scholarly journals A multi‐parent advanced generation inter‐cross ( MAGIC ) population for genetic analysis and improvement of cowpea ( Vigna unguiculata L. Walp.)

2018 ◽  
Vol 93 (6) ◽  
pp. 1129-1142 ◽  
Author(s):  
Bao‐Lam Huynh ◽  
Jeffrey D. Ehlers ◽  
Bevan Emma Huang ◽  
María Muñoz‐Amatriaín ◽  
Stefano Lonardi ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Vigna Unguiculata ◽  
Advanced Generation ◽  
Magic Population

scholarly journals Registration of a Cowpea [Vigna unguiculata (L.) Walp.] Multiparent Advanced Generation Intercross (MAGIC) Population

2019 ◽  
Vol 13 (2) ◽  
pp. 281-286 ◽  
Author(s):  
Bao-Lam Huynh ◽  
Jeffrey D. Ehlers ◽  
Timothy J. Close ◽  
Philip A. Roberts
Keyword(s):  
Vigna Unguiculata ◽  
Advanced Generation ◽  
Magic Population

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 Genetic analysis of seed proteins contents in cowpea (Vigna unguiculata L. Walp.)

2011 ◽  
Vol 10 (16) ◽  
pp. 3077-3086 ◽  
Author(s):  
Noubissieacute Tchiagam Jean Baptiste ◽  
Martin Bell Joseph ◽  
M Nassourou Antoine ◽  
Y Njintang Nicolas ◽  
Youmbi Emmanuel
Keyword(s):  
Genetic Analysis ◽  
Vigna Unguiculata ◽  
Seed Proteins

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 Genetic Analysis of Selected Mutants of Cowpea (<i>Vigna unguiculata</i> [L.] Walp) Using Simple Sequence Repeat and <i>rcb</i>L Markers

2018 ◽  
Vol 09 (13) ◽  
pp. 2728-2756 ◽  
Author(s):  
Festus Olakunle Olasupo ◽  
Christopher Olumuyiwa Ilori ◽  
Esther Adekemi Stanley ◽  
Temitope Esther Owoeye ◽  
David Okeh Igwe
Keyword(s):  
Genetic Analysis ◽  
Vigna Unguiculata ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Simple Sequence

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.

Genetic Analysis of Effect of Heat Stress on Genomic DNA from Cowpea (Vigna unguiculata (L) Walp.)

2015 ◽  
Vol 4 (4) ◽  
pp. 1-14
Author(s):  
Onasanya Amos ◽  
T Obafemi ◽  
A Ojo ◽  
M Abu ◽  
A Prebor ◽  
...  
Keyword(s):  
Heat Stress ◽  
Genetic Analysis ◽  
Vigna Unguiculata ◽  
Genomic Dna

scholarly journals Genetic Dissection for Maize Forage Digestibility Traits in a Multi-Parent Advanced Generation Intercross (MAGIC) Population

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 104
Author(s):  
Ana Lopez-Malvar ◽  
Rosa Ana Malvar ◽  
Ana Butron ◽  
Pedro Revilla ◽  
Sonia Pereira-Crespo ◽  
...  
Keyword(s):  
Organic Matter ◽  
Plant Cell Wall ◽  
Phenotypic Variability ◽  
Neutral Detergent Fiber ◽  
Wall Material ◽  
Forage Digestibility ◽  
A Genome ◽  
Limited Digestion ◽  
Advanced Generation ◽  
Magic Population

Forage feedstock is the greatest source of energy for livestock. Unfortunately, less than 50% of their fiber content is actually digested and assimilated by the ruminant animals. This recalcitrance is mainly due to the high concentration of plant cell wall material and to the limited digestion of the fiber by the microorganisms. A Genome-Wide Association Study (GWAS) was carried out in order to identify Single Nucleotide Polymorphisms (SNPs) associated with forage digestibility traits in a maize Multi-Parent Advanced Generation Intercross (MAGIC) population. We identified seven SNPs, corresponding to five Quantitative Trait Loci (QTL), associated to digestibility of the organic matter, 11 SNPs, clustered in eight QTLs, associated to Neutral Detergent Fiber (NDF) content and eight SNPs corresponding with four QTL associated with Acid Detergent Fiber (ADF). Candidate genes under the QTL for digestibility of the organic matter could be the ones involved in pectin degradation or phenylpropanoid pathway. Transcription factor genes were also proposed for the fiber QTL identified, in addition to genes induced by oxidative stress, or a gene involved in lignin modifications. Nevertheless, for the improvement of the traits under study, and based on the moderate heritability value and low percentage of the phenotypic variability explained by each QTL, a genomic selection strategy using markers evenly distributed across the whole genome is proposed.

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