Image_3_Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing.jpeg

Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.</p

Table_1_Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing.xlsx

Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.</p

Image_2_Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing.jpeg

Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.</p

Image_1_Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing.jpeg

Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.</p

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

28 février 19371937/02/28 (A38,N13222)

Allelic analysis of 768 cowpea accessions from 11 geographic regions and genotyped with 1,048 SNP markers.

<p>Allelic analysis of 768 cowpea accessions from 11 geographic regions and genotyped with 1,048 SNP markers.</p

Genetic Diversity and Population Structure of Cowpea (<i>Vigna unguiculata</i> L. Walp) - Fig 1

<p>(A) Delta K values for different numbers of populations assumed (K) in the STRUCTURE analysis. (B) Classification of 768 accessions into three populations using STRUCTURE 2.3.1. The distribution of the accessions to different populations is indicated by the color code. Numbers on the y-axis show the subgroup membership, and the x-axis shows the different accession.(C)Unrooted Neighbor-Joining (NJ) tree of the 768 accessions drawn by MEGA 6 and each colored shape represents one cluster matching the structure population (blue for Q1, red for Q2, yellow for Q3, and green for admixture).(D)the scatter diagram of Principal Component Analysis (PCA) of the 768 accessions, calculated by TASSEL and drawn by Excel and each colored spot is representative of one cluster Q1 to Q3 same as in (C).</p

Phylogenetic tree among 11 regions based on the genetic-distance matrix using the neighbor-joining method by Power Marker V3.25 and visualized using the software MEGA 6.

<p>The blue and yellow balls in each region represent the accession ratio of cluster Q3 ratio in region: blue for low (less than 10%) and red for high (greater than 20%) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160941#pone.0160941.t002" target="_blank">Table 2</a>).</p

Three parameters were estimated: (1) The number of spinach accessions in each cluster was list by region (up section in the table); (2) the percentage of accessions in each cluster was listed by region and the data were shown in each row (the middle section in the table); and (3) the percentage of accessions in each region was listed by cluster and the data were shown in each column (bottom section in the table) in the 343 world wide spinach genotypes including 268 USDA accessions, 45 F1 hybrids and 30 Arkansas lines.

<p>Three parameters were estimated: (1) The number of spinach accessions in each cluster was list by region (up section in the table); (2) the percentage of accessions in each cluster was listed by region and the data were shown in each row (the middle section in the table); and (3) the percentage of accessions in each region was listed by cluster and the data were shown in each column (bottom section in the table) in the 343 world wide spinach genotypes including 268 USDA accessions, 45 F1 hybrids and 30 Arkansas lines.</p

The traditional phylogenetic tree created by the Maximum Likelihood (ML) method from MEGA 6 in spinach germplasm accessions from 12 countries plus F1 hybrids and Arkansas lines.

<p>The traditional phylogenetic tree created by the Maximum Likelihood (ML) method from MEGA 6 in spinach germplasm accessions from 12 countries plus F1 hybrids and Arkansas lines.</p