<p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. T... more <p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. The matrix consists of 90K genotypic data where cells shaded in blue denote expression of the W9262-260D3 (solid-stem) allele, whereas cells shaded in red denote expression of the Kofa (hollow-stem) allele. The name and position of each 90K probe, the anchored physical position on WEW chromosome 3B, and the corresponding position on the common wheat consensus map are shown. Two dimensional (row and column) hierarchical cluster analysis was performed to group lines into haplotypes as indicated by the colorized dendogram along the top X-axis, whereas similarly marker order is shown along the left Y-axis. *Lines showing identical haplotypes (n = 45) were collapsed into a single haplotype (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175285#pone.0175285.s002" target="_blank">S2A Table</a>).</p
<p>Each color represents a sub-population. The first 56 axes explained 80% of the total var... more <p>Each color represents a sub-population. The first 56 axes explained 80% of the total variance.</p
<p>Seedling disease reaction to (a) W009 and (b) W015. (c) Final scoring of adult plant dis... more <p>Seedling disease reaction to (a) W009 and (b) W015. (c) Final scoring of adult plant disease severity collected on 27-Aug-2014 in Toluca, Mexico (MX-14_DH).</p
<p>(a) LSMeans for seedling disease severity of lines from three subpopulations that were i... more <p>(a) LSMeans for seedling disease severity of lines from three subpopulations that were inoculated with FC, W009, and W015. (b) LSMeans for adult plant disease severity of lines from three subpopulations, based on final ratings in 2013 (MX-13) and 2014 (MX-14). Bars that do not share a letter differ significantly (Fisher’s LSD, <i>P <</i> 0.05). Data are presented as mean ± standard error.</p
<p>Seedling stripe rust reaction to (a) isolate W009 (W009_DH) and (b) W015 (W015_DH), and ... more <p>Seedling stripe rust reaction to (a) isolate W009 (W009_DH) and (b) W015 (W015_DH), and (c) adult plant resistance in Mexico in 2014 (MX-14_DH). The ‘p’ represents the susceptible allele from Kofa, while ‘q’ represents the resistant allele from W9262-260D3, as determined using the peak markers for <i>QYr</i>.<i>usw-5B</i> (<i>wsnp_Ku_c4427_8029592</i>) and <i>QYr</i>.<i>usw-7B</i> (<i>BS00075300_51</i>). There were 34, 37, 39, and 39 lines with the ‘pp’, ‘qp’, ‘pq’ and ‘qq’ haplotype for <i>QYr</i>.<i>usw-5B</i> and <i>QYr</i>.<i>usw-7B</i>, respectively (a and b). Likewise, there were 73 lines with the ‘p’ haplotype and 76 lines with the ‘q’ haplotype for <i>QYr</i>.<i>usw-7B</i> (c). Bars that do not share a letter differ significantly (Fisher’s LSD, <i>P < 0</i>.<i>05</i>).</p
<p>Gene candidates for <i>QYr</i>.<i>usw-5B</i> and <i>QYr<... more <p>Gene candidates for <i>QYr</i>.<i>usw-5B</i> and <i>QYr</i>.<i>usw-7B</i> from the WEW genome.</p
<p>The positions of significant QTL on chromosome 5B (a) and 7B (b) are illustrated by diag... more <p>The positions of significant QTL on chromosome 5B (a) and 7B (b) are illustrated by diagonally hatched bars next to the chromosome, which are expanded to show map detail. Flanking markers are in bold. The dotted lines indicate the QTL significance thresholds. The QTL are labelled and colored according to three independent experiments involving stripe rust infection: two growth cabinet experiments using single isolates W009 (orange) or W015 (green) and a third field experiment performed in Mexico in 2014 (MX-14, pink).</p
In mammals, the pre-Sertoli celi of the male genital ridge is the first celi type to display sex ... more In mammals, the pre-Sertoli celi of the male genital ridge is the first celi type to display sex specific differentiation and gene expression. The genetic cascade driving the differentiation of pre-Sertoli ceils and testis formation is beginning to be unravelled, but many questions remain; a better understanding of the transcriptome of pre-Sertoli ceils immediately after sex determination is now essential. A mouse model expressing Red fluorescent Protein under the control of a hybrid mouse/pig $RY promoter (HybSRYp-RFP) was used to purify ceils from embryonic day 12.0 (e 12.0) male genital ridges. The transcriptomes of of these ceils was compared to age matched whole female genital ridge cells using Affymetrix Mouse Genome 430 2.0 microanays. The expression of genes considered markers for pre-Sertoli ceils, including Sox9, Mis, Dhh and Fgf9 were identified within the HybSRYp-RFP expressing ceil population, while markers for germ cells (Oct4, SSEA-]) and endothelial celis (Ntrk3) wer...
Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is... more Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to stripe rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for stripe rust resistance were identified on chromosome 7B (LOD 6.87-11.47) and chromosome 5B (LOD 3.88...
Insights from the annotated wheat genome Wheat is one of the major sources of food for much of th... more Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 ; see also p. eaar6089
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecul... more An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Association mapping is usually performed by testing the correlation between a single marker and p... more Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structu...
<p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. T... more <p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. The matrix consists of 90K genotypic data where cells shaded in blue denote expression of the W9262-260D3 (solid-stem) allele, whereas cells shaded in red denote expression of the Kofa (hollow-stem) allele. The name and position of each 90K probe, the anchored physical position on WEW chromosome 3B, and the corresponding position on the common wheat consensus map are shown. Two dimensional (row and column) hierarchical cluster analysis was performed to group lines into haplotypes as indicated by the colorized dendogram along the top X-axis, whereas similarly marker order is shown along the left Y-axis. *Lines showing identical haplotypes (n = 45) were collapsed into a single haplotype (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175285#pone.0175285.s002" target="_blank">S2A Table</a>).</p
<p>Each color represents a sub-population. The first 56 axes explained 80% of the total var... more <p>Each color represents a sub-population. The first 56 axes explained 80% of the total variance.</p
<p>Seedling disease reaction to (a) W009 and (b) W015. (c) Final scoring of adult plant dis... more <p>Seedling disease reaction to (a) W009 and (b) W015. (c) Final scoring of adult plant disease severity collected on 27-Aug-2014 in Toluca, Mexico (MX-14_DH).</p
<p>(a) LSMeans for seedling disease severity of lines from three subpopulations that were i... more <p>(a) LSMeans for seedling disease severity of lines from three subpopulations that were inoculated with FC, W009, and W015. (b) LSMeans for adult plant disease severity of lines from three subpopulations, based on final ratings in 2013 (MX-13) and 2014 (MX-14). Bars that do not share a letter differ significantly (Fisher’s LSD, <i>P <</i> 0.05). Data are presented as mean ± standard error.</p
<p>Seedling stripe rust reaction to (a) isolate W009 (W009_DH) and (b) W015 (W015_DH), and ... more <p>Seedling stripe rust reaction to (a) isolate W009 (W009_DH) and (b) W015 (W015_DH), and (c) adult plant resistance in Mexico in 2014 (MX-14_DH). The ‘p’ represents the susceptible allele from Kofa, while ‘q’ represents the resistant allele from W9262-260D3, as determined using the peak markers for <i>QYr</i>.<i>usw-5B</i> (<i>wsnp_Ku_c4427_8029592</i>) and <i>QYr</i>.<i>usw-7B</i> (<i>BS00075300_51</i>). There were 34, 37, 39, and 39 lines with the ‘pp’, ‘qp’, ‘pq’ and ‘qq’ haplotype for <i>QYr</i>.<i>usw-5B</i> and <i>QYr</i>.<i>usw-7B</i>, respectively (a and b). Likewise, there were 73 lines with the ‘p’ haplotype and 76 lines with the ‘q’ haplotype for <i>QYr</i>.<i>usw-7B</i> (c). Bars that do not share a letter differ significantly (Fisher’s LSD, <i>P < 0</i>.<i>05</i>).</p
<p>Gene candidates for <i>QYr</i>.<i>usw-5B</i> and <i>QYr<... more <p>Gene candidates for <i>QYr</i>.<i>usw-5B</i> and <i>QYr</i>.<i>usw-7B</i> from the WEW genome.</p
<p>The positions of significant QTL on chromosome 5B (a) and 7B (b) are illustrated by diag... more <p>The positions of significant QTL on chromosome 5B (a) and 7B (b) are illustrated by diagonally hatched bars next to the chromosome, which are expanded to show map detail. Flanking markers are in bold. The dotted lines indicate the QTL significance thresholds. The QTL are labelled and colored according to three independent experiments involving stripe rust infection: two growth cabinet experiments using single isolates W009 (orange) or W015 (green) and a third field experiment performed in Mexico in 2014 (MX-14, pink).</p
In mammals, the pre-Sertoli celi of the male genital ridge is the first celi type to display sex ... more In mammals, the pre-Sertoli celi of the male genital ridge is the first celi type to display sex specific differentiation and gene expression. The genetic cascade driving the differentiation of pre-Sertoli ceils and testis formation is beginning to be unravelled, but many questions remain; a better understanding of the transcriptome of pre-Sertoli ceils immediately after sex determination is now essential. A mouse model expressing Red fluorescent Protein under the control of a hybrid mouse/pig $RY promoter (HybSRYp-RFP) was used to purify ceils from embryonic day 12.0 (e 12.0) male genital ridges. The transcriptomes of of these ceils was compared to age matched whole female genital ridge cells using Affymetrix Mouse Genome 430 2.0 microanays. The expression of genes considered markers for pre-Sertoli ceils, including Sox9, Mis, Dhh and Fgf9 were identified within the HybSRYp-RFP expressing ceil population, while markers for germ cells (Oct4, SSEA-]) and endothelial celis (Ntrk3) wer...
Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is... more Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to stripe rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for stripe rust resistance were identified on chromosome 7B (LOD 6.87-11.47) and chromosome 5B (LOD 3.88...
Insights from the annotated wheat genome Wheat is one of the major sources of food for much of th... more Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science , this issue p. eaar7191 ; see also p. eaar6089
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecul... more An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Association mapping is usually performed by testing the correlation between a single marker and p... more Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structu...
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