Olin D. Anderson

Analysis of the bread wheat genome using whole-genome shotgun sequencing

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

BackgroundMicrosatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.ResultsA new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories.ConclusionBatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.

Rapid Production of Multiple Independent Lines of Fertile Transgenic Wheat (Triticum aestivum)

Improvement of wheat (Triticum aestivum) by biotechnological approaches is currently limited by a lack of efficient and reliable transformation methodology. In this report, we detail a protocol for transformation of a highly embryogenic wheat cultivar, Bobwhite. Calli derived from immature embryos, 0.5 to 1 mm long, were bombarded with microprojectiles coated with DNA containing as marker genes the bar gene, encoding phosphinothricin-resistance, and the gene encoding [beta]-glucuronidase (GUS), each under control of a maize ubiquitin promoter. The bombardment was performed 5 d after embryo excision, just after initiation of callus proliferation. The ability of plantlets to root in the presence of 1 or 3 mg/L of bialaphos was the most reliable selection criteria used to identify transformed plants. Stable transformation was confirmed by marker gene expression assays and the presence of the bar sequences in high molecular weight chromosomal DNA of the resultant plants. Nine independent lines of fertile transgenic wheat plants have been obtained thus far, at a frequency of 1 to 2 per 1000 embryos bombarded. On average, 168 d elapsed between embryo excision for bombardment and anthesis of the T0 plants. The transmission of both the resistance phenotype and bar DNA to the T1 generation verified that germline transformation had occurred.

Activity of a maize ubiquitin promoter in transgenic rice.

We have used the maize ubiquitin 1 promoter, first exon and first intron (UBI) for rice (Oryza sativa L. cv. Taipei 309) transformation experiments and studied its expression in transgenic calli and plants. UBI directed significantly higher levels of transient gene expression than other promoter/intron combinations used for rice transformation. We exploited these high levels of expression to identify stable transformants obtained from callus-derived protoplasts co-transfected with two chimeric genes. The genes consisted of UBI fused to the coding regions of the uidA and bar marker genes (UBI:GUS and UBI:BAR). UBI:GUS expression increased in response to thermal stress in both transfected protoplasts and transgenic rice calli. Histochemical localization of GUS activity revealed that UBI was most active in rapidly dividing cells. This promoter is expressed in many, but not all, rice tissues and undergoes important changes in activity during the development of transgenic rice plants.

The characterization and comparative analysis of high-molecular-weight glutenin genes from genomes A and B of a hexaploid bread wheat.

SummaryTwo high-molecular-weight subunit (HMWS) glutenin genes from the A and B genomes of the hexaploid bread wheat Triticum aestivum L. cv Cheyenne have been isolated and sequenced. Both of these genes are of the high Mr class (x-type) of HMW glutenins, and have not been previously reported. The entire set of six HMW genes from cultivar Cheyenne have now been isolated and characterized. An analysis of the Ax and Bx sequences shows that the Ax sequence is similar to the homoeologous gene from the D genome, while the Bx repeat structure is significantly different. The repetitive region of these proteins can be modelled as a series of interspersed copies of repeat modifs of 6, 9, and 15 amino acid residues. The evolution of these genes includes single-base substitutions over the entire coding region, plus insertion/deletions of single or blocks of repeats in the central repetitive domain.

Effect of temperature on expression of genes encoding enzymes for starch biosynthesis in developing wheat endosperm

The effect of high temperature on starch accumulation, starch granule populations, and expression of genes encoding key enzymes for starch biosynthesis was examined during grain development in wheat (Triticum aestivum L. cv. Butte 86). High temperature applied from anthesis to maturity reduced the duration of starch accumulation. Starch accumulation ceased approximately 6 days earlier for grain produced under a 37/17 8C (day/night) regimen and 21 days earlier under a 37/28 8C (day/night) regimen than for grain produced under a 24/17 8C (day/night) regimen. Compared to the 24/17 8C regimen, starch content was approximately 19% less for mature grain produced under the 37/17 8C regimen and 58% less under the 37/28 8C regimen. Based on relative volume, the smaller type B starch granules were the predominant class in mature grain produced under the 24/17 and 37/17 8C regimens, whereas the larger type A granules were predominant in grain produced under the 37/28 8C regimen. Under the 24/17 8C regimen, steady state transcript levels for ADP-glucose pyrophosphorylase, starch synthases I, II, and III, granule-bound starch synthase, and starch branching enzymes I and II were highest from 12/16 days post-anthesis (dpa). Under the 37/17 8C regimen, steady state levels of these transcripts followed the same temporal pattern, but were substantially lower. Under the 37/28 8C regimen, transcript levels peaked earlier, at 7 dpa. The high temperature regimens reduced the relativ el evels of transcripts for starch synthase more than the other starch biosynthetic enzymes. Published by Elsevier Science Ireland Ltd.

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

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

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.

The wheat low-molecular-weight glutenin genes : characterization of six new genes and progress in understanding gene family structure

Abstract Although the low-molecular-weight (LMW) glutenin subunits are important for aspects of wheat quality and dough processing, a detailed description of the DNA structure and encoded polypeptides of this multigene family is still lacking. We report progress in obtaining a more thorough description of the LMW-glutenin gene family from a single wheat cultivar (‘Cheyenne’). Six new genomic sequences are reported and compared with other LMW-glutenin DNA sequences. Subfamilies of sequences are identified, and an analysis of the repetitive domain of these polypeptides suggests a simple codon pattern with implications for modes of evolution of these repeat motifs. Southern analysis is used to estimate 30–40 members of this gene family in cv ‘Cheyenne’, and chromosome assignments are made for most restriction fragments, including the six sequenced genes. The known DNA sequences cluster into two groups, and most of the new sequences are tentatively identified as C-type LMW-glutenins. Representatives of the B-genome genes are still lacking.

The nucleotide and deduced amino acid sequences of an HMW glutenin subunit gene from chromosome 1B of bread wheat (Triticum aestivum L.) and comparison with those of genes from chromosomes 1A and 1D

SummaryThe nucleotide and deduced amino acid sequences of a high molecular weight glutenin subunit gene derived from chromosome 1B of bread wheat (Triticum aestivum L.) are reported. The encoded protein corresponds to the y-type subunit 1B9. Comparison of the 5′ upstream untranslated regions of this gene and a previously reported silent y-type gene derived from chromosome 1A showed a deletion of 85 bp in the latter. A sequence present in this region of the 1By 9 gene shows homology with part of the “-300 element” which is conserved in the 5′ upstream regions of other prolamin genes from barley, wheat and maize (Forde BG et al. 1985). It is suggested that the absence of this element is responsible for the lack of expression of the 1Ay gene. Comparison of the derived amino acid sequence with those reported previously for the silent 1Ay gene and the expressed x-type (1Dx2) and y-type (1Dy12) genes derived from chromosome 1D showed that the three y-type proteins are closely related. In contrast the x-type subunit (1Dx2) shows clear differences in the N-terminal region and in the number, type and organisation of repeats in the central repetitive domain.