic distances expanded greatly in wheat compared to rice. Wheat and barley diverged from each other 12 million years ago and both show similar changes in the Sh2/A1 region, suggesting that the break in colinearity as well as X1 duplications and genome expansion occurred in a common ancestor of the Triticeae species.

A single copy of a virus-derived transgene encoding hairpin RNA gives immunity to barley yellow dwarf virus

Summary Barley yellow dwarf virus-PAV (BYDV-PAV) is the most serious and widespread virus of cereals worldwide. Natural resistance genes against this luteovirus give inadequate control, and previous attempts to introduce synthetic resistance into cereals have produced variable results. In an attempt to generate barley with protection against BYDV-PAV, plants were transformed with a transgene designed to produce hairpin (hp)RNA containing BYDV-PAV sequences. From 25 independent barley lines transformed with the BYDV-PAV hpRNA construct, nine lines showed extreme resistance to the virus and the majority of these contained a single transgene. In the progeny of two independent transgenic lines, inheritance of a single transgene consistently correlated with protection against BYDV-PAV. This protection was rated as immunity because the virus could not be detected in the challenged plants by ELISA nor recovered by aphid feeding experiments. In the field, BYDV-PAV is sometimes associated with the related luteovirus Cereal yellow dwarf virus-RPV (CYDV-RPV). When the transgenic plants were challenged with BYDV-PAV and CYDV-RPV together, the plants were susceptible to CYDV-RPV but immune to BYDV-PAV. This shows that the immunity is virus-specific and not broken down by the presence of CYDV. It suggests that CYDV-RPV does not encode a silencing-suppressor gene or that its product does not protect BYDV-PAV against the plant's RNAi-like defence mechanism. Either way, our results indicate that the BYDV-PAV immunity will be robust in the field and is potentially useful in minimizing losses in cereal production worldwide.

Highly Recombinogenic Regions at Seed Storage Protein Loci on Chromosome 1DS of Aegilops tauschii, the D-Genome Donor of Wheat

A detailed RFLP map was constructed of the distal end of the short arm of chromosome 1D of Aegilops tauschii, the diploid D-genome donor species of hexaploid wheat. Ae. tauschii was used to overcome some of the limitations commonly associated with molecular studies of wheat such as low levels of DNA polymorphism. Detection of multiple loci by most RFLP probes suggests that gene duplication events have occurred throughout this chromosomal region. Large DNA fragments isolated from a BAC library of Ae. tauschii were used to determine the relationship between physical and genetic distance at seed storage protein loci located at the distal end of chromosome 1DS. Highly recombinogenic regions were identified where the ratio of physical to genetic distance was estimated to be &lt;20 kb/cM. These results are discussed in relation to the genome-wide estimate of the relationship between physical and genetic distance.

Resistance gene analogs within an introgressed chromosomal segment derived from Triticum ventricosum that confers resistance to nematode and rust pathogens in wheat

A resistance (R) gene-rich 2S chromosomal segment from Triticum ventricosum contains a cereal cyst nematode (CCN; Heterodera avenae) R gene locus CreX and a closely linked group of genes (Sr38, Yr17, and Lr37) that confer resistance to stem rust (Puccinia graminis f. sp. tritici), stripe rust (P. striiformis f. sp. tritici), and leaf rust (P. recondita f. sp. tritici) when introgressed into wheat. The 2S chromosomal segment from T. ventricosum is further delineated in translocations onto chromosome 2A of bread wheat, where the rust genes are retained but not the CreX gene. Using these critical genetic stocks, we have isolated family members of R gene analogs that are associated with either the 2S segment from T. ventricosum carrying the CreX locus or the rust genes. Derivatives of the Cre3 candidate R gene sequence and a rice (Oryza sativa) R gene analog that mapped to the 2S homologous chromosome groups in wheat were used to isolate related gene sequences from T. ventricosum that contain a nucleotide binding site-leucine rich repeat domain. The potential of these gene sequences as entry points for isolating candidate genes or gene family members of the CreX or rust genes and their further applications to plant breeding are discussed.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS-leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.

Aneuploid marker assignment in hexaploid oat with the C genome as a reference for determining remnant homoeology

Nullisomic lines of hexaploid oat Avena sativa L. (2n = 6x - 2 = 40, AACCDD) cultivar Sun II were used to assign 134 DNA sequences to 10 chromosome-associated syntenic groups. A limited set of ditelosomic lines allowed localization of subsets of these sequences to six chromosome arms. Advantages of using such aneuploids in mapping are in the assignment of gene families, monomorphic RFLP sequences, and oat linkage groups to chromosomes. The published hexaploid oat RFLP linkage map has 38 linkage groups, 17 more than expected on the basis of the haploid chromosome number. Using nullisomics, eight linkage groups were assigned to five physical chromosomes; using ditelosomics, three of these linkage groups were assigned to their respective chromosome arms. The A- and D-genome chromosome sets of oat are indistinguishable from each other based on different staining and genomic in situ hybridization techniques, while C-genome chromosomes are distinct. Because chromosomal rearrangements such as translocations and inversions have played an important role in the evolution of hexaploid oat, the distinction of C-genome chromosomes can be used to determine remnant homoeologous segments that exist in the other two genomes. Among the 10 syntenic groups identified, six chromosomes showed sequence homoeology believed to represent segmental homoeologous regions. Owing to various evolutionary forces, segmental homoeology instead of whole chromosome homoeology appears to best describe the genome organization in hexaploid oat.

Repeated DNA sequences isolated by microdissection. I. Karyotyping of barley (Hordeum vulgare L.)

We report on microdissection, cloning and sequence, and Southern and fluorescence in situ hybridization (FISH) analysis of one moderately and one highly amplified repetitive DNA element, pHvMWG2314 and pHvMWG2315, respectively, isolated from barley (Hordeum vulgare L.) chromosome arm 3HL. The pHvMWG2315 sequence hybridizes to all 14 telomeric or subtelomeric regions of the barley chromosomes as determined by FISH. The 50 different hybridization sites that include intercalary signals allow the discrimination of all 14 chromosome arms and the construction of a kariotype of barley. The tandemly repeated subtelomeric element of 331 bp exists in all Triticeae species tested (H. vulgare, Agropyron elongatum, Secale cereale, Triticum tauschii, T. turgidum, and T. aestivum). It is AT rich (66%), exibits 84% sequence homology to subfragments of the D genome ¿specific¿ 1-kb element pAs1 of T. tauscii and 75% homology to interspersed genome-specific DNA sequence pHcKB6 from H. chilence. The repetitive sequence pHvMWG2314 is moderately amplified in barley and highly amplified in hexaploid wheat. The in situ experiments revealed no distinct signals on barley chromosomes, indicating a dispersed character for the sequence. The significance of the results for the identification of chromosomes and chromosome aberrations in FISH experiments are discussed.

Comparative mapping in grasses. Wheat relationships

Conventionally, the genetics of species of the family Gramineae have been studied separately. Comparative mapping using DNA markers offers a method of combining the research efforts in each species. In this study, we developed consensus maps for members of the Triticeae tribe (Triticum aestivum, T. tauschii, and Hordeum spp.) and compared them to rice, maize and oat. The aneuploid stocks available in wheat are invaluable for comparative mapping because almost every DNA fragment can be allocated to a chromosome arm, thus preventing erroneous conclusions about probes that could not be mapped due to a lack of polymorphism between mapping parents. The orders of the markers detected by probes mapped in rice, maize and oat were conserved for 93, 92 and 94% of the length of Triticeae consensus maps, respectively. The chromosome segments duplicated within the maize genome by ancient polyploidization events were identified by homoeology of segments from two maize chromosomes to regions of one Triticeae chromosome. Homoeologous segments conserved across Triticeae species, rice, maize, and oat can be identified for each Triticeae chromosome. Putative orthologous loci for several simply inherited and quantitatively inherited traits in Gramineae species were identified.

A genetic map of rye chromosome 1R integrating RFLP and cytogenetic loci

A genetic map of rye, Secale cereale L., chromosome 1R covering 247 cM was constructed utilizing 27 RFLP and four C-band markers, including terminal C-bands. Genetic mapping of C-bands and the centromere, and in situ hybridization of three RFLP clones, allowed for the integration of the genetic and cytological maps. Eight contact points between the genetic and cytological maps revealed variation in the recombination distance to cytological distance ratio ranging between 0.25 and 1.95, a 7.8-fold difference. Recombination was found to be highest in the satellite region of 1RS and lowest in the most distal region of 1RL.

Comparison of wheat physical maps with barley linkage maps for group 7 chromosomes

Comparative genetic maps among the Triticeae or Gramineae provide the possibility for combining the genetics, mapping information and molecular-marker resources between different species. Dense genetic linkage maps of wheat and barley, which have a common array of molecular markers, along with deletion-based chromosome maps of Triticum aestivum L. will facilitate the construction of an integrated molecular marker-based map for the Triticeae. A set of 21 cDNA and genomic DNA clones, which had previously been used to map barley chromosome 1 (7H), were used to physically map wheat chromosomes 7A, 7B and 7D. A comparative map was constructed to estimate the degree of linkage conservation and synteny of chromosome segments between the group 7 chromosomes of the two species. The results reveal extensive homoeologies between these chromosomes, and the first evidence for an interstitial inversion on the short arm of a barley chromosome compared to the wheat homoeologue has been obtained. In a cytogenetically-based physical map of group 7 chromosomes that contain restriction-fragment-length polymorphic DNA (RFLP) and random amplified polymorphic DNA (RAPD) markers, the marker density in the most distal third of the chromosome arms was two-times higher than in the proximal region. The recombination rate in the distal third of each arm appears to be 8-15 times greater than in the proximal third of each arm where recombination of wheat chromosomes is suppressed.