A Novel QTL for Resistance to Phytophthora Crown Rot in Squash

Phytophthora capsici Leonian causes significant yield losses in commercial squash (Cucurbita pepo) production worldwide. The deployment of resistant cultivars can complement integrated management practices for P. capsici, but resistant cultivars are currently unavailable for growers. Moderate resistance to Phytophthora crown rot in a selection of accession PI 181761 (C. pepo) (designated line #181761-36P) is controlled by three dominant genes (R4, R5 and R6). Introgression of these loci into elite germplasm through marker-assisted selection (MAS) can accelerate the release of new C. pepo cultivars resistant to crown rot, but these tools are currently unavailable. Here we describe the identification of a quantitative trait locus (QTL), molecular markers and candidate genes associated with crown rot resistance in #181761-36P. Five hundred and twenty-three SNP markers were genotyped in an F2 (n = 83) population derived from a cross between #181761-36P (R) and Table Queen (S) using targeted genotyping by sequencing. A linkage map (2068.96 cM) consisting of twenty-one linkage groups and an average density of 8.1 markers/cM was developed for the F2 population. The F2:3 families were phenotyped in the greenhouse with a virulent strain of P. capsica, using the spore-spray method. A single QTL (QtlPC-C13) was consistently detected on LG 13 (chromosome 13) across three experiments and explained 17.92–21.47% of phenotypic variation observed in the population. Nine candidate disease resistance gene homologs were found within the confidence interval of QtlPC-C13. Single nucleotide polymorphism (SNP) markers within these genes were converted into Kompetitive Allele Specific PCR (KASP) assays and tested for association with resistance in the F2 population. One SNP marker (C002686) was significantly associated with resistance to crown rot in the F2 population (p < 0.05). This marker is a potential target for MAS for crown rot resistance in C. pepo.

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Adapting Genotyping-by-Sequencing for Rice F2 Populations

10.1101/055798 ◽

2016 ◽

Cited By ~ 1

Author(s):

Tomoyuki Furuta ◽

Motoyuki Ashikari ◽

Kshirod K. Jena ◽

Kazuyuki Doi ◽

Stefan Reuscher

Keyword(s):

Low Cost ◽

Genotyping By Sequencing ◽

Cost Effective ◽

Snp Markers ◽

Reduced Representation ◽

F2 Population ◽

Wild Rice Species ◽

Miseq Platform ◽

Mapping Populations ◽

Genotype A

ABSTRACTRapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species Oryza longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations we attempted to genotype a highly heterozygous F2 population. We show how species-and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average) we were able to generate up to 8,154 informative SNP markers in 1,081 F2 individuals. Additionally, the effects of enzyme choice, read coverage and data post-processing are evaluated. Using GBS-derived markers we were able to assemble a genetic map of 1,536 cM. To demonstrate the usefulness of our GBS pipeline we determined QTL for the number of tillers. We were able to map four QTLs to chromosomes 1, 3, 4 and 8 and confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform we show that the GBS method is flexible and cost-effective even for smaller laboratories

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Inheritance of Resistance to Phytophthora Crown Rot in Cucurbita pepo

HortScience ◽

10.21273/hortsci14021-19 ◽

2019 ◽

Vol 54 (7) ◽

pp. 1156-1158 ◽

Cited By ~ 3

Author(s):

Vincent Njung’e Michael ◽

Yuqing Fu ◽

Geoffrey Meru

Keyword(s):

Cucurbita Pepo ◽

Management Practices ◽

Integrated Management ◽

Phytophthora Capsici ◽

The United States ◽

Crown Rot ◽

Inheritance Of Resistance ◽

Phenotypic Data ◽

Backcross Populations ◽

Pathogen Populations

Phytophthora crown rot, caused by Phytophthora capsici Leonian, is a devastating disease in commercial squash (Cucurbita pepo L.) production across the United States. Current management practices rely heavily on the use of chemical fungicides, but existence of fungicide-resistant pathogen populations has rendered many chemicals ineffective. Host resistance is the best strategy for managing this disease; however, no commercial cultivars resistant to the pathogen are currently available. Resistance to Phytophthora crown rot in PI 181761 (C. pepo) is an important genetic resource for squash breeders worldwide; however, the underlying genetic basis of resistance in PI 186761 that would allow designing of sound breeding strategies is currently unknown. The goal of the current study was to determine the inheritance of resistance in breeding line #186761-36P, a resistant selection of PI 181761, using phenotypic data from F1, F2, and backcross populations derived from a cross between #181761-36P and a susceptible acorn-type cultivar, Table Queen. The results indicated that resistance in #181761-36P is controlled by three dominant genes (R4, R5, and R6). Introgression of these genes into susceptible cultivar groups of C. pepo will provide an important tool in the integrated management of Phytophthora crown rot.

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High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽

10.1186/s12864-021-07788-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gehendra Bhattarai ◽

Wei Yang ◽

Ainong Shi ◽

Chunda Feng ◽

Braham Dhillon ◽

...

Keyword(s):

Candidate Genes ◽

Downy Mildew ◽

Association Analysis ◽

Spinacia Oleracea ◽

Genotyping By Sequencing ◽

Significant Snps ◽

Snp Markers ◽

Resistance Locus ◽

Downy Mildew Resistance ◽

Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

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Identification of Three Putative Signal Transduction Genes Involved in R Gene-Specified Disease Resistance in Arabidopsis

Genetics ◽

10.1093/genetics/152.1.401 ◽

1999 ◽

Vol 152 (1) ◽

pp. 401-412 ◽

Cited By ~ 1

Author(s):

Randall F Warren ◽

Peter M Merritt ◽

Eric Holub ◽

Roger W Innes

Keyword(s):

Disease Resistance ◽

Pseudomonas Syringae ◽

Resistance Genes ◽

Virulent Strain ◽

Disease Resistance Genes ◽

Avirulence Gene ◽

Detectable Effect ◽

Disease Resistance Gene ◽

Protein Functions ◽

Signal Transduction Genes

Abstract The RPS5 disease resistance gene of Arabidopsis mediates recognition of Pseudomonas syringae strains that possess the avirulence gene avrPphB. By screening for loss of RPS5-specified resistance, we identified five pbs (avrPphB susceptible) mutants that represent three different genes. Mutations in PBS1 completely blocked RPS5-mediated resistance, but had little to no effect on resistance specified by other disease resistance genes, suggesting that PBS1 facilitates recognition of the avrPphB protein. The pbs2 mutation dramatically reduced resistance mediated by the RPS5 and RPM1 resistance genes, but had no detectable effect on resistance mediated by RPS4 and had an intermediate effect on RPS2-mediated resistance. The pbs2 mutation also had varying effects on resistance mediated by seven different RPP (recognition of Peronospora parasitica) genes. These data indicate that the PBS2 protein functions in a pathway that is important only to a subset of disease-resistance genes. The pbs3 mutation partially suppressed all four P. syringae-resistance genes (RPS5, RPM1, RPS2, and RPS4), and it had weak-to-intermediate effects on the RPP genes. In addition, the pbs3 mutant allowed higher bacterial growth in response to a virulent strain of P. syringae, indicating that the PBS3 gene product functions in a pathway involved in restricting the spread of both virulent and avirulent pathogens. The pbs mutations are recessive and have been mapped to chromosomes I (pbs2) and V (pbs1 and pbs3).

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Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

BMC Plant Biology ◽

10.1186/s12870-021-02932-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhengjie Chen ◽

Dengguo Tang ◽

Jixing Ni ◽

Peng Li ◽

Le Wang ◽

...

Keyword(s):

Marker Assisted Selection ◽

Inbred Lines ◽

Average Density ◽

Snp Markers ◽

Data Sets ◽

Rna Seq ◽

Specific Pcr ◽

Maize Inbred Lines ◽

Allele Specific ◽

Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

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Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽

10.3390/genes12071042 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1042

Author(s):

Zhuoying Weng ◽

Yang Yang ◽

Xi Wang ◽

Lina Wu ◽

Sijie Hua ◽

...

Keyword(s):

Fishery Management ◽

Genotyping By Sequencing ◽

Parentage Analysis ◽

Snp Markers ◽

Individual Identification ◽

Pedigree Information ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Polymorphic Snps ◽

Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

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Organic Farming and Cover-Crop Management Reduce Pest Predation in Austrian Vineyards

Insects ◽

10.3390/insects12030220 ◽

2021 ◽

Vol 12 (3) ◽

pp. 220

Author(s):

Jo Marie Reiff ◽

Sebastian Kolb ◽

Martin H. Entling ◽

Thomas Herndl ◽

Stefan Möth ◽

...

Keyword(s):

Organic Farming ◽

Pest Control ◽

Cover Crops ◽

Cover Crop ◽

Management Practices ◽

Integrated Management ◽

Lobesia Botrana ◽

Management Options ◽

Natural Pest Control ◽

Predation Rates

Habitat simplification and intensive use of pesticides are main drivers of global arthropod declines and are, thus, decreasing natural pest control. Organic farming, complex landscapes, and local vineyard management practices such as implementation of flower-rich cover-crop mixtures may be a promising approach to enhance predator abundance and, therefore, natural pest control. We examined the effect of organic versus integrated management, cover-crop diversity in the vineyard inter-rows, and landscape composition on the natural pest control of Lobesia botrana eggs and pupae. Predation of L. botrana pupae was reduced by organic farming and species-poor cover-crops by about 10%. Predation rates of L. botrana eggs did not differ significantly in any of the studied management options. Dominant predators were earwigs (Forficulidae), bush crickets (Tettigoniidae), and ants (Formicidae). Negative effects of organic viticulture are most likely related to the negative nontarget effects on arthropods related to the frequent sulfur and copper applications in combination with the avoidance of strongly damaging insecticides by integrated winegrowers. While a 10% difference in predation rates on a single pest stage is unlikely to have strong practical implications, our results show that the assumed effectiveness of environmentally friendly agriculture needs to be evaluated for specific crops and regions.

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Integrated Management of Downy Mildew on Slicing Cucumber With Fungicides and Host Resistance But Not Trellising

Plant Disease ◽

10.1094/pdis-02-19-0323-re ◽

2019 ◽

Vol 103 (10) ◽

pp. 2592-2598

Author(s):

Anthony P. Keinath

Keyword(s):

Downy Mildew ◽

Host Resistance ◽

Management Practices ◽

Integrated Management ◽

Cultivar Resistance ◽

Fall Season ◽

Fungicide Treatment ◽

Progress Curve ◽

Management Techniques ◽

The Mean

The objective of this study was to evaluate fungicide applications, host resistance, and trellising, alone and in combination, as management practices for downy mildew on slicing cucumber. A split-split plot experimental design was used with three and four replications in spring and fall 2017, respectively. The whole-plot treatment was fungicide, four applications of chlorothalonil (Bravo Weather Stik 6SC) alternated with three applications of cyazofamid (Ranman 400SC), or water. Split plots were nontrellised or trellised with four strings supported by stakes. Split-split plots were cultivar Bristol, which is intermediately resistant to downy mildew, or cultivar Speedway, which is susceptible to downy mildew with similar parentage as Bristol. In both seasons, area under the disease progress curve (AUDPC) values were lower with fungicides than water for both cultivars. In the spring, AUDPC for Bristol was lower than for Speedway regardless of fungicide treatment. In the fall, Bristol had a lower AUDPC than Speedway with fungicides, but the AUDPC did not differ between the two cultivars with water. The mean AUDPC for trellised plants (376.2) was lower than for nontrellised plants (434.0; P = 0.007). Fungicide applications increased marketable and total fruit weights in both seasons (P ≤ 0.0002). Marketable weight with fungicides was almost double (93% greater) the marketable weight with water. Marketable weight was 55% greater for Bristol than for Speedway in spring, but yields did not differ between cultivars in fall (season-by-cultivar interaction, P ≤ 0.0003). Because trellising had no effect on marketable yields (P = 0.11), trellising is not recommended for managing downy mildew on slicing cucumber. Of the three management techniques examined, fungicides had the largest effects on disease and yields, followed by cultivar resistance.

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Overexpression of Pto Induces a Salicylate-Independent Cell Death But Inhibits Necrotic Lesions Caused by Salicylate-Deficiency in Tomato Plants

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2002.15.7.654 ◽

2002 ◽

Vol 15 (7) ◽

pp. 654-661 ◽

Cited By ~ 16

Author(s):

Jianxiong Li ◽

Libo Shan ◽

Jian-Min Zhou ◽

Xiaoyan Tang

Keyword(s):

Cell Death ◽

Disease Resistance ◽

Pseudomonas Syringae ◽

Virulent Strain ◽

Gene Activation ◽

Cellular Damage ◽

Minor Role ◽

Disease Resistance Gene ◽

Tomato Plants ◽

Spontaneous Cell Death

Tomato plants overexpressing the disease resistance gene Pto (35S∷Pto) exhibit spontaneous cell death, accumulation of salicylic acid (SA), elevated expression of pathogenesis-related genes, and enhanced resistance to a broad range of pathogens. Because salicylate plays an important role in the cell death and defense activation in many lesion mimic mutants, we investigated the interaction of SA-mediated processes and the 35S∷Pto-mediated defense pathway by introducing the nahG transgene that encodes salicylate hydroxylase. Here, we show that SA is not required for the 35S∷Pto-activated microscopic cell death and plays a minor role in defense gene activation and general disease resistance in 35S∷Pto plants. In contrast, temperature greatly affects the spontaneous cell death and general resistance in 35S∷Pto plants, and high temperature inhibits the cell death. The NahG tomato plants develop spontaneous, unconstrained necrotic lesions on leaves. These lesions also are initiated by the inoculation of a virulent strain of Pseudomonas syringae pv. tomato. However, the NahG-dependent necrotic lesions are inhibited in the NahG/35S∷Pto plants. This inhibition is most pronounced under conditions favoring the 35S∷Pto-mediated spontaneous cell death development. These results indicate that the signaling pathways activated by Pto overexpression suppress the cellular damage that is caused by SA depletion. We also found that ethylene is dispensable for the 35S∷Pto-mediated general defense.

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Mitigación de daños provocados por fauna silvestre en cultivos agrícolas en un bosque montano de Bolivia

Revista de Biología Tropical ◽

10.15517/rbt.v62i4.12983 ◽

2014 ◽

Vol 62 (4) ◽

pp. 1495 ◽

Cited By ~ 2

Author(s):

Eddy Pérez L. ◽

Luis F. Pacheco

Keyword(s):

Management Practices ◽

Integrated Management ◽

Management Strategies ◽

Species Conservation ◽

Agricultural Practices ◽

Dasypus Novemcinctus ◽

Natural Area ◽

Rural People ◽

Sapajus Apella ◽

Pecari Tajacu

Wildlife is often blamed for causing damage to human activities, including agricultural practices and the result may be a conflict between human interests and species conservation. A formal assessment of the magnitude of damage is necessary to adequately conduct management practices and an assessment of the efficiency of different management practices, is necessary to enable managers to mitigate the conflict with rural people. This study was carried out to evaluate the effectiveness of agricultural management practices and controlled hunting in reducing damage to subsistence annual crops at the Cotapata National Park and Natural Area of Integrated Management. The design included seven fields with modified agricultural practices, four fields subjected to control hunting, and five fields held as controls. We registered cultivar type, density, frequency of visiting species to the field, crops lost to wildlife, species responsible for damage, and crop biomass. Most frequent species in the fields were Dasyprocta punctata and Dasypus novemcinctus. Hunted plots were visited 1.6 times more frequently than agriculturally managed plots. Crop lost to wildlife averaged 7.28% at agriculturally managed plots, 4.59% in plots subjected to hunting, and 27.61% in control plots. Species mainly responsible for damage were Pecari tajacu, D. punctata, and Sapajus apella. We concluded that both management strategies were effective to reduce damage by >50% as compared to unmanaged crop plots.

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