Biomedical subjects

Daryl J Somers

Publications and source records attributed to Daryl J Somers.

8 recordsLinked to original sources

PubMed2006

Fine mapping Fhb1, a major gene controlling fusarium head blight resistance in bread wheat (Triticum aestivum L.).

A major fusarium head blight (FHB) resistance gene Fhb1 (syn. Qfhs.ndsu-3BS) was fine mapped on the distal segment of chromosome 3BS of spring wheat (Triticum aestivum L.) as a Mendelian factor. FHB resistant parents, Sumai 3 and Nyubai, were used as sources of this gene. Two mapping populations were developed to facilitate segregation of Qfhs.ndsu-3BS in either a fixed resistant (Sumai 3*5/Thatcher) (S/T) or fixed susceptible (HC374/3*98B69-L47) (HC/98) genetic background (HC374 = Wuhan1/Nyubai) for Type II resistance. Type II resistance (disease spread within the spike) was phenotyped in the greenhouse using single floret injections with a mixture of macro-conidia of three virulent strains of Fusarium graminearum. Due to the limited heterogeneity in the genetic background of the crosses and based on the spread of infection, fixed recombinants in the interval between molecular markers XGWM533 and XGWM493 on 3BS could be assigned to discrete "resistant" and "susceptible" classes. The phenotypic distribution was bimodal with progeny clearly resembling either the resistant or susceptible parent. Marker order for the two maps was identical with the exception of marker STS-3BS 142, which was not polymorphic in the HC/98 population. The major gene Fhb1 was successfully fine mapped on chromosome 3BS in the same location in the two populations within a 1.27-cM interval (S/T) and a 6.05-cM interval (HC/98). Fine mapping of Fhb1 in wheat provides tightly linked markers that can reduce linkage drag associated with marker-assisted selection of Fhb1 and assist in the isolation, sequencing and functional identification of the underlying resistance gene.

Chromosomes, Plant↗

PubMed2005

Assembling complex genotypes to resist Fusarium in wheat (Triticum aestivum L.).

Fusarium head blight of wheat is a major deterrent to wheat production world-wide. The genetics of FHB resistance in wheat are becoming clear and there is a good understanding of the genome location of FHB resistance QTL from different sources such as Sumai3, Wuhan, Nyubai and Frontana. All the components needed for assembling complex genotypes through large-scale molecular breeding experiments are now available. This experiment used high throughput microsatellite genotyping and half-seed analysis to process four independent crosses through a molecular breeding strategy to introduce multiple pest resistance genes into Canadian wheat. This included two backcrosses and selection for a total of six FHB resistance QTL, orange blossom wheat midge resistance (Sm1) and leaf rust resistance (Lr21). In addition, the fixation of the elite genetic background was monitored with 45-76 markers to accelerate restoration of the genetic background at each backcross. The strategy resulted in 87% fixation of the elite genetic background on average at the BC2F1 generation and successfully introduced all of the chromosome segments containing FHB, Sm1 and Lr21 resistance genes. The molecular breeding strategy was completed in 25 months, at an equal pace to conventional crossing and selection of spring wheat.

Breeding↗

PubMed2005

Genetic characterization of QTL associated with resistance to Fusarium head blight in a doubled-haploid spring wheat population.

Fusarium head blight (FHB) is one of the most important fungal wheat diseases worldwide. Understanding the genetics of FHB resistance is the key to facilitating the introgression of different FHB resistance genes into adapted wheat. The objectives of the present study were to detect and map quantitative trait loci (QTL) associated with FHB resistance genes and characterize the genetic components of the QTL in a doubled-haploid (DH) spring wheat population using both single-locus and two-locus analysis. A mapping population, consisting of 174 DH lines from the cross between DH181 (resistant) and AC Foremost (susceptible), was evaluated for type I resistance to initial infection during a 2-year period in spray-inoculated field trials, for Type II resistance to fungal spread within the spike in 3 greenhouse experiments using single-floret inoculation, and for resistance to kernel infection in a 2001 field trial. One-locus QTL analysis revealed 7 QTL for type I resistance on chromosome arms 2DS, 3AS, 3BS, 3BC (centromeric), 4DL, 5AS, and 6BS, 4 QTL for type II resistance on chromosomes 2DS, 3BS, 6BS, and 7BL, and 6 QTL for resistance to kernel infection on chromosomes 1DL, 2DS, 3BS, 3BC, 4DL, and 6BS. Two-locus QTL analysis detected 8 QTL with main effects and 4 additive by additive epistatic interactions for FHB resistance and identified novel FHB resistance genes for the first time on chromosomes 1DL, 4AL, and 4DL. Neither significant QTL by environment interactions nor epistatic QTL by environment interactions were found for either type I or type II resistance. The additive effects of QTL explained most of the phenotypic variance for FHB resistance. Marker-assisted selection for the favored alleles at multiple genomic regions appears to be a promising tool to accelerate the introgression and pyramiding of different FHB resistance genes into adapted wheat genetic backgrounds.

Chromosome Mapping↗

PubMed2004

A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.).

A microsatellite consensus map was constructed by joining four independent genetic maps of bread wheat. Three of the maps were F(1)-derived, doubled-haploid line populations and the fourth population was 'Synthetic' x 'Opata', an F(6)-derived, recombinant-inbred line population. Microsatellite markers from different research groups including the Wheat Microsatellite Consortium, GWM, GDM, CFA, CFD, and BARC were used in the mapping. A sufficient number of common loci between genetic maps, ranging from 52 to 232 loci, were mapped on different populations to facilitate joining the maps. Four genetic maps were developed using MapMaker V3.0 and JoinMap V3.0. The software CMap, a comparative map viewer, was used to align the four maps and identify potential errors based on consensus. JoinMap V3.0 was used to calculate marker order and recombination distances based on the consensus of the four maps. A total of 1,235 microsatellite loci were mapped, covering 2,569 cM, giving an average interval distance of 2.2 cM. This consensus map represents the highest-density public microsatellite map of wheat and is accompanied by an allele database showing the parent allele sizes for every marker mapped. This enables users to predict allele sizes in new breeding populations and develop molecular breeding and genomics strategies.

Bread↗

PubMed2004

In silico physical mapping software for the Triticum aestivum genome.

The large size of the Triticum aestivum genome makes it unlikely that a complete genome sequence for wheat will be available in the near future. Exploiting the conserved genome organization between wheat and rice and existing genomic resources, we have constructed in silico physical mapping software for wheat, assigning a gross physical location(s) into chromosome bins to 22,626 representative wheat gene sequences. To validate the predictions from the software we compared the predicted locations of ten ESTs to their positions experimentally determined by SNP marker analysis. Six of the sequences were correctly positioned on the map including four that demonstrated a high level of colinearity with their orthologous rice genomic region. This tool will facilitate the development of molecular markers for regions of interest and the creation of map-based cloning strategies in areas demonstrating high levels of sequence conservation and organization between wheat and rice.

Computational Biology↗

PubMed2003

Mining single-nucleotide polymorphisms from hexaploid wheat ESTs.

Single-nucleotide polymorphisms (SNPs) represent a new form of functional marker, particularly when they are derived from expressed sequence tags (ESTs). A bioinformatics strategy was developed to discover SNPs within a large wheat EST database and to demonstrate the utility of SNPs in genetic mapping and genetic diversity applications. A collection of > 90000 wheat ESTs was assembled into contiguous sequences (contigs), and 45 random contigs were then visually inspected to identify primer pairs capable of amplifying specific alleles. We estimate that homoeologue sequence variants occurred 1 in 24 bp and the frequency of SNPs between wheat genotypes was 1 SNP/540 bp (theta = 0.0069). Furthermore, we estimate that one diagnostic SNP test can be developed from every contig with 10-60 EST members. Thus, EST databases are an abundant source of SNP markers. Polymorphism information content for SNPs ranged from 0.04 to 0.50 and ESTs could be mapped into a framework of microsatellite markers using segregating populations. The results showed that SNPs in wheat can be discovered in ESTs, validated, and be applied to conventional genetic studies.

Base Sequence↗

PubMed2003

Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat.

Fusarium head blight of wheat is an extremely damaging disease, causing severe losses in seed yield and quality. The objective of the current study was to examine and characterize alternate sources of resistance to Fusarium head blight (FHB). Ninety-one F1-derived doubled haploid lines from the cross Triticum aestivum 'Wuhan-1' x Triticum aestivum 'Maringa' were examined for disease reaction to Fusarium graminearum by single-floret injection in replicated greenhouse trials and by spray inoculation in replicated field trials. Field and greenhouse experiments were also used to collect agronomic and spike morphology characteristics. Seed samples from field plots were used for deoxynivalenol (DON) determination. A total of 328 polymorphic microsatellite loci were used to construct a genetic linkage map in this population and together these data were used to identify QTL controlling FHB resistance, accumulation of DON, and agronomic and spike morphology traits. The analysis identified QTL for different types of FHB resistance in four intervals on chromosomes 2DL, 3BS, and 4B. The QTLs on 4B and 3BS proximal to the centromere are novel and not reported elsewhere. QTL controlling accumulation of DON independent of FHB resistance were located on chromosomes 2DS and 5AS. Lines carrying FHB resistance alleles on 2DL and 3BS showed a 32% decrease in disease spread after single-floret injection. Lines carrying FHB resistance alleles on 3BS and 4B showed a 27% decrease from the mean in field infection. Finally, lines carrying favourable alleles on 3BS and 5AS, showed a 17% reduction in DON accumulation. The results support a polygenic and quantitative mode of inheritance and report novel FHB resistance loci. The data also suggest that resistance to FHB infection and DON accumulation may be controlled, in part, by independent loci and (or) genes.

Chromosome Mapping↗

PubMed2002

Identification of repetitive, genome-specific probes in crucifer oilseed species.

Direct amplification of minisatellite DNA by PCR (DAMD PCR) was used to amplify and subsequently clone several fragments of DNA from crucifer species. The PCR-derived fragments of DNA were generated using known minisatellite core sequences as PCR primers. Southern hybridization of these putative minisatellite DNA fragments revealed that many were genome-specific; they hybridized with high affinity only to the genomic DNA of the species from which they were cloned. The DNA fragments were believed to be dispersed in the genome, based on smear-like hybridization signals on EcoRI-, BamHI-, and HindIII-digested genomic DNA. Genome-specific probes were specifically isolated from Brassica rapa (A genome), Brassica nigra (B genome), and Sinapis alba in addition to several other crucifer species. The sequence of a B. rapa specific probe (pBr17.1.3A) contained a minisatellite region that could be divided into three tandem repeats; each repeat contained between two and five subrepeats and each subrepeat shared a highly conserved core region of 29 bp. This minisatellite sequence also hybridized with high affinity to the A genome species B. napus and B. juncea. This research showed that dispersed, genome-specific probes can be isolated using DAMD PCR and that these probes could be used to detect and quantify alien DNA present in progeny from intergeneric or interspecific crosses.

Base Sequence↗