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A scoping review on tools and methods for trait prioritization in crop breeding programmes.

ABSTRACT: Trait prioritization studies have guided research, development and investment decisions for public-sector crop breeding programmes since the 1970s, but the research design, methods and tools underpinning these studies are not well understood. We used PRISMA-ScR (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols) to evaluate research on trait ranking for major crops over the past 40 years (1980-2023). Data extraction and descriptive analysis on 657 papers show uneven attention to crops, lack of systematic sex disaggregation and regional bias. The lack of standardized trait data taxonomy across studies, and inconsistent research design and data collection practices make cross-comparison of findings impossible. In addition, network mapping of authors and donors shows patterns of concentration and the presence of silos within research areas. This study contributes to the next generation of innovation in trait preference studies to produce more inclusive, demand-driven varietal design that moves beyond trait prioritization focused on productivity and yield.

SUBMITTER: Occelli M

PROVIDER: S-EPMC10954539 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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A scoping review on tools and methods for trait prioritization in crop breeding programmes.

Occelli M M Mukerjee R R Miller C C Porciello J J Puerto S S Garner E E Guerra M M Gomez M I MI Tufan H A HA

Nature plants 20240222 3

Trait prioritization studies have guided research, development and investment decisions for public-sector crop breeding programmes since the 1970s, but the research design, methods and tools underpinning these studies are not well understood. We used PRISMA-ScR (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols) to evaluate research on trait ranking for major crops over the past 40 years (1980-2023). Data extraction and descriptive analysis on 657 papers show uneven att ...[more]

PMID: 38388675

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Project description:We investigated the benefit from introgression of external lines into a cereal breeding programme and strategies that accelerated introgression of the favourable alleles while minimising linkage drag using stochastic computer simulation. We simulated genomic selection for disease resistance and grain yield in two environments with a high level of genotype-by-environment interaction (G × E) for the latter trait, using genomic data of a historical barley breeding programme as the base generation. Two populations (existing and external) were created from this base population with different allele frequencies for few (N = 10) major and many (N ~ 990) minor simulated disease quantitative trait loci (QTL). The major disease QTL only existed in the external population and lines from the external population were introgressed into the existing population which had minor disease QTL with low, medium and high allele frequencies. The study revealed that the benefit of introgression depended on the level of genetic variation for the target trait in the existing cereal breeding programme. Introgression of external resources into the existing population was beneficial only when the existing population lacked variation in disease resistance or when minor disease QTL were already at medium or high frequency. When minor disease QTL were at low frequencies, no extra genetic gain was achieved from introgression. More benefit in the disease trait was obtained from the introgression if the major disease QTL had larger effect sizes, more selection emphasis was applied on disease resistance, or more external lines were introgressed. While our strategies to increase introgression of major disease QTL were generally successful, most were not able to completely avoid negative impacts on selection for grain yield with the only exception being when major introgression QTL effects were very large. Breeding programmes are advised to carefully consider the level of genetic variation in a trait available in their breeding programme before deciding to introgress germplasms.

Project description:BackgroundSystematic reviews (SRs) are time-consuming and labor-intensive to perform. With the growing number of scientific publications, the SR development process becomes even more laborious. This is problematic because timely SR evidence is essential for decision-making in evidence-based healthcare and policymaking. Numerous methods and tools that accelerate SR development have recently emerged. To date, no scoping review has been conducted to provide a comprehensive summary of methods and ready-to-use tools to improve efficiency in SR production.ObjectiveTo present an overview of primary studies that evaluated the use of ready-to-use applications of tools or review methods to improve efficiency in the review process.MethodsWe conducted a scoping review. An information specialist performed a systematic literature search in four databases, supplemented with citation-based and grey literature searching. We included studies reporting the performance of methods and ready-to-use tools for improving efficiency when producing or updating a SR in the health field. We performed dual, independent title and abstract screening, full-text selection, and data extraction. The results were analyzed descriptively and presented narratively.ResultsWe included 103 studies: 51 studies reported on methods, 54 studies on tools, and 2 studies reported on both methods and tools to make SR production more efficient. A total of 72 studies evaluated the validity (n = 69) or usability (n = 3) of one method (n = 33) or tool (n = 39), and 31 studies performed comparative analyses of different methods (n = 15) or tools (n = 16). 20 studies conducted prospective evaluations in real-time workflows. Most studies evaluated methods or tools that aimed at screening titles and abstracts (n = 42) and literature searching (n = 24), while for other steps of the SR process, only a few studies were found. Regarding the outcomes included, most studies reported on validity outcomes (n = 84), while outcomes such as impact on results (n = 23), time-saving (n = 24), usability (n = 13), and cost-saving (n = 3) were less often evaluated.ConclusionFor title and abstract screening and literature searching, various evaluated methods and tools are available that aim at improving the efficiency of SR production. However, only few studies have addressed the influence of these methods and tools in real-world workflows. Few studies exist that evaluate methods or tools supporting the remaining tasks. Additionally, while validity outcomes are frequently reported, there is a lack of evaluation regarding other outcomes.

Project description:BackgroundPatient prioritization is a strategy used to manage access to healthcare services. Patient prioritization tools (PPT) contribute to supporting the prioritization decision process, and to its transparency and fairness. Patient prioritization tools can take various forms and are highly dependent on the particular context of application. Consequently, the sets of criteria change from one context to another, especially when used in non-emergency settings. This paper systematically synthesizes and analyzes the published evidence concerning the development and challenges related to the validation and implementation of PPTs in non-emergency settings.MethodsWe conducted a systematic mixed studies review. We searched evidence in five databases to select articles based on eligibility criteria, and information of included articles was extracted using an extraction grid. The methodological quality of the studies was assessed by using the Mixed Methods Appraisal Tool. The article selection process, data extraction, and quality appraisal were performed by at least two reviewers independently.ResultsWe included 48 studies listing 34 different patient prioritization tools. Most of them are designed for managing access to elective surgeries in hospital settings. Two-thirds of the tools were investigated based on reliability or validity. Inconclusive results were found regarding the impact of PPTs on patient waiting times. Advantages associated with PPT use were found mostly in relationship to acceptability of the tools by clinicians and increased transparency and equity for patients.ConclusionsThis review describes the development and validation processes of PPTs used in non-urgent healthcare settings. Despite the large number of PPTs studied, implementation into clinical practice seems to be an open challenge. Based on the findings of this review, recommendations are proposed to develop, validate, and implement such tools in clinical settings.Systematic review registrationPROSPERO CRD42018107205.

Dataset Information

A scoping review on tools and methods for trait prioritization in crop breeding programmes.

Publications

A scoping review on tools and methods for trait prioritization in crop breeding programmes.

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