scholarly journals Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa)

2020 ◽  
Author(s):  
Carla Colque-Little ◽  
Miguel Correa Abondano ◽  
Ole Søgard Lund ◽  
Daniel Buchvaldt Amby ◽  
Hans-Peter Piepho ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Downy Mildew ◽  
Mixed Models ◽  
Genetic Basis ◽  
Chenopodium Quinoa ◽  
South American ◽  
Sources Of Resistance ◽  
Saponin Content ◽  
Genome Wide ◽  
Grain Crop

AbstractBackgroundQuinoa (Chenopodium quinoa Willd.) is an ancient grain crop that is tolerant to abiotic stress and has favorable nutritional properties. Downy mildew is the main disease of quinoa and is caused by infections of the biotrophic oomycete Peronospora variabilis Gaüm. Since the disease causes major yield losses, identifying sources of downy mildew tolerance in genetic resources and understanding its genetic basis are important goals in quinoa breeding.ResultsWe infected 132 South American genotypes, three Danish cultivars and the weedy relative C. album with a single isolate of P. variabilis under greenhouse conditions and observed a large variation in disease traits like severity of infection, which ranged from 5% to 83%. Linear mixed models revealed a significant effect of genotypes on disease traits with high heritabilities (0.72 to 0.81). Factors like altitude at site of origin or seed saponin content did not correlate with mildew tolerance, but stomatal width was weakly correlated with severity of infection. Despite the strong genotypic effects on mildew tolerance, genome-wide association mapping with 88 genotypes failed to identify significant marker-trait associations indicating a polygenic architecture of mildew tolerance.ConclusionsThe strong genetic effects on mildew tolerance allow to identify genetic resources, which are valuable sources of resistance in future quinoa breeding.

scholarly journals Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Carla Colque-Little ◽  
Miguel Correa Abondano ◽  
Ole Søgaard Lund ◽  
Daniel Buchvaldt Amby ◽  
Hans-Peter Piepho ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Downy Mildew ◽  
Mixed Models ◽  
Genetic Basis ◽  
Chenopodium Quinoa ◽  
South American ◽  
Sources Of Resistance ◽  
Saponin Content ◽  
Genome Wide ◽  
Grain Crop

Abstract Background Quinoa (Chenopodium quinoa Willd.) is an ancient grain crop that is tolerant to abiotic stress and has favorable nutritional properties. Downy mildew is the main disease of quinoa and is caused by infections of the biotrophic oomycete Peronospora variabilis Gaüm. Since the disease causes major yield losses, identifying sources of downy mildew tolerance in genetic resources and understanding its genetic basis are important goals in quinoa breeding. Results We infected 132 South American genotypes, three Danish cultivars and the weedy relative C. album with a single isolate of P. variabilis under greenhouse conditions and observed a large variation in disease traits like severity of infection, which ranged from 5 to 83%. Linear mixed models revealed a significant effect of genotypes on disease traits with high heritabilities (0.72 to 0.81). Factors like altitude at site of origin or seed saponin content did not correlate with mildew tolerance, but stomatal width was weakly correlated with severity of infection. Despite the strong genotypic effects on mildew tolerance, genome-wide association mapping with 88 genotypes failed to identify significant marker-trait associations indicating a polygenic architecture of mildew tolerance. Conclusions The strong genetic effects on mildew tolerance allow to identify genetic resources, which are valuable sources of resistance in future quinoa breeding.

scholarly journals Molecular Detection of Peronospora variabilis in Quinoa Seed and Phylogeny of the Quinoa Downy Mildew Pathogen in South America and the United States

2014 ◽  
Vol 104 (4) ◽  
pp. 379-386 ◽  
Author(s):  
Anna L. Testen ◽  
María del Mar Jiménez-Gasco ◽  
José B. Ochoa ◽  
Paul A. Backman
Keyword(s):  
United States ◽  
South America ◽  
Downy Mildew ◽  
Detection Method ◽  
Chenopodium Quinoa ◽  
The United States ◽  
Human Consumption ◽  
South American ◽  
Geographical Differences ◽  
Polymerase Chain

Quinoa (Chenopodium quinoa) is an important export of the Andean region, and its key disease is quinoa downy mildew, caused by Peronospora variabilis. P. variabilis oospores can be seedborne and rapid methods to detect seedborne P. variabilis have not been developed. In this research, a polymerase chain reaction (PCR)-based detection method was developed to detect seedborne P. variabilis and a sequencing-based method was used to validate the PCR-based method. P. variabilis was detected in 31 of 33 quinoa seed lots using the PCR-based method and in 32 of 33 quinoa seed lots using the sequencing-based method. Thirty-one of the quinoa seed lots tested in this study were sold for human consumption, with seed originating from six different countries. Internal transcribed spacer (ITS) and cytochrome c oxidase subunit 2 (COX2) phylogenies were examined to determine whether geographical differences occurred in P. variabilis populations originating from Ecuador, Bolivia, and the United States. No geographical differences were observed in the ITS-derived phylogeny but the COX2 phylogeny indicated that geographical differences existed between U.S. and South American samples. Both ITS and COX2 phylogenies supported the existence of a Peronospora sp., distinct from P. variabilis, that causes systemic-like downy mildew symptoms on quinoa in Ecuador. The results of these studies allow for a better understanding of P. variabilis populations in South America and identified a new causal agent for quinoa downy mildew. The PCR-based seed detection method allows for the development of P. variabilis-free quinoa seed, which may prove important for management of quinoa downy mildew.

scholarly journals Fast and Powerful Genome Wide Association Analysis of Dense Genetic Data with High Dimensional Imaging Phenotypes

2017 ◽  
Author(s):  
Habib Ganjgahi ◽  
Anderson M. Winkler ◽  
David C. Glahn ◽  
John Blangero ◽  
Brian Donohue ◽  
...  
Keyword(s):  
Mixed Models ◽  
Multiple Testing ◽  
Genetic Basis ◽  
Genome Wide Association ◽  
High Dimensional ◽  
Mixed Effect ◽  
Mixed Effect Models ◽  
Genome Wide ◽  
The Brain ◽  
Linear Mixed Effect Models

ABSTRACTGenome wide association (GWA) analysis of brain imaging phenotypes can advance our understanding of the genetic basis of normal and disorder-related variation in the brain. GWA approaches typically use linear mixed effect models to account for non-independence amongst subjects due to factors such as family relatedness and population structure. The use of these models with high-dimensional imaging phenotypes presents enormous challenges in terms of computational intensity and the need to account multiple testing in both the imaging and genetic domain. Here we present method that makes mixed models practical with high-dimensional traits by a combination of a transformation applied to the data and model, and the use of a non-iterative variance component estimator. With such speed enhancements permutation tests are feasible, which allows inference on powerful spatial tests like the cluster size statistic.

ALLOCATION OF SOURCES AND DONORS OF ECONOMICALLY VALUABLE TRAITS FROM THE COLLECTION MATERIAL OF CUCUMBER TO CREATE HIGHLY PRODUCTIVE VARIETIES AND HYBRIDS

1970 ◽  
pp. 45-49
Author(s):  
N. V. Kulyakina ◽  
G. A. Kuzmitskaya ◽  
T. K. Yurechko
Keyword(s):  
Genetic Resources ◽  
Downy Mildew ◽  
Geographical Origin ◽  
Plant Genetic Resources ◽  
Eastern Region ◽  
Biotic And Abiotic Stress ◽  
Climate Conditions ◽  
Damage Degree ◽  
Economically Valuable Traits ◽  
Far Eastern

The downy mildew (peronosporosis) is the most dangerous and harmful cucumber disease in the Far-Eastern region. Its harmfulness is the highest during the period of flowering – fruiting, because it may completely ruin the cucumber plants both in open and protected ground. Use of cucumber sorts with effective genes that are resistant to the disease is the most efficient way to fight cucumber peronosporosis. In this connection the publication adduces the facts of study the sorts and hybrids of different ecological and geographical origin from the genetic resources collection of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in comparison with three zoned sorts of DV NIISH selection – Mig, Khabar, Amurchonok. The aim of researches – to identify the sort samples cucumber according to the main economically valuable traits and also to the degree resistance of genetypes to the main disease of the culture in the region – downy mildew (peronosporosis), for allow to select the source material for the creation of sorts and hybrids, highly productive and resistant to biotic and abiotic stress environmental factors in the monsoon climate conditions of Khabarovsk region. The perspective genetypes having both the resistance to the diseases and productivity are not revealed as a result of the evaluation of the collection of cucumber samples according to their susceptibility by fungus diseases and productivity. Slavyanskiy (Belarus) is more resistant to peronosporosis, especially in 2016 year conditions, although it was inferior to the damage degree of disease to the zoned sorts – Mig, Khabar, Amurchonok. This perspective sample is planned to be used as a source of donors of the main economically valuable traits in a further selective work.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽  
2021 ◽  
Vol 253 (4) ◽  
Author(s):  
Mingzhao Zhu ◽  
Shujin Lu ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Downy Mildew ◽  
Fusarium Wilt ◽  
Black Spot ◽  
Housekeeping Genes ◽  
Chitinase Gene ◽  
Genome Wide ◽  
A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

scholarly journals Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

2021 ◽  
Vol 22 (8) ◽  
pp. 4266
Author(s):  
Yan Liu ◽  
Dalong Li ◽  
Na Yang ◽  
Xiaolong Zhu ◽  
Kexin Han ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Chinese Cabbage ◽  
Plant Disease Resistance ◽  
Expression Profiles ◽  
Black Rot ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Effector Triggered Immunity ◽  
Gene Structures ◽  
Bacteria And Fungi

The nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS–LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC–NBS–LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC–NBS–LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC–NBS–LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC–NBS–LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC–NBS–LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC–NBS–LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

scholarly journals The Genetic Basis of Hypertriglyceridemia

2021 ◽  
Vol 23 (8) ◽  
Author(s):  
Germán D. Carrasquilla ◽  
Malene Revsbech Christiansen ◽  
Tuomas O. Kilpeläinen
Keyword(s):  
Genetic Basis ◽  
Association Studies ◽  
Cumulative Effect ◽  
Genome Wide Association Studies ◽  
Genetic Loci ◽  
Risk Variants ◽  
Genome Wide ◽  
Severe Hypertriglyceridemia ◽  
Increased Risk ◽  
Polygenic Scores

Abstract Purpose of Review Hypertriglyceridemia is a common dyslipidemia associated with an increased risk of cardiovascular disease and pancreatitis. Severe hypertriglyceridemia may sometimes be a monogenic condition. However, in the vast majority of patients, hypertriglyceridemia is due to the cumulative effect of multiple genetic risk variants along with lifestyle factors, medications, and disease conditions that elevate triglyceride levels. In this review, we will summarize recent progress in the understanding of the genetic basis of hypertriglyceridemia. Recent Findings More than 300 genetic loci have been identified for association with triglyceride levels in large genome-wide association studies. Studies combining the loci into polygenic scores have demonstrated that some hypertriglyceridemia phenotypes previously attributed to monogenic inheritance have a polygenic basis. The new genetic discoveries have opened avenues for the development of more effective triglyceride-lowering treatments and raised interest towards genetic screening and tailored treatments against hypertriglyceridemia. Summary The discovery of multiple genetic loci associated with elevated triglyceride levels has led to improved understanding of the genetic basis of hypertriglyceridemia and opened new translational opportunities.

scholarly journals Widespread Infection with Hemotropic Mycoplasmas in Free-Ranging Dogs and Wild Foxes Across Six Bioclimatic Regions of Chile

2021 ◽  
Vol 9 (5) ◽  
pp. 919
Author(s):  
Sophia Di Cataldo ◽  
Aitor Cevidanes ◽  
Claudia Ulloa-Contreras ◽  
Irene Sacristán ◽  
Diego Peñaloza-Madrid ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Mixed Models ◽  
Rhipicephalus Sanguineus ◽  
Species Group ◽  
South American ◽  
Adult Age ◽  
Network Analyses ◽  
Male Sex ◽  
Free Ranging ◽  
Sequence Types

Blood samples of 626 rural dogs, 140 Andean foxes (Lycalopex culpaeus), and 83 South American grey foxes (L. griseus) from six bioregions of Chile spanning 3000 km were screened for Mycoplasma DNA by conventional PCR and sequencing. Risk factors of infection were inferred using Generalized Linear Mixed Models and genetic structure by network analyses. Overall, Mycoplasma haemocanis/Mycoplasma haemofelis (Mhc/Mhf) and Candidatus Mycoplasma haematoparvum (CMhp) observed prevalence was 23.8% and 12.8% in dogs, 20.1% and 7.2% in Andean foxes, and 26.5% and 8.4% in grey foxes, respectively. Both hemoplasmas were confirmed in all the bioregions, with higher prevalence in those where ticks from the Rhipicephalus sanguineus species group were absent. Candidatus M. haematominutum and a Mycoplasma sp. previously found in South American carnivores were detected in one fox each. Although the most prevalent Mhc/Mhf and CMhp sequence types were shared between dogs and foxes, network analysis revealed genetic structure of Mhc/Mhf between hosts in some regions. Male sex was associated with a higher risk of Mhc/Mhf and CMhp infection in dogs, and adult age with CMhp infection, suggesting that direct transmission is relevant. No risk factor was identified in foxes. Our study provides novel information about canine hemoplasmas with relevance in distribution, transmission routes, and cross-species transmission.

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