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 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 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 QTL identification for nine seed-related traits in Brassica juncea using a multiparent advanced generation intercross (MAGIC) population

2021 ◽  
Vol 57 (No. 1) ◽  
pp. 9-18
Author(s):  
Haifei Zhao ◽  
Wei Yan ◽  
Kunjiang Yu ◽  
Tianya Wang ◽  
Aimal Nawaz Khattak ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Acid Detergent Lignin ◽  
Seed Maturity ◽  
Biparental Population ◽  
Acid Detergent Fibre ◽  
Mapping Gene ◽  
Qtl Identification ◽  
Advanced Generation ◽  
Thousand Seed Weight ◽  
Magic Population

Agronomic traits are usually determined by multiple quantitative trait loci (QTLs) that can have pleiotropic effects. A multiparent advanced generation intercross (MAGIC) population is well suited for genetically analysing the effects of multiple QTLs on the traits of interest because it contains more QTL alleles than a biparental population and can overcome the problem of confounding the population structure of the natural germplasm population. We previously developed the B. juncea MAGIC population, derived from eight B. juncea lines with great diversity in agronomic and quality traits. In this study, we show that the B. juncea MAGIC population is also effective for the evaluation of multiple QTLs for complex agronomic traits in B. juncea. A total of twenty-two QTLs for nine seed-related traits were identified, including one QTL for each oil content, seed number per silique and thousand-seed weight; two QTLs for each acid detergent lignin and neutral detergent fibre; three QTLs for each acid detergent fibre and protein content; four QTLs for the seed maturity time; and five QTLs for the white index. Some of these QTLs overlapped. These results should be helpful for further fine mapping, gene cloning, plant breeding and marker-assisted selection (MAS) in B. juncea.

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.

Genetic Mapping of Agronomic Traits Using Recombinant Inbred Lines of Soybean

Crop Science ◽  
1996 ◽  
Vol 36 (5) ◽  
pp. 1327-1336 ◽  
Author(s):  
L. M. Mansur ◽  
J. H. Orf ◽  
K. Chase ◽  
T. Jarvik ◽  
P. B. Cregan ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Recombinant Inbred ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Inbred Lines

scholarly journals Relationships between Stalk Resistance and Corn Borers, Agronomic Traits, and Cell Wall Hydroxycinnamates in a Set of Recombinant Inbred Lines from a Maize MAGIC Population

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1132
Author(s):  
Ana López-Malvar ◽  
Zoila Reséndiz ◽  
Rogelio Santiago ◽  
José Cruz Jiménez-Galindo ◽  
Rosa Ana Malvar
Keyword(s):  
Cell Wall ◽  
Recombinant Inbred ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Corn Borer ◽  
Corn Borers ◽  
Grain Moisture ◽  
Resistant Lines ◽  
Magic Population

Corn borers are the most important pest affecting maize. Resistance to corn borer attack may compromise plant fitness being detrimental for some important agronomic traits such as yield. Against the attack of this pest, cell wall-bound hydroxycinnamates have been previously described as a possible defense mechanism. In this study, agronomic characterization and cell wall-bound hydroxycinnamates quantification was performed in a subset of Recombinant Inbred Lines (RILs) from a Multiparent Advanced Generation Intercross (MAGIC) population that showed contrasting behavior against corn borer attack. Resistant lines showed greater concentration of p-coumaric acid, the only hydroxycinnamate that could have a role in the resistance in these particular materials. In addition, results indicated that resistant lines showed precocity, low grain moisture at harvest, and reduced plant height, thus, selecting for resistance may be detrimental for yield. In this way, a breeding strategy directly targeting grain yield in order to tolerate corn borer attack would be the recommended one.

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 Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Santiago Diaz ◽  
Daniel Ariza-Suarez ◽  
Paulo Izquierdo ◽  
Juan David Lobaton ◽  
Juan Fernando de la Hoz ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Common Bean ◽  
Harvest Index ◽  
Agronomic Traits ◽  
Smallholder Farmers ◽  
Climate Change Scenarios ◽  
Drought Conditions ◽  
Major Qtl ◽  
Magic Population ◽  
Pod Harvest Index

Abstract Background Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major production constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans. Results A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation. Conclusions This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community.

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
Sign in / Sign up

Export Citation Format

Share Document