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

2020 ◽  
Vol 139 (4) ◽  
pp. 779-789 ◽  
Author(s):  
Wei Yan ◽  
Haifei Zhao ◽  
Kunjiang Yu ◽  
Tianya Wang ◽  
Aimal Nawaz Khattak ◽  
...  
Keyword(s):  
Brassica Juncea ◽  
Complex Traits ◽  
Glucosinolate Content ◽  
Advanced Generation ◽  
Magic Population

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 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 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

Centennial Brown brown condiment mustard

2009 ◽  
Vol 89 (2) ◽  
pp. 337-340 ◽  
Author(s):  
G. Rakow ◽  
J. P. Raney ◽  
D. Rode ◽  
J. Relf-Eckstein
Keyword(s):  
Grain Yield ◽  
Brassica Juncea ◽  
Seed Quality ◽  
Leptosphaeria Maculans ◽  
Research Centre ◽  
Glucosinolate Content ◽  
Market Place ◽  
Improvement Program ◽  
Canadian Prairies ◽  
White Rust

Brown condiment mustard (Common Brown) has about 10% lower grain yield than oriental condiment mustard (yellow seeded), which both belong to the same species [Brassica juncea (L.) Czern.]. Yield improvements in brown condiment mustard are therefore of great importance. The Saskatoon Research Centre of AAFC initiated a condiment brown mustard improvement program in 1996 applying pedigree selection of single plants from the condiment brown mustard cultivar Blaze, which resulted in the selection and registration of the cultivar Centennial Brown. Centennial Brown yielded 3.2% more grain than the landrace Common Brown, on average over 81 location years in 9 yr of condiment mustard Co-op tests (1999–2007) and was well adapted to the mustard-growing areas of the Canadian prairies. Support for registration was based on 6 yr of Co-op tests. Centennial Brown had the same maturity (91 d) and was 5 cm taller (116 cm) than Common Brown. It had 1.5% lower fixed oil (36.6%) and 1.2% greater protein content (30.0%) compared with Common Brown. It had 0.4 g heavier seed (2.96 g 1000 seed-1) than Common Brown. Centennial Brown had 0.9 mg g seed-1 greater allyl glucosinolate content than Common Brown (9.15 mg g seed-1). Green seed counts were low in Centennial Brown (0.64%) compared with Common Brown (0.79%). This was confirmed in chlorophyll content measurements, 4.76 mg kg-1 for Centennial Brown and 5.24 mg kg-1 for Common Brown. Centennial Brown was resistant to blackleg disease [Leptosphaeria maculans (Desm.) Ces. et de Not.] and highly susceptible to the B. juncea races of white rust [Albugo candida (Pers.) Kuntze], equal to Common Brown. Centennial Brown will quickly replace Common Brown in the market place because of its increased grain yield and much superior seed quality. Key words: Brassica juncea (L.) Czern., cultivar description, grain yield, seed quality

DEVELOPMENT OF LOW GLUCOSINOLATE MUSTARD

1990 ◽  
Vol 70 (2) ◽  
pp. 419-424 ◽  
Author(s):  
H. K. LOVE ◽  
G. RAKOW ◽  
J. P. RANEY ◽  
R. K. DOWNEY
Keyword(s):  
Gas Chromatography ◽  
Brassica Juncea ◽  
Interspecific Cross ◽  
Plant Morphology ◽  
Glucosinolate Content ◽  
Aliphatic Glucosinolates ◽  
Plant Grown ◽  
Type 3 ◽  
Canola Quality ◽  
Aliphatic Glucosinolate

The objective of this study was to develop low glucosinolate mustard (Brassica juncea Coss.). This was accomplished through an interspecific cross between an Indian type 3-butenyl glucosinolate containing B. juncea selection and a "Bronowski-gene(s)" containing low glucosinolate B. campestris L. followed by backcrossing to the B. juncea parent. Seed of BC1F2 plants, and selected plants of BC1F3 and BC1F4 generations were analyzed for glucosinolate content by gas chromatography. Total aliphatic glucosinolate contents of individual BC1F2 plants ranged from 57 to 204 μmol g−1 meal. A single BC1F3 plant grown from the BC1F2 plant with the lowest glucosinolate content, identified as 1058, was found to contain less than 1 μmol g−1 meal of total aliphatic glucosinolates. The glucosinolate content in individual plants of the BC1F4 generation of plant 1058 ranged from 0.8 to 2.9 μmol g−1 meal. Field grown progeny of 1058 at three locations in 1987 and at one location in 1988 in Saskatchewan contained less than 10 μmol g−1 meal of total aliphatic glucosinolates. Therefore, the low glucosinolate characteristic of selection 1058 can be considered genetically stable. Progeny of plant 1058 had plant morphology and seed coat reticulation of B. juncea, but poor fertility (< 5 seeds per pod). The development of this low glucosinolate plant is an achievement that should allow the breeding of canola quality oilseed B. juncea mustard.Key words: Mustard, glucosinolate, Brassica juncea, interspecific cross

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.

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.

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