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

Root restriction accelerates genomic target identification in quinoa under controlled conditions

Quinoa (Chenopodium quinoa) is a nutritious and resilient crop that displays a high genetic and phenotypic variation. As the popularity of this crop increases, there is a growing need to integrate classic and modern breeding tools to favor its improvement. We tested root restriction as a method to reduce plant size and enable high-throughput phenotypic screening of large sets of quinoa plants under controlled conditions. We verified how increasing root restriction does not affect the prediction of field behavior with respect to other standard greenhouse cultivation procedures. We then combined the phenotypic information obtained with our root restriction system with whole-genome re-sequencing data to characterize a quinoa diversity panel of 100 accessions and showed that phenotypic data obtained from root-restricted plants provide real insights into quinoa genetics. Finally, we carried out a genome-wide association study (GWAS) and identified a previously described locus for betalain biosynthesis, as well as other candidate loci linked to betalain biosynthesis and seed size. Overall, we showed that a phenotyping system based on root restriction can aid the identification of genomic targets in quinoa, which can complement and inform field trials for certain traits. This work supports further breeding and faster improvement of quinoa.

Genome assembly of a diversity panel of Chenopodium quinoa

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.

Unraveling Quinoa (Chenopodium quinoa Willd.) Defense Against Downy Mildew (Peronospora variabilis): Comparative Molecular Analysis of Resistant "Hualhuas" and Susceptible "Real" Cultivars

Quinoa (Chenopodium quinoa Willd.) is a new, promising non-conventional useful crop; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle limiting its productivity in Egypt. Identifying and utilizing resistant quinoa cultivars appear to be reliable and cost-efficient strategies for controlling downy mildew, particularly in resource-limited farmers' fields. This study aimed to evaluate the differential resistance of the Peruvian "Hualhuas" and Bolivian "Real" quinoa cultivars to P. variabilis infection under laboratory conditions to provide precise insight into their basic defense mechanism(s). Inoculated "Hualhuas" plants displayed complete resistance against P. variabilis, with no visible symptoms (incompatible reaction), while those of "Real" plants revealed high susceptibility (compatible reaction), with typical downy mildew lesions on their leaf surfaces. Disease incidence reached about 66% in the inoculated "Real" plants, with most inoculated leaves having lesions of grades 4 and 5 covering up to 90% of their leaf surfaces. Susceptibility indices reached up to 66% in the inoculated "Real" plants. Resistance to P. variabilis observed in the "Hualhuas" plants may have been largely attributed to elevated endogenous H2O2 levels, increased peroxidase (POX) activity and abundance, enhanced phenylalanine ammonia-lyase (PAL) activity and expression, as well as the upregulation of the pathogen-related protein 10 gene (PR-10). The results of this study indicate that the quinoa cultivar "Hualhuas" not only is a promising candidate for sustainable control of quinoa downy mildew but also, through a deep understanding of its molecular resistance mechanisms, would provide a possible route to enhance downy mildew resistance in other genotypes.

A Quantitative Real-Time PCR Method to Detect the Quinoa Downy Mildew Pathogen, Peronospora variabilis

Quinoa downy mildew, caused by Peronospora variabilis, is the most devastating disease of quinoa globally. Rapid, sensitive diagnostic methods are needed to detect and quantify this pathogen in seeds and plant tissue. A hydrolysis probe-based quantitative real-time PCR (qPCR) assay including a competitive internal control was developed for P. variabilis detection. This assay could detect as low as 20 ag of DNA or approximately 25 internal transcribed spacer (ITS) copies per reaction with efficiencies ranging from 93.9 to 98.2%. No nontarget amplification was observed when tested against DNA from other downy mildew pathogens and related oomycetes. P. variabilis strains from multiple countries were detected using this assay. The assay was successfully applied to quantify the pathogen in quinoa seeds from a field trial conducted in the state of Washington. Downy mildew disease was recorded on all 14 genotypes, with the genotypes 104.88 and 106.49 recording the highest area under the disease progress curve values (mean ± SE; 3,236 ± 303 and 2,851 ± 198, respectively) and J6 and Dutchess recording the lowest (441 ± 107 and 409 ± 129, respectively). Seed washes obtained from field samples were subjected to the qPCR assay, and the pathogen was detected in all samples. The highest pathogen ITS copy number was recorded with 106.49 (194,934 ± 38,171), and the lowest was observed in Pasto (5,971 ± 1,435) and Riobamba (9,954 ± 4,243). This qPCR assay could lead to improved detection and quantification of P. variabilis as well as increased understanding of quinoa-P. variabilis interactions and epidemiology.

Genome-wide association study, combined with bulk segregant analysis, identify plant receptors and defense related genes as candidate genes for downy mildew resistance in quinoa

BACKGROUND

Downy mildew is the most relevant disease of quinoa and the most widespread. Though, little is known about the genetics of resistance to this disease. The objective of this study was to identify the genomic regions controlling downy mildew resistance in quinoa and candidate genes for this trait. With this aim we carried out a GWAS analysis in a collection formed by 211 quinoa accessions from different origins. This approach was combined with inheritance studies and Bulk Segregant Analysis (BSA) in a segregating population.

RESULTS

GWAS analysis identified 26 genomic regions associated with the trait. Inheritance studies in a F2 population segregating for resistance revealed the existence of a major single dominant gene controlling downy mildew complete resistance in quinoa accession PI614911. Through BSA, this gene was found to be located in chromosome 4, in a region also identified by GWAS. Furthermore, several plant receptors and resistance genes were found to be located into the genomic regions identified by GWAS and are postulated as candidate genes for resistance.

CONCLUSIONS

Until now, little was known about the genetic control of downy mildew resistance in quinoa. A previous inheritance study suggested that resistance to this disease was a quantitative polygenic trait and previous GWAS analyses were unable to identify accurate markers for this disease. In our study we demonstrate the existence of, at least, one major gene conferring resistance to this disease, identify the genomic regions involved in the trait and provide plausible candidate genes involved in defense. Therefore, this study significantly increases our knowledge about the genetics of downy mildew resistance and provides relevant information for breeding for this important trait.

kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS

Genome-wide association studies (GWAS) have been widely used to identify genetic variation associated with complex traits. Despite its success and popularity, the traditional GWAS approach comes with a variety of limitations. For this reason, newer methods for GWAS have been developed, including the use of pan-genomes instead of a reference genome and the utilization of markers beyond single-nucleotide polymorphisms, such as structural variations and k-mers. The k-mers-based GWAS approach has especially gained attention from researchers in recent years. However, these new methodologies can be complicated and challenging to implement. Here, we present kGWASflow, a modular, user-friendly, and scalable workflow to perform GWAS using k-mers. We adopted an existing kmersGWAS method into an easier and more accessible workflow using management tools like Snakemake and Conda and eliminated the challenges caused by missing dependencies and version conflicts. kGWASflow increases the reproducibility of the kmersGWAS method by automating each step with Snakemake and using containerization tools like Docker. The workflow encompasses supplemental components such as quality control, read-trimming procedures, and generating summary statistics. kGWASflow also offers post-GWAS analysis options to identify the genomic location and context of trait-associated k-mers. kGWASflow can be applied to any organism and requires minimal programming skills. kGWASflow is freely available on GitHub (https://github.com/akcorut/kGWASflow) and Bioconda (https://anaconda.org/bioconda/kgwasflow).

k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean

Genome-wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a given trait in crop species. Assessing genetic variants other than single-nucleotide polymorphisms (SNPs) could alleviate this problem. In this study, we tested the potential of structural variant (SV)- and k-mer-based GWAS in soybean by applying these methods as well as conventional SNP/indel-based GWAS to 13 traits. We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k-mer-based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to Phytophthora sojae. In our dataset, SV-based GWAS did not add value compared to k-mer-based GWAS and may not be worth the time and computational resources invested. Despite promising results, significant challenges remain regarding the downstream analysis of k-mer-based GWAS. Notably, better methods are needed to associate significant k-mers with sequence variation. Our results suggest that coupling k-mer- and SNP/indel-based GWAS is a powerful approach for discovering candidate genes in crop species.

New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health

As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.

Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen

Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.

Challenges and Perspectives for Integrating Quinoa into the Agri-Food System

Quinoa is a highly nutritious and abiotic stress-tolerant crop that can be used to ensure food security for the rapidly growing world population under changing climate conditions. Various experiments, based on morphology, phenology, physiology, and yield-related attributes, are being conducted across the globe to check its adoptability under stressful environmental conditions. High weed infestation, early stand establishment, photoperiod sensitivity, loss of seed viability after harvest, and heat stress during its reproductive stage are major constraints to its cultivation. The presence of saponin on its outer surface is also a significant restriction to its local consumption. Scientists are using modern breeding programs, such as participatory approaches, to understand and define breeding goals to promote quinoa adaptation under marginalized conditions. Despite its rich nutritional value, there is still a need to create awareness among people and industries about its nutritional profile and potential for revenue generation. In the future, the breeding of the sweet and larger-grain quinoa varietals will be an option for avoiding the cleaning of saponins, but with the risk of having more pests in the field. There is also a need to focus on mechanized farming systems for the cultivation, harvesting, and processing of quinoa to facilitate and expand its cultivation and consumption across the globe, considering its high genetic diversity.

Characterization of Alternaria alternata and Alternaria scrophulariae Brown Spot in Colombian quinoa (Chenopodium quinoa)

Alternaria is a saprophytic and opportunistic fungus with a worldwide distribution that can affect the quality of various agricultural products, such as fruits, cereals, and pseudocereals. This research was carried out to investigate the population of this genus associated with quinoa cultivation in plots located in the Boyacá department (Colombia), the country's third-largest quinoa-producing department. The present study found 17 Alternaria isolates, of which 13 were identified as A. alternata and 4 as A. scrophulariae (formerly A. conjuncta) employed molecular markers of internal transcribed spacer (ITS) region and translation elongation factor 1α (TEF-1α). In the pathogenicity test under greenhouse conditions, all the Alternaria isolates showed some degree of pathogenicity on Piartal quinoa cultivar plants although no significant differences were found in isolates. The severity indices ranged from 2 to 5, and the percentage of affected leaves per plant ranged between 15% and 40%. This fungus affected the foliar tissue of quinoa, resulting in chlorotic and necrotic spots, symptoms that can generate a reduction in the quality and productivity of crops. This is the first time that the pathogenicity of Alternaria spp. in the Piartal variety has been described and the first report of this genera in quinoa crops of Colombia.

Chenopodium quinoa, a New Host for Alternaria Section Alternata and Alternaria Section Infectoriae Causing Yellow Leaf Blotch Disease

Quinoa (Chenopodium quinoa Willd.) is a native American crop mainly grown in the Andes of Bolivia and Peru. During the last decades, the cultivation of quinoa has expanded to more than 125 countries. Since then, several diseases of quinoa have been characterized. A leaf disease was observed on quinoa plants growing in an experimental plot in Eastern Denmark in 2018. The symptoms produced by the associated fungi consisted of small yellow blotches on the upper surface of leaves with a pale chlorotic halo surrounding the lesion. These studies used a combination of morphology, molecular diagnostics, and pathogenicity tests to identify two different Alternaria species belonging to Alternaria sections Infectoriae and Alternata as the causal agent of observed disease symptoms. To the best of our knowledge, this is the first report of Alternaria spp. as foliar pathogens of quinoa. Our findings indicate the need for additional studies to determine potential risks to quinoa production.

Yield, phenology and triterpene saponins in Colombian quinoa

Exploring yield, phenology and their relationship with secondary metabolites in seeds provides a fundamental analysis that expands knowledge on the nutritional quality of seeds and the effect on productive potential. This knowledge is fundamental when improving or selecting nutritionally important crops, including Chenopodium quinoa Willd, which has excellent nutritional properties and contributes to global food security. This species contains saponins, a metabolite that imparts a bitter taste and can be highly toxic to consumers in large quantities. Therefore, the identification and selection of genotypes according to their saponin contents and outstanding agronomic characteristics are fundamental objectives for the genetic improvement programs of these species. Therefore, the objective of this research was to evaluate the characteristics of the grain, the phenology and the saponin content of 30 C. quinoa accessions with an aim to select or relate genotypes according to their yield and grain quality. The accessions were sown using randomized complete blocks (RCB) with nine repetitions for each material. Seven FAO-defined descriptors were evaluated to characterize the grain and physiological maturity. Saponin was extracted using microwave, and the quantification was done with high-performance liquid chromatography (HPLC) which a UV-VIS detector at 277 nm wavelength. The accessions were classified according to their phenology: semi-late (56.7%), late (36.7%), and semi-early (3.3%). The total triterpene saponin content varied from 0.018 to 0.537%. The multivariate and cluster analyses formed groups of accessions with good yields (>62.02 g of seeds per plant) and desirable grain morphological characteristics. The more suitable accessions for the production of saponins are Quinoa semiamarga (0.537%), Quinoa peruana (0.412%) and Amarilla de maranganí (0.305%). Quinoa real and Quinoa primavera are more suitable for food products, which can be used as parents in future quinoa genetic improvement programs in Colombia.

Resequencing worldwide spinach germplasm for identification of field resistance QTLs to downy mildew and assessment of genomic selection methods

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete Peronospora effusa. In the past two decades, new pathogen races have repeatedly overcome the resistance used in newly released cultivars, urging the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew pathogens and are effective against some pathogen races/isolates. This work aimed to evaluate the worldwide USDA spinach germplasm collections and commercial cultivars for resistance to downy mildew pathogen in the field condition under natural inoculum pressure and conduct genome wide association analysis (GWAS) to identify resistance-associated genomic regions (alleles). Another objective was to evaluate the prediction accuracy (PA) using several genomic prediction (GP) methods to assess the potential implementation of genomic selection (GS) to improve spinach breeding for resistance to downy mildew pathogen. More than four hundred diverse spinach genotypes comprising USDA germplasm accessions and commercial cultivars were evaluated for resistance to downy mildew pathogen between 2017-2019 in Salinas Valley, California and Yuma, Arizona. GWAS was performed using single nucleotide polymorphism (SNP) markers identified via whole genome resequencing (WGR) in GAPIT and TASSEL programs; detected 14, 12, 5, and 10 significantly associated SNP markers with the resistance from four tested environments, respectively; and the QTL alleles were detected at the previously reported region of chromosome 3 in three of the four experiments. In parallel, PA was assessed using six GP models and seven unique marker datasets for field resistance to downy mildew pathogen across four tested environments. The results suggest the suitability of GS to improve field resistance to downy mildew pathogen. The QTL, SNP markers, and PA estimates provide new information in spinach breeding to select resistant plants and breeding lines through marker-assisted selection (MAS) and GS, eventually helping to accumulate beneficial alleles for durable disease resistance.

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with F_ST divergence of 0.36 and LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study using multi-year phenotyping trials uncovered 600 SNPs stably associated with 17 traits. Two candidate genes are associated with thousand seed weight, and a resistance gene analog is associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits important for adaptation. This work demonstrates the use of re-sequencing data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomics-enabled quinoa breeding.

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

Assessment of Phenotypic Diversity in the USDA Collection of Quinoa Links Genotypic Adaptation to Germplasm Origin

Quinoa’s germplasm evaluation is the first step towards determining its suitability under new environmental conditions. The aim of this study was to introduce suitable germplasm to the lowland areas of the Faisalabad Plain that could then be used to introduce quinoa more effectively to that region. A set of 117 quinoa genotypes belonging to the USDA quinoa collection was evaluated for 11 phenotypic quantitative traits (grain yield (Y), its biological and numerical components plus phenological variables) in a RCBD during two consecutive growing seasons at the University of Agriculture, Faisalabad, Pakistan under mid-autumn sowings. Genotypic performance changed across the years, however most phenotypic traits showed high heritability, from 0.75 for Harvest Index (HI) to 0.97 for aerial biomass (B) and Y. Ordination and cluster analyses differentiated four groups dominated by genotypes from: Peru and the Bolivian Highlands (G1); the Bolivian Highlands (G2); the Ballón collection (regarded as a cross between Bolivian and Sea Level (Chilean) genotypes) plus Bolivian Highlands (G3); and Ballón plus Sea Level (G4), this latter group being the most differentiated one. This genetic structure shared similarities with previous groups identified using SSR markers and G×E data from an international quinoa test. G4 genotypes showed the highest Y associated with higher B and seed numbers (SN), while HI made a significant contribution to yield determination in G2 and seed weight (SW) in G3. G1 and G2 showed the lowest Y associated with a lower B and SN. Moreover, SW showed a strongly negative association with SN in G2. Accordingly, G4 followed by G3 are better suited to the lowland areas of Faisalabad plain and the physiological traits underlying yield determination among genotypic groups should be considered in future breeding programs.

Multiple evolutionary origins of glyphosate resistance in Lolium multiflorum

The multitude of herbicide resistance patterns that have evolved in different weed species is a remarkable example of the rapid adaptation to anthropogenic-driven disturbance. Recently, resistance to glyphosate was identified in multiple populations of Lolium multiflorum in Oregon. We used phenotypic approaches, as well as population genomic and gene expression analyses, to determine whether known mechanisms were responsible for glyphosate resistance and whether resistance phenotypes evolved independently in different populations, and to identify potential loci contributing to resistance. We found no evidence of genetic alterations or expression changes at known target and non-target-site resistance mechanisms of glyphosate. Population genomic analyses indicated that resistant populations tended to have largely distinct ancestry from one another, suggesting that glyphosate resistance did not spread among populations by gene flow. Rather, resistance appears to have evolved independently on different genetic backgrounds. We also detected potential loci associated with the resistance phenotype, some of which encode proteins with potential effects on herbicide metabolism. Our results suggest that Oregon populations of L. multiflorum evolved resistance to glyphosate due to a novel mechanism. Future studies that characterize the gene or genes involved in resistance will be necessary to confirm this conclusion.

Evaluation of Disease Severity and Molecular Relationships Between Peronospora variabilis Isolates on Chenopodium Species in New Hampshire

Quinoa is a potential new crop for New England; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle for cultivation. The objectives of this study were to evaluate differential resistance within the Chenopodium genus, identify novel sources of resistance for use in future genetic studies or breeding programs, and investigate phylogenetic relationships of P. variabilis isolates from different Chenopodium hosts. The long-term goal of this research is to develop a resistant variety of quinoa to be grown in New England. Field trials conducted at the University of New Hampshire evaluated downy mildew disease severity on 10 Chenopodium accessions representing four species. Disease severity for each treatment was compared and significant differences in disease severity were observed between accessions. C. berlandieri var. macrocalycium ecotypes collected from Rye Beach, New Hampshire and Appledore Island, Maine exhibited the lowest disease severity over the growing season. P. variabilis was isolated from each accession, and COX2 sequences were compared. Phylogenetic analyses suggest no effect of host species on P. variabilis sequence similarity; however, isolates are shown to cluster by geographic location. This research provides the first step in identifying potential New England native sources of resistance to downy mildew within the genus Chenopodium and provides preliminary information needed to further investigate resistance at the genomic level in Chenopodium spp.

Genotype-Dependent Variation of Nutritional Quality-Related Traits in Quinoa Seeds

Exploiting the relationship between the nutritional properties of seeds and the genetic background constitutes an essential analysis, which contributes to broadening our knowledge regarding the control of the nutritional quality of seeds or any other edible plant structure. This is an important aspect when aiming at improving the nutritional characteristics of crops, including those of Chenopodium quinoa Willd. (quinoa), which has the potential to contribute to food security worldwide. Previous works have already described changes in the nutritional properties of quinoa seeds due to the influence of the environment, the genotype, or their interaction. However, there is an important limitation in the analyses carried out, including the outcomes that can be translated into agronomical practices and their effect on seed quality. In the present study, several seed nutritional-related parameters were analyzed in 15 quinoa cultivars grown in a particular environmental context. Important agronomical and nutritional differences were found among cultivars, such as variations in mineral or protein contents and seed viability. More importantly, our analyses revealed key correlations between seed quality-related traits in some cultivars, including those that relate yield and antioxidants or yield and the germination rate. These results highlight the importance of considering the genotypic variation in quinoa when selecting improved quinoa varieties with the best nutritional characteristics for new cultivation environments.

R. Patiranage D, Johansen K, Schmöckel SM, Bertero D, Oakey H, Colque-Little C, Afzal I, Raubach S, Miller N, Streich J, Amby DB, Emrani N, Warmington M, Mousa MAA, Wu D, Jacobson D, Andreasen C, Jung C, Murphy K, Bazile D, Tester M, on behalf of the Quinoa Phenotyping Consortium. Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.

A Review of Chenopodium quinoa (Willd.) Diseases-An Updated Perspective

The journey of the Andean crop quinoa (Chenopodium quinoa Willd.) to unfamiliar environments and the combination of higher temperatures, sudden changes in weather, intense precipitation, and reduced water in the soil has increased the risk of observing new and emerging diseases associated with this crop. Several diseases of quinoa have been reported in the last decade. These include Ascochyta caulina, Cercospora cf. chenopodii, Colletotrichum nigrum, C. truncatum, and Pseudomonas syringae. The taxonomy of other diseases remains unclear or is characterized primarily at the genus level. Symptoms, microscopy, and pathogenicity, supported by molecular tools, constitute accurate plant disease diagnostics in the 21st century. Scientists and farmers will benefit from an update on the phytopathological research regarding a crop that has been neglected for many years. This review aims to compile the existing information and make accurate associations between specific symptoms and causal agents of disease. In addition, we place an emphasis on downy mildew and its phenotyping, as it continues to be the most economically important and studied disease affecting quinoa worldwide. The information herein will allow for the appropriate execution of breeding programs and control measures.

Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans

The wild tomato species Solanum chilense is divided into geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype versus pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance can be observed between but also within populations at the level of individual plants. Our data also did not reveal complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggests that the observed quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is the result of basal defense responses that depend on the host genotype and are pathogen isolate-unspecific.