TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Jan 18, 2016
New SNP markers that can be used for marker-assisted selection and map-based cloning saturate the... more New SNP markers that can be used for marker-assisted selection and map-based cloning saturate the chromosome region carrying SrCad , a wheat gene that confers resistance to Ug99 stem rust. Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a devastating disease of wheat worldwide. Development of cultivars with effective resistance has been the primary means to control this disease, but the appearance of new virulent strains such as Ug99 has rendered most wheat varieties vulnerable. The stem rust resistance gene SrCad located on chromosome arm 6DS has provided excellent resistance to various strains of Ug99 in field nurseries conducted in Njoro, Kenya since 2005. Three genetic populations were used to identify SNP markers closely linked to the SrCad locus. Of 220 SNP markers evaluated, 27 were found to be located within a 2 cM region surrounding SrCad. The diagnostic potential of these SNPs was evaluated in a diverse set of 50 wheat lines that were primarily of Canadian ...
Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the g... more Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis. We first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number. Slow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials.
In Canada, flax is an oilseed crop known for its high content of omega-3 (alpha linolenic acid), ... more In Canada, flax is an oilseed crop known for its high content of omega-3 (alpha linolenic acid), an essential fatty acid associated with numerous health attributes. In Europe, flax is mostly grown as a fibre crop used in the fabrication of linen and other high quality technical fibre products. Flax’s latin name, Linum usitatissimum, means “most useful” which indeed reflects the usefulness of this dual purpose crop. Flax’s estimated genome size of 373Mb is smaller than rice and makes it a good target for rapid advancement using genomics tools. Here, we developed 1,082 SSR markers from EST and BAC end sequences. Between 389 and 466 SSR markers were mapped on three segregating populations. A consensus SSR map of 774 SSR markers grouped in 15 linkage groups spanning ~2,060 cM was constructed. A Reduced Genome Representation (RGR) combined with a Genotyping by Sequencing (GBS) approach was used to develop SNP-based maps of two segregating populations. The CDC Bethune/Macbeth RIL populati...
The Plant journal : for cell and molecular biology, Jan 7, 2015
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hin... more Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6,278 BACs in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15,622 BACs representing the minimal tiling path of 72,052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data...
International journal of molecular sciences, Jan 14, 2015
Plants have developed effective mechanisms to recognize and respond to infections caused by patho... more Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cl...
Phenotypic studies have shown that cold acclimation in wheat and its relatives start at different... more Phenotypic studies have shown that cold acclimation in wheat and its relatives start at different temperatures. To gain insight into the underlying mechanisms that regulate the induction of cold-acclimation process in cereals we compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar) cultivars that vary in tolerance to cold. Global expression of genes in the crowns of juvenile plants cold-acclimated at four different temperatures (6oC, 9 oC, 12 oC, 15 oC and 18 oC) for 12-hrs, 60-hrs and 380-hrs was examined. Expression of genes associated with induction of cold-acclimation at different temperatures will be presented.
The gene family of C-repeat binding factors (CBFs) has been established to play a prominent role ... more The gene family of C-repeat binding factors (CBFs) has been established to play a prominent role in cold acclimation in plants. The expression of CBF genes in hexaploid wheat was investigated by comparing the response to cold acclimation of four near-isogenic lines previously generated from two cultivars, spring Manitou (a non-hardy spring wheat) and winter Norstar (a very cold-hardy winter wheat), wherein the major vernalization locus Vrn-A1 was swapped. The CBF cluster on the linked Fr2 locus was not included in the swapped Vrn-A1 region, thus was fixed in the Norstar and Manitou backgrounds. These lines allowed us to examine the effect of the Vrn1 locus on the expression of 16 CBF genes without the confounding effects of genetic variations outside of the swapped region. We showed that CBFs exhibit different temporal regulations during cold treatment, hence were not functionally equivalent. The expression of four of the CBFs was not detected in the crown. CBFI, CBFII-5.2, CBFIIIc-...
The number of days to maturity or maturity date (Mat) is a quantitative trait and an important de... more The number of days to maturity or maturity date (Mat) is a quantitative trait and an important determinant of a cultivar’s suitability to a specific growing region. A doubled haploid (DH) population of 183 progeny derived from a cross between Canadian spring wheats RL4452/AC Domain was screened for QTL with 12,252 SNP markers from a 90K Infinium iSelect Custom Beadchip. A significant Mat QTL was mapped to a region on 7DS that also coincided with a heading date (Hd) and a falling number (FN) QTL. Markers flanking the Mat QTL interval on 7DS are ~12 cM apart, and this region is orthologous to a ~3 mb region on chromosome 1 of Brachypodium distachyon, and to chromosome 6 of rice. Efforts to saturate this region on 7DS in order to identify and clone underlying genes that are related to maturity are ongoing. These involve (a) identifying SNPs from an orthologous region of the diploid A. tauschii D genome, and (b) utilizing varietal SNPs via an exome capture strategy that involves screeni...
The type 2 modified augmented design (MAD) was used to phenotype seed yield, oil content and fatt... more The type 2 modified augmented design (MAD) was used to phenotype seed yield, oil content and fatty acid compositions in a collection of 120 flax genotypes at two locations during three years. All six experiments had the same design, in which whole plots were arranged in 10 rows and 10 columns and each whole plot was split into five paralleled rectangular subplots with a control subplot in the centre of each whole plot. Two additional subplot controls were allocated at random in each of five randomly selected whole plots. Relative efficiency (RE) of adjusted versus unadjusted observations was evaluated for all six experiments. The RE was redefined as a ratio of pooled variance within both plot and subplot controls of the unadjusted values to that of the adjusted values. Two adjustment methods based on the row and column effect of plot controls (M1) and the regression of the test plots on the plot control (M3), were assessed to adjust for soil heterogeneity. The analysis of variance (...
Lr16 is a widely deployed leaf rust resistance gene that is effective against the North American ... more Lr16 is a widely deployed leaf rust resistance gene that is effective against the North American Puccinia triticina population when in combination with Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the pustule. Previously sequenced seedling leaf rust resistance genes (e.g Lr1, Lr10 and Lr21) were Resistance Gene Analog (RGA)-like genes. Lr16 has been mapped to the telomeric region of wheat chromosome bin 2BS3. We used two populations to fine map Lr16: an F6‐derived recombinant inbred line (RIL) population consisting of 1872 lines from the cross between Canadian wheat lines BW278 and “AC Foremost” and a Doubled Haploid (DH) population with 957 lines from the cross between wheat varieties “AC Majestic” and “Glenlea”. The gene was localized to 1.5cM and 3.4cM intervals in BW278/AC foremost and AC Majestic/Glenlea populations respectively. To better delineate the Lr16 interval, single nucleotide poly...
Flax (Linum usitatissimum L., 2n = 2x =30) is a self-pollinated annual species of the Linaceae fa... more Flax (Linum usitatissimum L., 2n = 2x =30) is a self-pollinated annual species of the Linaceae family. It is a dual purpose crop grown for its seed oil (linseed) and/or its stem fibres from which linen and other products are made. Linseeds are rich in omega-3 fatty acids (55-57%) essential for humans and ideal for the production of biodegradable products such as linoleum flooring and paints. The genome size of the flax variety CDC Bethune was estimated at ~373Mb based on flow cytometry (Wang et al. 2012). This genome was sequenced using a whole genome shotgun (WGS) sequencing strategy on the Illumina sequencing platform (Wang et al. 2012). A total of 302 Mb in 116,602 contigs or 318 Mb in 88,384 scaffolds was obtained, representing ~81% of the flax genome. The remaining ~70 Mb were gaps within and between scaffolds. All contigs or scaffolds were unordered and some of them, especially long scaffolds, were mis-assembled. In order to refine the genome assembly, we identified mis-assemb...
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Jan 18, 2016
New SNP markers that can be used for marker-assisted selection and map-based cloning saturate the... more New SNP markers that can be used for marker-assisted selection and map-based cloning saturate the chromosome region carrying SrCad , a wheat gene that confers resistance to Ug99 stem rust. Wheat stem rust, caused by Puccinia graminis f. sp. tritici, is a devastating disease of wheat worldwide. Development of cultivars with effective resistance has been the primary means to control this disease, but the appearance of new virulent strains such as Ug99 has rendered most wheat varieties vulnerable. The stem rust resistance gene SrCad located on chromosome arm 6DS has provided excellent resistance to various strains of Ug99 in field nurseries conducted in Njoro, Kenya since 2005. Three genetic populations were used to identify SNP markers closely linked to the SrCad locus. Of 220 SNP markers evaluated, 27 were found to be located within a 2 cM region surrounding SrCad. The diagnostic potential of these SNPs was evaluated in a diverse set of 50 wheat lines that were primarily of Canadian ...
Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the g... more Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis. We first constructed a genetic map for walnut, a woody perennial. All linkage groups were short, and recombination rates were greatly reduced in the centromeric regions. We then used the genetic map to construct a walnut bacterial artificial chromosome (BAC) clone-based physical map, which contained 15,203 exonic BAC-end sequences, and quantified with it synteny between the walnut genome and genomes of three long-lived woody perennials, Vitis vinifera, Populus trichocarpa, and Malus domestica, and three short-lived herbs, Cucumis sativus, Medicago truncatula, and Fragaria vesca. Each measure of synteny we used showed that the genomes of woody perennials were less diverged from the walnut genome than those of herbs. We also estimated the nucleotide substitution rate at silent codon positions in the walnut lineage. It was one-fifth and one-sixth of published nucleotide substitution rates in the Medicago and Arabidopsis lineages, respectively. We uncovered a whole-genome duplication in the walnut lineage, dated it to the neighborhood of the Cretaceous-Tertiary boundary, and allocated the 16 walnut chromosomes into eight homoeologous pairs. We pointed out that during polyploidy-dysploidy cycles, the dominant tendency is to reduce the chromosome number. Slow rates of nucleotide substitution are accompanied by slow rates of synteny erosion during genome divergence in woody perennials.
In Canada, flax is an oilseed crop known for its high content of omega-3 (alpha linolenic acid), ... more In Canada, flax is an oilseed crop known for its high content of omega-3 (alpha linolenic acid), an essential fatty acid associated with numerous health attributes. In Europe, flax is mostly grown as a fibre crop used in the fabrication of linen and other high quality technical fibre products. Flax’s latin name, Linum usitatissimum, means “most useful” which indeed reflects the usefulness of this dual purpose crop. Flax’s estimated genome size of 373Mb is smaller than rice and makes it a good target for rapid advancement using genomics tools. Here, we developed 1,082 SSR markers from EST and BAC end sequences. Between 389 and 466 SSR markers were mapped on three segregating populations. A consensus SSR map of 774 SSR markers grouped in 15 linkage groups spanning ~2,060 cM was constructed. A Reduced Genome Representation (RGR) combined with a Genotyping by Sequencing (GBS) approach was used to develop SNP-based maps of two segregating populations. The CDC Bethune/Macbeth RIL populati...
The Plant journal : for cell and molecular biology, Jan 7, 2015
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hin... more Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6,278 BACs in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15,622 BACs representing the minimal tiling path of 72,052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data...
International journal of molecular sciences, Jan 14, 2015
Plants have developed effective mechanisms to recognize and respond to infections caused by patho... more Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cl...
Phenotypic studies have shown that cold acclimation in wheat and its relatives start at different... more Phenotypic studies have shown that cold acclimation in wheat and its relatives start at different temperatures. To gain insight into the underlying mechanisms that regulate the induction of cold-acclimation process in cereals we compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar) cultivars that vary in tolerance to cold. Global expression of genes in the crowns of juvenile plants cold-acclimated at four different temperatures (6oC, 9 oC, 12 oC, 15 oC and 18 oC) for 12-hrs, 60-hrs and 380-hrs was examined. Expression of genes associated with induction of cold-acclimation at different temperatures will be presented.
The gene family of C-repeat binding factors (CBFs) has been established to play a prominent role ... more The gene family of C-repeat binding factors (CBFs) has been established to play a prominent role in cold acclimation in plants. The expression of CBF genes in hexaploid wheat was investigated by comparing the response to cold acclimation of four near-isogenic lines previously generated from two cultivars, spring Manitou (a non-hardy spring wheat) and winter Norstar (a very cold-hardy winter wheat), wherein the major vernalization locus Vrn-A1 was swapped. The CBF cluster on the linked Fr2 locus was not included in the swapped Vrn-A1 region, thus was fixed in the Norstar and Manitou backgrounds. These lines allowed us to examine the effect of the Vrn1 locus on the expression of 16 CBF genes without the confounding effects of genetic variations outside of the swapped region. We showed that CBFs exhibit different temporal regulations during cold treatment, hence were not functionally equivalent. The expression of four of the CBFs was not detected in the crown. CBFI, CBFII-5.2, CBFIIIc-...
The number of days to maturity or maturity date (Mat) is a quantitative trait and an important de... more The number of days to maturity or maturity date (Mat) is a quantitative trait and an important determinant of a cultivar’s suitability to a specific growing region. A doubled haploid (DH) population of 183 progeny derived from a cross between Canadian spring wheats RL4452/AC Domain was screened for QTL with 12,252 SNP markers from a 90K Infinium iSelect Custom Beadchip. A significant Mat QTL was mapped to a region on 7DS that also coincided with a heading date (Hd) and a falling number (FN) QTL. Markers flanking the Mat QTL interval on 7DS are ~12 cM apart, and this region is orthologous to a ~3 mb region on chromosome 1 of Brachypodium distachyon, and to chromosome 6 of rice. Efforts to saturate this region on 7DS in order to identify and clone underlying genes that are related to maturity are ongoing. These involve (a) identifying SNPs from an orthologous region of the diploid A. tauschii D genome, and (b) utilizing varietal SNPs via an exome capture strategy that involves screeni...
The type 2 modified augmented design (MAD) was used to phenotype seed yield, oil content and fatt... more The type 2 modified augmented design (MAD) was used to phenotype seed yield, oil content and fatty acid compositions in a collection of 120 flax genotypes at two locations during three years. All six experiments had the same design, in which whole plots were arranged in 10 rows and 10 columns and each whole plot was split into five paralleled rectangular subplots with a control subplot in the centre of each whole plot. Two additional subplot controls were allocated at random in each of five randomly selected whole plots. Relative efficiency (RE) of adjusted versus unadjusted observations was evaluated for all six experiments. The RE was redefined as a ratio of pooled variance within both plot and subplot controls of the unadjusted values to that of the adjusted values. Two adjustment methods based on the row and column effect of plot controls (M1) and the regression of the test plots on the plot control (M3), were assessed to adjust for soil heterogeneity. The analysis of variance (...
Lr16 is a widely deployed leaf rust resistance gene that is effective against the North American ... more Lr16 is a widely deployed leaf rust resistance gene that is effective against the North American Puccinia triticina population when in combination with Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the pustule. Previously sequenced seedling leaf rust resistance genes (e.g Lr1, Lr10 and Lr21) were Resistance Gene Analog (RGA)-like genes. Lr16 has been mapped to the telomeric region of wheat chromosome bin 2BS3. We used two populations to fine map Lr16: an F6‐derived recombinant inbred line (RIL) population consisting of 1872 lines from the cross between Canadian wheat lines BW278 and “AC Foremost” and a Doubled Haploid (DH) population with 957 lines from the cross between wheat varieties “AC Majestic” and “Glenlea”. The gene was localized to 1.5cM and 3.4cM intervals in BW278/AC foremost and AC Majestic/Glenlea populations respectively. To better delineate the Lr16 interval, single nucleotide poly...
Flax (Linum usitatissimum L., 2n = 2x =30) is a self-pollinated annual species of the Linaceae fa... more Flax (Linum usitatissimum L., 2n = 2x =30) is a self-pollinated annual species of the Linaceae family. It is a dual purpose crop grown for its seed oil (linseed) and/or its stem fibres from which linen and other products are made. Linseeds are rich in omega-3 fatty acids (55-57%) essential for humans and ideal for the production of biodegradable products such as linoleum flooring and paints. The genome size of the flax variety CDC Bethune was estimated at ~373Mb based on flow cytometry (Wang et al. 2012). This genome was sequenced using a whole genome shotgun (WGS) sequencing strategy on the Illumina sequencing platform (Wang et al. 2012). A total of 302 Mb in 116,602 contigs or 318 Mb in 88,384 scaffolds was obtained, representing ~81% of the flax genome. The remaining ~70 Mb were gaps within and between scaffolds. All contigs or scaffolds were unordered and some of them, especially long scaffolds, were mis-assembled. In order to refine the genome assembly, we identified mis-assemb...
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