High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Flowering Dogwood (Cornus florida)

Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding for resistance has been recognized as an ideal strategy for controlling the disease in C. florida, but efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. In this study, we mapped quantitative trait loci (QTL) associated with PM resistance/tolerance in two full sibling populations segregating for PM response: Rutgers H4AR15P25 (P25) × Rutgers H4AR15R28 (P28) (n = 195) and Rutgers H4AR15R25 × Rutgers H4AR15P35 (P35) (n = 83). High-density genetic linkage maps were constructed for the mapping populations using double digest restriction-site associated DNA sequencing-derived single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). The P25 × P28 map consisted of 2265 markers, spanning 1520 cM and 11 linkage groups (LGs) with an average marker spacing of 0.69 cM. The P25 × P35 map was constructed with 1788 markers, spanning 1256 cM and 11 LGs, with an average marker spacing of 0.72 cM. The maps had 604 markers in common and exhibited excellent collinearity. Through multiple QTL model mapping, one major QTL (LOD = 11.36 and R2 = 58.9%) was identified in P25 × P35. Furthermore, a minor QTL (LOD = 3.30 and R2 = 7.8%) was detected in P25 × P28. Due to their proximity onLG3, these QTL may be designating the same locus or tightly linked loci. The negative additive effects of both QTL signify that the PM susceptible male parents were contributing susceptibility alleles to the progeny. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs

High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Flowering Dogwood (<i>Cornus florida</i>)

Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding for resistance has been recognized as an ideal strategy for controlling the disease in C. florida, but efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. In this study, we mapped quantitative trait loci (QTL) associated with PM resistance/tolerance in two full sibling populations segregating for PM response: Rutgers H4AR15P25 (P25) × Rutgers H4AR15R28 (P28) (n = 195) and Rutgers H4AR15R25 × Rutgers H4AR15P35 (P35) (n = 83). High-density genetic linkage maps were constructed for the mapping populations using double digest restriction-site associated DNA sequencing-derived single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). The P25 × P28 map consisted of 2265 markers, spanning 1520 cM and 11 linkage groups (LGs) with an average marker spacing of 0.69 cM. The P25 × P35 map was constructed with 1788 markers, spanning 1256 cM and 11 LGs, with an average marker spacing of 0.72 cM. The maps had 604 markers in common and exhibited excellent collinearity. Through multiple QTL model mapping, one major QTL (LOD = 11.36 and R2 = 58.9%) was identified in P25 × P35. Furthermore, a minor QTL (LOD = 3.30 and R2 = 7.8%) was detected in P25 × P28. Due to their proximity onLG3, these QTL may be designating the same locus or tightly linked loci. The negative additive effects of both QTL signify that the PM susceptible male parents were contributing susceptibility alleles to the progeny. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs

Additional file 1: of Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm

Description of 180-accession panel of Ocimum spp., cluster membership and response to downy mildew (Peronospora belbahrii) reported as disease severity. (PDF 115 kb

Additional file 5: of Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm

Genotype data. Binary matrix of accessions (rows) and alleles (columns). (XLSX 186 kb

Additional file 2: of Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm

Primer sequences and melting temperatures (Tm) for the EST-SSRs used in this study. (PDF 52 kb

Sea turtle populations and poaching implications on Playa Norte, Tortuguero, Costa Rica 2009-2011

Sea turtle populations continue to be under threat globally from organised poaching for human consumption and financial gain. In the northeast of Costa Rica four species of sea turtle nest annually at one of the country’s most popular tourism destinations, Tortuguero. Over a four year nesting population survey, completed with anti-poaching strategies, we show that sea turtle poaching levels on the edge of the national park beach zones are maintained at a similar frequency annually and potentially could increase. Harvesting of sea turtles on the Atlantic coasts of Costa Rica is prohibited. Unsustainable poaching of adult sea turtles and their nests during years of poorer adult abundance has an unknown potential to damage future populations by degrading the number of nests that could hatch and the subsequent recruitment of hatchling turtles. We raise concern over the dwindling future of hawksbill turtles (Eretmochelys imbricata) on the beaches surrounding Tortuguero National Park

A first linkage map and downy mildew resistance QTL discovery for sweet basil (<i>Ocimum basilicum</i>) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq)

<div><p>Limited understanding of sweet basil (<i>Ocimum basilicum</i> L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (<i>Peronospora belbahrii</i>) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F₂ mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an <i>O</i>. <i>basilicum</i> allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37–55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, <i>dm11</i>.<i>1</i> explained 21–28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL <i>dm9</i>.<i>1</i> and <i>dm14</i>.<i>1</i> explained 5–16% and 4–18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL <i>dm11</i>.<i>1</i> increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.</p></div

Detection of major downy mildew resistance QTL <i>dm11</i>.<i>1</i> across three environments.

<p>LOD scores for genome-wide scan using square-root transformed phenotype data from three environments: NJSN14 (northern New Jersey; 2014), NJRA14 (southern New Jersey; 2014) and NJRA15 (southern New Jersey; 2015). Significant LOD thresholds (α = 0.05) were calculated by permutation tests with 1,000 iterations and are shown with red, dashed horizontal lines.</p

Frequency distribution of disease severity in the MRI x SB22 F₂ mapping population across three environments.

<p>Codes for each environment are shown on the x-axis and correspond to data recorded in 2014 in southern New Jersey (NJRA14), 2015 in southern New Jersey (NJRA15) and northern New Jersey in 2014 (NJSN14). Disease severity measured on a scale in which 0 = lowest possible severity score and 1 = highest possible severity score.</p

Effect and interaction plots for three QTL detected in environment NJSN14.

<p>MRI x SB22 F₂ genotype means (circles) ± 1 SE (error bars) for (A) minor QTL <i>dm9</i>.1, (B) major QTL <i>dm11</i>.<i>1</i> and (C) minor <i>dm14</i>.<i>1</i>. Two-QTL genotype by genotype means ± 1 SE for (D) <i>dm11</i>.<i>1</i> by <i>dm9</i>.<i>1</i> and (E) <i>dm11</i>.<i>1</i> by <i>dm14</i>.<i>1</i>. Allele ‘a’ is inherited from downy mildew resistant grandparent MRI and allele ‘b’ is inherited from susceptible grandparent SB22. Error bars represent ±1 SE.</p