Generation and Characterization of the Western Regional Research Center Brachypodium T-DNA Insertional Mutant Collection

The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.     

GenoProfiler: batch processing of high-throughput capillary fingerprinting data

High-throughput content fingerprinting techniques employing capillary electrophoresis place new demands on the editing of fingerprint files for the downstream contig assembly program, FPC. A cross-platform software application, GenoProfiler, was developed for automated editing of sized fingerprinting profiles generated by the ABI Genetic Analyzers. The batch-processing module extracts the sized fragment information directly from the ABI raw trace files, or from data files exported from GeneMapper or other size calling software, removes the background noise and undesired fragments, and generates fragment size files compatible with the FPC software. AVAILABILITY: http://wheat.pw.usda.gov/PhysicalMapping/     

Thinopyrum 7Ai-1-derived small chromatin with Barley Yellow Dwarf Virus (BYDV) resistance gene integrated into the wheat genome with retrotransposon

Thinopyrum intermedium is a useful source of resistance genes for Barley Yellow Dwarf Virus (BYDV), one of the most damaging wheat diseases. In this study, wheat/Th. intermedium translocation lines with a BYDV resistance gene were developed using the Th. intermedium 7Ai-1 chromosome. Genomic in situ hybridization (GISH), using a Th. intermedium total genomic DNA probe, enabled detection of 7Ai-1-derived small chro-matins containing a BYDV resistance gene, which were translocated onto the end of wheat chromosomes in the lines Y95011 and Y960843. Random amplified polymorphic DNA (RAPD) analyses using 120 random 10-mer primers were conducted to compare the BYDV-resistant translocation lines with susceptible lines. Two primers amplified the DNA fragments specific to the resistant line that would be useful as molecular markers to identify 7Ai-1-derived BYDV resistance chromatin in the wheat genome. Additionally, the isolated Th. intermedium-specific retrotransposon-like sequence pTi28 can be used to identify Th. intermedium chromatin transferred to the wheat genome.     

Development of a D genome specific marker resource for diploid and hexaploid wheat

Background

Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome.

Results

In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci.

Conclusions

In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website (http://probes.pw.usda.gov/ATRJM/) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1852-2) contains supplementary material, which is available to authorized users.Keyword: Wheat deletion bins, Molecular markers, Repeat junction markers, NimbleGen array, Recombination, Genetic map     

Anther culture and Hordeum bulbosum-derived barley doubled haploids mutations and methylation

Anther culture and Hordeum bulbosum-derived doubled haploid (DH) lines of barley (Hordeum vulgare L.) were analyzed for RFLP and RAPD polymorphisms. Polymorphisms were not detected in the anther culture-or H. bulbosum-derived DH lines among 273 RFLP and 89 polymerase chain reaction (PCR)-amplified DNA fragments assayed. It was calculated that base substitution or small deletion/insertion mutations had not been induced among 401 640 by screened. Large deletion/insertion mutations were not observed among 33 Mb screened. Polymorphisms were observed when DNA was digested with the methylation-sensitive restriction enzymes HpaII and MspI: these RFLPs originated primarily from the anther culture-derived doubled haploids. The data indicate that heritable DNA methylation changes had occurred during DH production, particularly with the anther culture method.     

Method for mapping a partial lethal-factor locus on a molecular-marker linkage map of a backcross and doubled-haploid population

 Distorted segregation has been repeatedly observed in various plant species in molecular-marker linkage mapping where distant crosses were made. It may be caused by a partial lethal-factor acting in the filial generations. A method is presented for estimating the recombination values between a partial lethal-factor locus and a linked molecular marker and the relative viability or fertilization ability of zygotes or gametes, respectively affected by the partial lethal factor in backcross (BC) and doubled-haploid (DH) populations using the maximum-likelihood method associated with the expectation maximization (EM) algorithm. The method was applied to segregation data of molecular markers for a population of 150 DH lines developed from the ‘Steptoe’בMorex’ cross in barley. The presence of a partial lethal-factor locus, located on chromosome 4, causing partial selection was suggested. This locus was tightly linked to the ABG500B marker, and the chance of fertilization of female gametes possessing the partial lethal factor was, on average, 59.8% that of a normal one. Two additional partial lethal factors were found on chromosome 5. Received: 3 December 1997 / Accepted: 25 February 1998     

The agronomic performance of wheat doubled haploid lines derived from wheat x maize crosses

Summary The agronomic performance of 9 doubled haploid (DH) lines of Chinese Spring, 6 DH lines of Hope, 14 DH lines of the single chromosome substitution line Chinese Spring (Hope 5 A) and their respective parents was analyzed under field conditions. Seventeen Chinese Spring DH lines derived from wheat x Hordeum bulbosum crosses were also included for comparison. No significant variation was detected in either population of Chinese Spring DH lines and neither DH population differed from its parent. The Hope DH lines differed significantly for tiller biomass, spikelet number per ear, ear grain weight and 50-grain weight. However, all the variation could be attributed to the poor performance of only one line. Chinese Spring (Hope 5 A) DH lines showed significant variation for ear emergence time, but this was probably due to genetic heterogeneity in the parental stock. Overall, the results suggest that most DH lines produced by the wheat x maize method resemble their wheat parent, and that the variation induced in DH production is likely to be similar to that found in DHs from wheat x Hordeum bulbosum crosses.     

Nitrogen addition has a stronger effect on stoichiometries of non-structural carbohydrates,nitrogen and phosphorus in <Emphasis Type="Italic">Bothriochloa ischaemum</Emphasis> than elevated CO<Subscript>2</Subscript>

The current study attempted to obtain candidate doubled haploid (DH) wheat lines by serially combining two approaches: conventional chemical mutagenesis and anther culture. Additionally, the salt tolerance levels were examined between stress-treated (100 mM NaCl) and non-treated DH groups. For the molecular analysis, IRAP markers were used to characterize retrotransposon insertion polymorphisms induced by haploidization, chromosome doubling, and/or mutagenesis in the DH lines. Various sodium azide (NaN₃) concentrations (from 0 to 5 mM) were applied to seeds of the Pehlivan wheat cultivar to obtain an M₁ generation mutant population. Anther culture was set up from the M₁ mutant population. Green plant regeneration, the frequency of selected candidate mutants within the DH form and the levels of salt tolerance between samples were screened. A total of eight thousand anthers were cultured, and sixteen candidate salt-tolerant DH mutant lines, twenty-seven candidate DH mutant lines with different characteristics and one hundred and two candidate DH lines with morphologically normal appearances were obtained from the NaN₃-mutagenized population. The IRAP patterns were quite similar between the control DH lines, and the genetic differences between the controls and DHs originating from possible mutants showed close relatedness. According to previous studies, chemical mutagenesis and anther culture were combined for the first time to detect candidate salt tolerant genotypes at the DH stage. This approach might also be useful for determining the threshold dose and efficiency of wheat mutagens.     

Microsatellite analysis of wheat chromosome 2D allows the reconstruction of chromosomal inheritance in pedigrees of breeding programmes

Fusarium head blight (FHB, scab) is a fungal disease of wheat and other small cereals that is found in both temperate and semi-tropical regions. FHB causes severe yield and quality losses, but the most-serious concern is the possible mycotoxin contamination of cereal food and feed. Breeding for FHB resistance by conventional selection is feasible, but tedious and expensive. This study was conducted to identify and map DNA markers associated with FHB resistance genes in wheat. A population of 364 F₁-derived doubled-haploid (DH) lines from the cross ’CM-82036’ (resistant)/’Remus’ (susceptible) was evaluated for Type II resistance (spread within the spike) during 2 years under field conditions. Marker analysis was performed on 239 randomly chosen DH lines. Different marker types were applied, with an emphasis on AFLP and SSR markers. Analysis of variance, as well as simple and composite interval mapping, were applied. Three genomic regions were found significantly associated with FHB resistance. The most-prominent effect was detected on the short arm of chromosome 3B, explaining up to 60% of the phenotypic variance for Type II FHB resistance. A further QTL was located on chromosome 5A and a third one on 1B. The QTL regions on 3B and 5A were tagged with flanking SSR markers, the 1B QTL was found associated with the high-molecular-weight glutenin locus. These results indicate that FHB resistance is under control of a few major QTLs operating together with unknown numbers of minor genes. Marker-assisted selection for these major QTLs involved in FHB resistance appears feasible and should accelerate the development of resistant and agronomically improved wheat cultivars. Received: 25 January 2001 / Accepted: 18 February 2001     

Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five intersubspecific (indica?/?japonica) crosses, including two F₂ populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129–629 markers. Segregation distortion was determined based on chi-square analysis (P?<?0.01) and was observed at 6.8–31.8% of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated.     

GrainGenes 2.0. an improved resource for the small-grains community

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.     

Mapping Ds insertions in barley using a sequence-based approach

A transposon tagging system, based upon maize Ac/Ds elements, was developed in barley (Hordeum vulgare subsp. vulgare). The long-term objective of this project is to identify a set of lines with Ds insertions dispersed throughout the genome as a comprehensive tool for gene discovery and reverse genetics. AcTPase and Ds-bar elements were introduced into immature embryos of Golden Promise by biolistic transformation. Subsequent transposition and segregation of Ds away from AcTPase and the original site of integration resulted in new lines, each containing a stabilized Ds element in a new location. The sequence of the genomic DNA flanking the Ds elements was obtained by inverse PCR and TAIL-PCR. Using a sequence-based mapping strategy, we determined the genome locations of the Ds insertions in 19 independent lines using primarily restriction digest-based assays of PCR-amplified single nucleotide polymorphisms and PCR-based assays of insertions or deletions.The proncipal strategy was to identify and map sequence polymorphisms in the regions corresponding to the flanking DNA using the Oregon Wolfe Barley mapping population. The mapping results obtained by the sequence-based approach were confirmed by RFLP analyses in four of the lines. In addition, cloned DNA sequences corresponding to the flanking DNA were used to assign map locations to Morex-derived genomic BAC library inserts, thus integrating genetic and physical maps of barley. BLAST search results indicate that the majority of the transposed Ds elements are found within predicted or known coding sequences. Transposon tagging in barley using Ac/Ds thus promises to provide a useful tool for studies on the functional genomics of the Triticeae.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by M.-A. GrandbastienThe first three authors contributed equally to this work     

Identification of novel tan spot resistance QTLs using an SSR-based linkage map of tetraploid wheat

Durum wheat (Triticum turgidum L. subsp. durum, 2n = 4x = 28, AABB) is an important cereal used for making pasta products. Compared with bread wheat, durum wheat receives less attention in genetic and genomic studies. In this research, a tetraploid wheat doubled haploid (DH) population derived from the cross between the durum wheat cultivar ‘Lebsock’ and the T. turgidum subsp. carthlicum (2n = 4x = 28, AABB) accession PI 94749 was developed. The population consisted of 146 lines and was used to construct linkage maps of all 14 chromosomes. The maps consisted of 280 SSR markers and spanned 2,034.1 cM with an average density of one marker per 7.2 cM. The DH population and the whole genome linkage maps were then used to identify QTLs associated with tan spot resistance. The DH population was inoculated separately with two Ptr ToxA-producing isolates (Pti2 and 86-124) representing races 1 and 2, respectively, of Pyrenophora tritici-repentis, and five resistance QTLs were detected on chromosome arms 3AS, 3BL, 5AL and 7BL. Together, the QTLs explained a total of 46 and 41% of the phenotypic variation for reaction to Pti2 and 86-124, respectively. The Tsn1-Ptr ToxA interaction was not a significant factor in tan spot development in this population, and none of the QTLs corresponded to previously identified loci known to confer insensitivity to host-selective toxins (HSTs) produced by P. tritici-repentis. This result, together with those of other similar studies, indicates that the wheat–P. tritici-repentis pathosystem involves more factors than currently published host-toxin interactions. The DH population and genetic maps reported here will be useful for genetic dissection of important agronomic traits as well as the identification and development of markers for marker-assisted selection (MAS).     

Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses.

Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.     

Comparison of bread wheat lines selected by doubled haploid, single-seed descent and pedigree selection methods

 Yield performance of each group of ten spring bread wheat lines selected by doubled haploid (DH), single-seed descent (SSD) and pedigree selection (PS) methods from three F₁ crosses was compared with the aim of evaluating the DH method in breeding programs. Populations of 65–97 DH lines and 110 SSD lines per cross were used for selection. PS lines were developed by repeated selections from 1500 F₂ plants. Yield evaluation was performed at the F₆ generation of SSD and PS lines along with DH lines in a 2-year field experiment. It took only 2 years from the planting of wheat materials for DH production to the planting of selected DH lines for yield evaluation. There was no significant difference in grain yield between DH lines and PS lines selected from an F₁ cross whose parental varieties were closely related in their pedigrees. In two crosses with low coefficients of parentage and a large variation in their progenies, grain yield of selected DH lines was significantly lower than those of selected SSD and PS lines. These results confirm that the DH method can save time in obtaining recombinant inbred lines ready for yield evaluation. However, a larger DH population is required to achieve the same level of genetic advance with the PS method in crosses containing greater genetic variation. Received: 23 December 1997 / Accepted: 12 March 1998