Genomic selection (GS) uses genomewide molecular markers to predict breeding values and make selections of individuals or breeding lines prior to phenotyping. Here we show that ...genotyping‐by‐sequencing (GBS) can be used for de novo genotyping of breeding panels and to develop accurate GS models, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS we discovered 41,371 single nucleotide polymorphisms (SNPs) in a set of 254 advanced breeding lines from CIMMYT's semiarid wheat breeding program. Four different methods were evaluated for imputing missing marker scores in this set of unmapped markers, including random forest regression and a newly developed multivariate‐normal expectation‐maximization algorithm, which gave more accurate imputation than heterozygous or mean imputation at the marker level, although no significant differences were observed in the accuracy of genomic‐estimated breeding values (GEBVs) among imputation methods. Genomic‐estimated breeding value prediction accuracies with GBS were 0.28 to 0.45 for grain yield, an improvement of 0.1 to 0.2 over an established marker platform for wheat. Genotyping‐by‐sequencing combines marker discovery and genotyping of large populations, making it an excellent marker platform for breeding applications even in the absence of a reference genome sequence or previous polymorphism discovery. In addition, the flexibility and low cost of GBS make this an ideal approach for genomics‐assisted breeding.
Key message
The principal phenotypic determinants of market class in carrot—the size and shape of the root—are under primarily additive, but also highly polygenic, genetic control.
The size and shape ...of carrot roots are the primary determinants not only of yield, but also market class. These quantitative phenotypes have historically been challenging to objectively evaluate, and thus subjective visual assessment of market class remains the primary method by which selection for these traits is performed. However, advancements in digital image analysis have recently made possible the high-throughput quantification of size and shape attributes. It is therefore now feasible to utilize modern methods of genetic analysis to investigate the genetic control of root morphology. To this end, this study utilized both genome wide association analysis (GWAS) and genomic-estimated breeding values (GEBVs) and demonstrated that the components of market class are highly polygenic traits, likely under the influence of many small effect QTL. Relatively large proportions of additive genetic variance for many of the component phenotypes support high predictive ability of GEBVs; average prediction ability across underlying market class traits was 0.67. GWAS identified multiple QTL for four of the phenotypes which compose market class: length, aspect ratio, maximum width, and root fill, a previously uncharacterized trait which represents the size-independent portion of carrot root shape. By combining digital image analysis with GWAS and GEBVs, this study represents a novel advance in our understanding of the genetic control of market class in carrot. The immediate practical utility and viability of genomic selection for carrot market class is also described, and concrete guidelines for the design of training populations are provided.
Sustainable management of genetic resources is a crucial issue in the global context of food security. On-farm conservation is now widely acknowledged as a relevant strategy to reach this goal ...because it maintains evolutionary forces within and between the different components of the agricultural system. Seed exchanges between farmers play a key role in this process but are complicated to study over different agricultural contexts. This review begins by illustrating how interdisciplinary approaches combining ethnobotany and genetics helps provide a detailed analysis of the role of social and genetic dynamic interactions related to seed exchanges in traditional farming systems with farmer-led on-farm conservation. Secondly, the evolution of crop genetic diversity management is described in the context of industrialized farming systems. We follow the evolution of crop biodiversity perception by involved actors using a socio-historical perspective. After the agricultural shift from a traditional to a productivist model, recent social developments such as citizen science and participatory research movements are emerging and are strongly concerned by the question of biodiversity. These emerging trends which recognize and value seed exchanges between farmers show similarities to farmer-to-farmer seed exchanges in traditional farming systems. To what extent are these systems comparable? To fully benefit from studies in both traditional and industrialized contexts, it will be critical to develop an interdisciplinary framework to rigorously compare seed exchange systems and more generally farmer-led on-farm conservation strategies in diverse agricultural systems.
The aim is to evaluate the published evidence on whether methotrexate (MTX) use causes progressive fibrotic interstitial lung disease (fILD). This PRISMA-compliant systematic review has been ...registered electronically with PROSPERO 2018 ID CRD42018087838, Centre of review and dissemination at the University of York. A total of 29 articles met the inclusion criteria. Thirteen articles were found to support the claim that MTX causes fILD. They all had a low Downs and Black quality score (< 6/27). Their ‘risk of bias’ assessment scores indicated serious to critical risk of bias. The 16 articles rejecting the claim that MTX causes fILD were of higher quality as indicated by their Downs and Black score. Their ‘risk of bias’ assessment scores suggested only a low to moderate risk of bias. This systematic literature review supports the finding that MTX does not cause fILD in humans. Three studies suggest that MTX treatment may actually improve outcomes in patients with rheumatoid arthritis (RA) associated fILD by slowing down ILD progression.
Root shape in carrot (
Daucus carota
subsp.
sativus
), which ranges from long and tapered to short and blunt, has been used for at least several centuries to classify carrot cultivars. The ...subjectivity involved in determining market class hinders the establishment of metric-based standards and is ill-suited to dissecting the genetic basis of such quantitative phenotypes. Advances in digital image acquisition and analysis has enabled new methods for quantifying sizes of plant structures and shapes, but in order to dissect the genetic control of the shape features that define market class in carrot, a tool is required that quantifies the specific shape features used by humans in distinguishing between classes. This study reports the construction and demonstration of the first such platform, which facilitates rapid phenotyping of traits that are measurable by hand, such as length and width, as well as principal component analysis (PCA) of the root contour and its curvature. This latter approach is of particular interest, as it enabled the detection of a novel and significant quantitative trait, defined here as root fill, which accounts for 85% of the variation in root shape. Curvature analysis was demonstrated to be an effective method for precise measurement of the broadness of the carrot shoulder, and degree of tip fill; the first principal component of the respective curvature profiles captured 87% and 84% of the total variance. This platform’s performance was validated in two experimental panels. First, a diverse, global collection of germplasm was used to assess its capacity to identify market classes through clustering analysis. Second, a diallel mating design between inbred breeding lines of differing market classes was used to estimate the heritability of the key phenotypes that define market class, which revealed significant variation in the narrow-sense heritability of size and shape traits, ranging from 0.14 for total root size, to 0.84 for aspect ratio. These results demonstrate the value of high-throughput digital phenotyping in characterizing the genetic control of complex quantitative phenotypes.
•We used an international wheat breeding trial dataset from stress environments.•Genome-wide markers were used to estimate genetic relatedness among genotypes.•Genomic selection (GS) models were used ...to make global predictions for yield.•Joint GS and G×E models did not improve targeting of lines to environments.•In simulated data GS and G×E models improved predictions for different environments.
Genomic selection (GS) offers breeders the possibility of using historic data and unbalanced breeding trials to form training populations for predicting the performance of new lines. However, when using datasets that are unbalanced over time and space, there is increasing exposure to different genotype – environment combinations and interactions that may make predictions less accurate. Global cross-validated genomic prediction accuracies may be high when using large historic datasets but accuracies for individual years using a forward-prediction approach, or accuracies for individual locations, are often much lower. The objective of this study was to evaluate the overall accuracy of genomic predictions for untested genotypes using an unbalanced dataset to train a genomic selection model, and to explore ways of combining genomic selection and genotype-by-environment (G×E) interaction models to better target untested lines to different locations. Using the International Center for Maize and Wheat Improvement's (CIMMYT) Semi-Arid Wheat Yield Trials (SAWYT) we assessed the accuracy of genomic predictions and the potential to subset these nurseries using the concept of mega-environments (ME) adapted to a genomic selection context. We found that there was no difference in accuracy between models accounting for G×E interactions and global models. Data-driven methods of clustering locations based on similarities in genomic predictions also failed to improve accuracies within clusters. Using a simulation based on the empirical SAWYT data, we found that if there were different true genotypic values between clusters, there was an advantage to modeling G×E in prediction models. In the SAWYT dataset it appears that there is not a consistent pattern of genotype-by-environment interaction among the ME, and this dataset is not balanced enough to partition into new clusters that have predictive power.
Cover crop-based reduced tillage (CCBRT) systems can provide multiple benefits in cucurbit cropping systems, including potential to reduce spread of soil-borne pathogens, minimize erosion, and ...decrease weed pressure. Despite benefits and farmer interest, adoption has been limited, in part due to inconsistent weed suppression and potential for reduced yields. Prior studies have suggested that N competition, allelopathy, and lower temperature may be factors in reducing vegetable yield in CCBRT systems. A strip tillage approach has been suggested as one strategy that could mitigate those issues, but cucurbit yields using these systems have shown mixed results in prior studies, some of which did not include other important considerations for growers such as the impact on weed and pest pressure. In 2018 and 2019, CCBRT strip till practices for organic acorn winter squash (
Cucurbita pepo
L.) production were assessed in Wisconsin on certified organic land. Combinations of different between-row (aisle) and in-row mulches were compared to attempt to identify reduced tillage combinations that effectively manage weeds while resulting in yields comparable to full tillage production, testing our hypothesis that no differences between production systems would be observed due to strip tillage and plastic mulch warming soil and minimizing competition while promoting cash crop growth. Aisle treatments included roller-crimped cereal rye (
Secale cereale
L.) mulch, straw mulch and cultivated bare ground, and in-row treatments included plastic mulch, ground straw mulch, and cultivated ground. Weed and pest counts, weed management time, and yields were compared between treatments. Plots managed with rye and straw in the aisles had significantly less weed pressure as compared to cultivated aisle treatments, although rye required more weed management time than ground straw mulch. In addition, rye resulted in lower marketable yield due to higher proportion unmarketable fruit in 2018, likely related to a 25 cm rain event 2 weeks prior to harvest. A significant row mulch × aisle mulch interaction was observed for marketable fruit m
−1
, showing that yield was not significantly affected by the type of in-row mulch in plots with crimped rye mulch in the aisle. Pressure from squash bugs (
Anasa tristis
) was also higher in treatments with organic or synthetic mulches (straw in aisles or rows, rye in aisles, and plastic in rows). Our results support previous evidence that crimped rye can be an effective mulching strategy to reduce weed pressure, with more efficient management than traditional straw mulch. However, crimped rye systems may have negative implications for yield and pest pressure regardless of the use of a strip-tillage approach, indicating that more research is needed to refine the production system.
In agricultural systems, biodiversity includes diversity within species and among species and provides many benefits for production, resilience and conservation. This article addresses the effects of ...a strategy of
in situ conservation called dynamic management (DM) on population evolution, adaptation and diversity. Two French DM initiatives are considered, the first one corresponding to an experimental context, the second to an on-farm management. Results from a study over 26 years of experimental DM of bread wheat (
Triticum aestivum L.) are first presented, including the evolution of agronomic traits and genetic diversity at neutral and fitness related loci. While this experiment greatly increased scientific knowledge of the effects of natural selection on cultivated populations, it also showed that population conservation cannot rely only on a network of experimental stations. In collaboration with a farmers’ network in France, researchers have begun studying the effects of on-farm DM (conservation and selection) on diversity and adaptation. Results from these studies show that on-farm DM is a key element for the long-term conservation and use of agricultural biodiversity. This method of
in situ conservation deserves more attention in industrialised countries.
L’importance de l’agrobiodiversité, c’est-à-dire la biodiversité présente dans les espaces agricoles, fait l’objet d’une reconnaissance toute récente. Cette biodiversité, qui englobe à la fois la diversité observée à l’intérieur des espèces et la richesse en espèces, est à l’origine de nombreux bénéfices pour les fonctions de production, résilience et conservation des espaces agricoles. Dans cet article, nous nous intéressons aux principaux effets d’une stratégie de conservation in situ de l’agrobiodiversité, la gestion dynamique (GD), sur l’évolution de la diversité et l’adaptation des populations. Notre analyse est construite sur la base de deux initiatives françaises de GD, l’une dans un contexte expérimental, et la seconde se déroulant à la ferme. Une première approche expérimentale de GD est menée depuis 26 années sur le blé tendre (
Triticum aestivum L.), et a fait l’objet de nombreuses études, portant sur l’évolution des caractères agronomiques et de la diversité génétique de locus neutres ou sélectionnés. Cette expérience a contribué à la meilleure connaissance des effets de la sélection naturelle sur les populations cultivées, mais elle a également montré qu’un réseau de stations expérimentales ne pouvait constituer l’unique dispositif de conservation de populations cultivées. En collaboration avec un réseau d’agriculteurs français, les scientifiques ont initié l’étude de l’effet de la conservation à la ferme et de la sélection participative sur la diversité et l’adaptation des populations. Les résultats des premières études montrent que la conservation in situ à la ferme et la sélection participative sont des éléments essentiels pour la conservation à long terme et l’utilisation de la biodiversité agricole, un rôle encore peu reconnu dans les pays industrialisés.
Full-scale food production in cities: is it an impossibility? Or is it a panacea for all that ails urban communities? Today, it's a reality, but many people still don't know how much of an impact ...this emerging food system is having on cities and their residents. This book showcases the work of the farmers, activists, urban planners, and city officials in the United States and Canada who are advancing food production. They have realized that, when it's done right, farming in cities can enhance the local ecology, foster cohesive communities, and improve the quality of life for urban residents.Implementing urban agriculture often requires change in the physical, political, and social-organizational landscape. Beginning with a look at how and why city people grew their own food in the early twentieth century, the contributors toCities of Farmersexamine the role of local and regional regulations and politics, especially the creation of food policy councils, in making cities into fertile ground for farming. The authors describe how food is produced and distributed in cities via institutions as diverse as commercial farms, community gardens, farmers' markets, and regional food hubs. Growing food in vacant lots and on rooftops affects labor, capital investment, and human capital formation, and as a result urban agriculture intersects with land values and efforts to build affordable housing. It also can contribute to cultural renewal and improved health.This book enables readers to understand and contribute to their local food system, whether they are raising vegetables in a community garden, setting up a farmers' market, or formulating regulations for farming and composting within city limits.CONTRIBUTORSCatherine Brinkley, Benjamin W. Chrisinger, Nevin Cohen, Michèle Companion, Lindsey Day-Farnsworth, Janine de la Salle, Luke Drake, Sheila Golden, Randel D. Hanson, Megan Horst, Nurgul Fitzgerald, Becca B. R. Jablonski, Laura Lawson, Kara Martin, Nathan McClintock, Alfonso Morales, Jayson Otto, Anne Pfeiffer, Anne Roubal, Todd M. Schmit, Erin Silva, Michael Simpson, Lauren Suerth, Dory Thrasher, Katinka Wijsman
Objectives. To review all the current evidence of LEF-induced pneumonitis (LEIP) which will help rheumatologists recognize suspected cases of LEIP and to influence clinical guidelines. Methods. ...Thirty-two reported cases of LEIP (13 males and 19 females) were identified from a literature search and classified using Searles and McKendry's classification criteria. Their clinical characteristics were reviewed. Results. All patients had a history of either exposure to MTX or interstitial lung disease (ILD) or both and all patients had RA. Most patients (82%) had LEIP within the first 20 weeks of initiation of LEF. All patients who had a loading dose LEF and most patients with ILD developed LEIP early (within 12 weeks of exposure). Case mortality was 19%. Two patients had previous MTX-induced pneumonitis (MTX-P) prior to initiation of LEF; both died from LEIP. There was a high mortality in the following groups of patients: diffuse alveolar damage (DAD) on histological examination, pre-existing ILD and ground glass shadowing on high resolution computerised tomography (HRCT). Treatment with cholestyramine did not appear to alter clinical outcome. Conclusions. LEIP usually occurs within the first 20 weeks of initiation of LEF. Clinical features of patients who died were pre-existing ILD, ground glass shadowing on HRCT and DAD on histological examination, and these could be poor prognostic indicators. Patients need to be made aware of this rare complication. LEF should not be used in patients with previous MTX-P and should be used with caution in patients with ILD.
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