scholarly journals Crafting for a better MAGIC: systematic design and test for multiparental advanced generation inter-cross population

2021 ◽  
Author(s):  
Chin Jian Yang ◽  
Rodney N. Edmondson ◽  
Hans-Peter Piepho ◽  
Wayne Powell ◽  
Ian Mackay
Keyword(s):  
Complex Traits ◽  
Recombinant Inbred Lines ◽  
Haplotype Diversity ◽  
R Package ◽  
Shiny App ◽  
New Varieties ◽  
Creativity And Innovation ◽  
Advanced Generation ◽  
Population Design ◽  
Magic Population

AbstractMultiparental advanced generation inter-cross (MAGIC) populations are valuable crop resources with a wide array of research uses including genetic mapping of complex traits, management of genetic resources and breeding of new varieties. Multiple founders are crossed to create a rich mosaic of highly recombined founder genomes in the MAGIC recombinant inbred lines (RILs). Many variations of MAGIC population designs exist; however, a large proportion of the currently available populations have been created empirically and based on similar designs. In our evaluations of five MAGIC populations, we found that the choice of designs has a large impact on the recombination landscape in the RILs. The most popular design used in many MAGIC populations has been shown to have a bias in recombinant haplotypes and low level of unique recombinant haplotypes, and therefore is not recommended. To address this problem and provide a remedy for the future, we have developed the “magicdesign” R package for creating and testing any MAGIC population design via simulation. A Shiny app version of the package is available as well. Our “magicdesign” package provides a unifying tool and a framework for creativity and innovation in MAGIC population designs. For example, using this package, we demonstrate that MAGIC population designs can be found which are very effective in creating haplotype diversity without the requirement for very large crossing programmes. Further, we show that interspersing cycles of crossing with cycles of selfing is effective in increasing haplotype diversity. These approaches are applicable in species which are hard to cross or in which resources are limited.

scholarly journals Crafting for a better MAGIC: systematic design and test for multiparental advanced generation inter-cross population

2021 ◽  
Author(s):  
Chin Jian Yang ◽  
Rodney N Edmondson ◽  
Hans-Peter Piepho ◽  
Wayne Powell ◽  
Ian Mackay
Keyword(s):  
Complex Traits ◽  
Recombinant Inbred Lines ◽  
Haplotype Diversity ◽  
R Package ◽  
Shiny App ◽  
New Varieties ◽  
Creativity And Innovation ◽  
Advanced Generation ◽  
Population Design ◽  
Magic Population

Abstract Multiparental advanced generation inter-cross (MAGIC) populations are valuable crop resources with a wide array of research uses including genetic mapping of complex traits, management of genetic resources and breeding of new varieties. Multiple founders are crossed to create a rich mosaic of highly recombined founder genomes in the MAGIC recombinant inbred lines (RILs). Many variations of MAGIC population designs exist; however, a large proportion of the currently available populations have been created empirically and based on similar designs. In our evaluations of five MAGIC populations, we found that the choice of designs has a large impact on the recombination landscape in the RILs. The most popular design used in many MAGIC populations has been shown to have a bias in recombinant haplotypes and low level of unique recombinant haplotypes, and therefore is not recommended. To address this problem and provide a remedy for the future, we have developed the “magicdesign” R package for creating and testing any MAGIC population design via simulation. A Shiny app version of the package is available as well. Our “magicdesign” package provides a unifying tool and a framework for creativity and innovation in MAGIC population designs. For example, using this package, we demonstrate that MAGIC population designs can be found which are very effective in creating haplotype diversity without the requirement for very large crossing programs. Further, we show that interspersing cycles of crossing with cycles of selfing is effective in increasing haplotype diversity. These approaches are applicable in species which are hard to cross or in which resources are limited.

scholarly journals Development of a multiparent advanced generation intercross (MAGIC) population for genetic exploitation of complex traits in Brassica juncea: glucosinolate content as an example

2019 ◽  
Author(s):  
Tianya Wang ◽  
Wei Wan ◽  
Kunjiang Yu ◽  
Aimal Nawaz Khattak ◽  
Botao Ye ◽  
...  
Keyword(s):  
Association Mapping ◽  
Complex Traits ◽  
Quantitative Traits ◽  
Recombinant Inbred Lines ◽  
Glucosinolate Content ◽  
Intron Length Polymorphism ◽  
Whole Process ◽  
Specific Pcr ◽  
Advanced Generation ◽  
Magic Population

AbstractMultiparent advanced generation intercross (MAGIC) populations have recently been developed to allow the high-resolution mapping of complex quantitative traits. This article describes the development of one MAGIC population and verifies its potential application for mapping quantitative trait loci (QTLs) in B. juncea. The population was developed from eight founders with diverse traits and composed of 408 F6 recombinant inbred lines (RILs). To develop one rapid and simplified way for using the MAGIC population, a subset of 133 RILs as the primary mapping population were genotyped using 346 intron-length polymorphism (ILP) polymorphic markers. The population lacks significant signatures of population structure that are suitable for the analysis of complex traits. Genome-wide association mapping (GWAS) identified three major glucosinolate (GSL) QTLs of QGsl.ig01.1 on J01 for indole GSL (IG), QGsl.atg09.1 on J09 and QGsl.atg11.1 on J11 for aliphatic GSL (AG) and total GSL (TG). The candidate genes for QGsl.ig01.1, QGsl.atg09.1 and QGsl.atg11.1 are GSH1, GSL-ALK and MYB28, which are involved in converting glutamate and cysteine to γ–EC, the accumulation of glucoraphanin, and the whole process of AG metabolism, respectively. One effective method for association mapping of quantitative traits in the B. juncea MAGIC population is also suggested by utilization of the remaining 275 RILs and incorporation of the novel kompetitive allele specific PCR (KASP) technique. In addition to its QTL mapping purpose, the MAGIC population could also be potentially utilized in variety development by breeders.

scholarly journals Association mapping for maize stover yield and saccharification efficiency using a multiparent advanced generation intercross (MAGIC) population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. López-Malvar ◽  
A. Butron ◽  
R. A. Malvar ◽  
S. J. McQueen-Mason ◽  
L. Faas ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Nucleotide Polymorphisms ◽  
Maize Stover ◽  
A Genome ◽  
Stover Yield ◽  
Saccharification Efficiency ◽  
Advanced Generation ◽  
Magic Population

AbstractCellulosic ethanol derived from fast growing C4 grasses could become an alternative to finite fossil fuels. With the potential to generate a major source of lignocellulosic biomass, maize has gained importance as an outstanding model plant for studying the complex cell wall network and also to optimize crop breeding strategies in bioenergy grasses. A genome-wide association study (GWAS) was conducted using a subset of 408 Recombinant Inbred Lines (RILs) from a Multi-Parent Advanced Generation Intercross (MAGIC) Population in order to identify single nucleotide polymorphisms (SNPs) associated with yield and saccharification efficiency of maize stover. We identified 13 SNPs significantly associated with increased stover yield that corresponded to 13 QTL, and 2 SNPs significantly associated with improved saccharification efficiency, that could be clustered into 2 QTL. We have pointed out the most interesting SNPs to be implemented in breeding programs based on results from analyses of averaged and yearly data. Association mapping in this MAGIC population highlight genomic regions directly linked to traits that influence the final use of maize. Markers linked to these QTL could be used in genomic or marker-assisted selection programs to improve biomass quality for ethanol production. This study opens a possible optimisation path for improving the viability of second-generation biofuels.

scholarly journals A multi-parent advanced generation inter-cross population for genetic analysis of multiple traits in cowpea (Vigna unguiculata L. Walp.)

2017 ◽  
Author(s):  
Bao-Lam Huynh ◽  
Jeffrey D. Ehlers ◽  
Maria Munoz-Amatriain ◽  
Stefano Lonardi ◽  
Jansen R. P. Santos ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Vigna Unguiculata ◽  
Seed Quality ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Sub Saharan Africa ◽  
Yield Potential ◽  
Breeding Populations ◽  
Advanced Generation ◽  
Magic Population

AbstractDevelopment and analysis of Multiparent Advanced Generation Inter-Cross (MAGIC) populations have been conducted with several crop plants to harness the potential for dissecting the genetic structure of traits and improving breeding populations. We developed a first MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in sub-Saharan Africa (SSA) where cowpea is vitally important in the human diet and in local economies. The eight parents were inter-crossed using structured matings to ensure the population would have balanced representation from each of the founder parents, followed by single-seed descent, resulting in 365 F8 recombinant inbred lines (RILs) each carrying a mosaic of genome blocks contributed from all founders. This was confirmed by SNP genotyping with the cowpea Illumina 60K iSelect BeadArray. Following filtering to eliminate duplicates, sister lines and accidental selfing events, a core set of 305 F8 RILs was chosen as the primary population. The F8 lines were on average 99.74% homozygous while also diverse in agronomic traits including flowering time, growth habit, maturity, yield potential and seed characteristics across environments. Trait-associated SNPs were identified for most of the parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by genetic mapping in biparental RIL populations. The distribution of recombination frequency varied considerably between chromosomes, with recombination hotspots distributed mostly in the telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain and high-resolution genetic mapping for gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.

scholarly journals The complex genetic architecture of recombination and structural variation in wheat uncovered using a large 8-founder MAGIC population

2019 ◽  
Author(s):  
Rohan Shah ◽  
B Emma Huang ◽  
Alex Whan ◽  
Marcus Newberry ◽  
Klara Verbyla ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Structural Variation ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Genetic Effects ◽  
Ongoing Research ◽  
Significant Qtls ◽  
Magic Population

AbstractBackgroundIdentifying the genetic architecture of complex traits requires access to populations with sufficient genetic diversity and recombination. Multi-parent Advanced Generation InterCross (MAGIC) populations are a powerful resource due to their balanced population structure, allelic diversity and enhanced recombination. However, implementing a MAGIC population in complex polyploids such as wheat is not trivial, as wheat harbours many introgressions, inversions and other genetic factors that interfere with linkage mapping.ResultsBy utilising a comprehensive crossing strategy, additional rounds of mixing and novel genotype calling approaches, we developed a bread wheat eight parent MAGIC population made up of more than 3000 fully genotyped recombinant inbred lines derived from 2151 distinct crosses, and achieved a dense genetic map covering the complete genome. Further rounds of inter-crossing led to increased recombination in inbred lines, as expected. The comprehensive and novel approaches taken in the development and analysis of this population provide a platform for genetic discovery in bread wheat. We identify previously unreported structural variation highlighted by segregation distortion, along with the identification of epistatic allelic interactions between specific founders. We demonstrate the ability to conduct high resolution QTL mapping using the number of recombination events as a trait, and identify several significant QTLs explaining greater than 50% of the variance.ConclusionsWe report on a novel and effective resource for genomic and trait exploration in hexaploid wheat, that can be used to detect small genetic effects and epistatic interactions due to the high level of recombination and large number of lines. The interactions and genetic effects identified provide a basis for ongoing research to understand the basis of allelic frequencies across the genome, particularly where economically important loci are involved.

PROSPECTS FOR THE USE OF REMOTE CROSS IN THE CITRUS CROPS SELECTION

1970 ◽  
pp. 46-49 ◽  
Author(s):  
R. V. Kulyan
Keyword(s):  
Complex Traits ◽  
Germplasm Collection ◽  
Early Maturity ◽  
Russian Research Institute ◽  
Citrus Germplasm ◽  
The Status ◽  
New Varieties ◽  
Primary Test ◽  
Growing Conditions ◽  
Positive Traits

The Russian Research Institute of Floriculture and Subtropical Crops has the citrus germplasm collection, in total over 150 genotypes of various origins including 30 wild and semi-wild relatives. As a result of controlled hybridization in 17 crossings combinations of with the participation of relatives of citrus plants, new 769 hybrid offspring were obtained, which combine the traits of both the maternal and paternal genotypes. Analyzing the populations, promising combinations were highlighted: C. reticulata × Fortunella margarita (47.1%); C. x natsudaidai × 3252 (42.1%) and C. reticulata × C. reticulata ‘Cleopatra’ (40.9%) to create the gene pool of distant hybrids. From the mentioned combinations of crossings the greatest percent of seedlings which phenotypes tend to cultivated varieties was received. This hybrid material is a valuable source for isolating forms that are resistant to extreme environmental factors. According to phenotypic characteristics, hybrids were divided into three categories: I – Cultural, II – Semi-wild and III – Wild. Of the first category, the largest number 87 prospective forms were selected, and can be of interest for further breeding. As a result of the study of interspecific hybrid seedlings, 137 promising forms have been identified, which are carriers the complex traits such as dwarfism, thornless, early maturity and increased winter hardiness. From this set 17 genotypes were selected, which received the status of an elite forms, which successfully pass the primary test, and will be also useful in further breeding work for creating sources with a complex of positive traits and on breeding new varieties of citrus crops resistant to growing conditions.

scholarly journals BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

2021 ◽  
Vol 22 (S6) ◽  
Author(s):  
Yasmine Mansour ◽  
Annie Chateau ◽  
Anna-Sophie Fiston-Lavier
Keyword(s):  
Data Quality ◽  
Data Science ◽  
Fruit Fly ◽  
R Package ◽  
Model Organisms ◽  
Data Quality Control ◽  
Recombination Rates ◽  
Functional Dynamics ◽  
Shiny App ◽  
User Friendly

Abstract Background Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated with several chromatin states. However, eu-heterochromatin boundaries are not available nor easily provided for non-model organisms, especially for newly sequenced ones. Hence, we miss accurate local recombination rates necessary to address evolutionary questions. Results Here, we propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, called BREC (heterochromatin Boundaries and RECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is based on pure statistics and is data-driven, implying that good input data quality remains a strong requirement. Therefore, a data pre-processing module (data quality control and cleaning) is provided. Experiments show that BREC handles different markers' density and distribution issues. Conclusions BREC's heterochromatin boundaries have been validated with cytological equivalents experimentally generated on the fruit fly Drosophila melanogaster genome, for which BREC returns congruent corresponding values. Also, BREC's recombination rates have been compared with previously reported estimates. Based on the promising results, we believe our tool has the potential to help bring data science into the service of genome biology and evolution. We introduce BREC within an R-package and a Shiny web-based user-friendly application yielding a fast, easy-to-use, and broadly accessible resource. The BREC R-package is available at the GitHub repository https://github.com/GenomeStructureOrganization.

scholarly journals RIL-StEp: epistasis analysis of rice recombinant inbred lines (RILs) reveals candidate interacting genes that control seed hull color and leaf chlorophyll content

2021 ◽  
Author(s):  
Toshiyuki Sakai ◽  
Akira Abe ◽  
Motoki Shimizu ◽  
Ryohei Terauchi
Keyword(s):  
Chlorophyll Content ◽  
Recombinant Inbred ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Gene Interactions ◽  
Leaf Chlorophyll Content ◽  
Leaf Chlorophyll ◽  
Seed Hull

Abstract Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines (RILs) excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms.

scholarly journals PRISMA2020: an R package and Shiny app for producing PRISMA 2020-compliant flow diagrams, with interactivity for optimised digital transparency and Open Synthesis

2021 ◽  
Author(s):  
Neal R Haddaway ◽  
Matthew J Page ◽  
Christopher C Pritchard ◽  
Luke A McGuinness
Keyword(s):  
Systematic Review ◽  
Systematic Reviews ◽  
Science Communication ◽  
Review Process ◽  
Evidence Synthesis ◽  
R Package ◽  
Web Based ◽  
Shiny App ◽  
Data Files ◽  
Flow Diagrams

Background Reporting standards, such as PRISMA aim to ensure that the methods and results of systematic reviews are described in sufficient detail to allow full transparency. Flow diagrams in evidence syntheses allow the reader to rapidly understand the core procedures used in a review and examine the attrition of irrelevant records throughout the review process. Recent research suggests that use of flow diagrams in systematic reviews is poor and of low quality and called for standardised templates to facilitate better reporting in flow diagrams. The increasing options for interactivity provided by the Internet gives us an opportunity to support easy-to-use evidence synthesis tools, and here we report on the development of tools for the production of PRISMA 2020-compliant systematic review flow diagrams. Methods and Findings We developed a free-to-use, Open Source R package and web-based Shiny app to allow users to design PRISMA flow diagrams for their own systematic reviews. Our tools allow users to produce standardised visualisations that transparently document the methods and results of a systematic review process in a variety of formats. In addition, we provide the opportunity to produce interactive, web-based flow diagrams (exported as HTML files), that allow readers to click on boxes of the diagram and navigate to further details on methods, results or data files. We provide an interactive example here; https://driscoll.ntu.ac.uk/prisma/. Conclusions We have developed a user-friendly suite of tools for producing PRISMA 2020-compliant flow diagrams for users with coding experience and, importantly, for users without prior experience in coding by making use of Shiny. These free-to-use tools will make it easier to produce clear and PRISMA 2020-compliant systematic review flow diagrams. Significantly, users can also produce interactive flow diagrams for the first time, allowing readers of their reviews to smoothly and swiftly explore and navigate to further details of the methods and results of a review. We believe these tools will increase use of PRISMA flow diagrams, improve the compliance and quality of flow diagrams, and facilitate strong science communication of the methods and results of systematic reviews by making use of interactivity. We encourage the systematic review community to make use of these tools, and provide feedback to streamline and improve their usability and efficiency.

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