Development of a multiparent advanced generation intercross (MAGIC) population for genetic exploitation of complex traits in <i>Brassica juncea</i>: Glucosinolate content as an example

Yan, Wei; Zhao, Haifei; Yu, Kunjiang; Wang, Tianya; Khattak, Aimal Nawaz; Tian, Entang

doi:10.1111/pbr.12820

Cited by 10 publications

(7 citation statements)

References 79 publications

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“…Glucosinolate content (Yan et al 2020) Cotton Fibre quality (Islam et al 2016;Thyssen et al 2019) Fibre length (Naoumkina et al 2019) Root-knot nematode resistance (Wubben et al 2019) Fibre maturity and fineness (Kim et al 2020) Verticillium wilt resistance (Zhang et al 2020) Cowpea Flowering time, growth habit, flower colour, leaf shape and seed characteristics (Huynh et al 2018) Durum wheat Grain yield (Milner et al 2016) Faba Corn borer resistance (Jiménez-Galindo et al…”

Section: Imputation In Mpps: the Power Of Haplotypesmentioning

confidence: 99%

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Scott¹,

Ladejobi²,

et al. 2020

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Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding. Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a

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Section: Imputation In Mpps: the Power Of Haplotypesmentioning

confidence: 99%

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Scott¹,

Ladejobi²,

et al. 2020

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“…For controlling populations and family structures, this software implements general linear model and mixed linear model approaches. This useful software has been widely used for rice, cotton, wheat, sorghum, and Brassica juncea MAGIC population analyses [ 35 , 40 , 85 , 86 , 87 ]. Furthermore, some R packages are also available to conduct GWAS such as the so-called Genome Association and Prediction Integrated Tool (GAPIT) that implements advanced statistical methods, including mixed linear models [ 88 ].…”

Section: Analysis Software For Genetic Gap Construction and Qtl Mamentioning

confidence: 99%

“…In the case of oil seed crops, a rapeseed MAGIC population was developed with 680 F6 final RILs to study disease resistance, yield potential, plant architecture, and ecological adaptability [ 104 ]. Recently, a Chinese mustard ( Brassica juncea ) MAGIC population was developed with a final population size of 408 F6 RILs mainly focused on glucosinolate-related traits to improve fruit quality [ 87 ]. Relevant QTLs were used to predict candidate genes associated with glucosinolate synthesis.…”

Section: An Appraisal Of Magic Populations Developed and Evaluatedmentioning

confidence: 99%

The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material

Arrones

Vilanova

Plazas

et al. 2020

Biology

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The compelling need to increase global agricultural production requires new breeding approaches that facilitate exploiting the diversity available in the plant genetic resources. Multi-parent advanced generation inter-cross (MAGIC) populations are large sets of recombinant inbred lines (RILs) that are a genetic mosaic of multiple founder parents. MAGIC populations display emerging features over experimental bi-parental and germplasm populations in combining significant levels of genetic recombination, a lack of genetic structure, and high genetic and phenotypic diversity. The development of MAGIC populations can be performed using “funnel” or “diallel” cross-designs, which are of great relevance choosing appropriate parents and defining optimal population sizes. Significant advances in specific software development are facilitating the genetic analysis of the complex genetic constitutions of MAGIC populations. Despite the complexity and the resources required in their development, due to their potential and interest for breeding, the number of MAGIC populations available and under development is continuously growing, with 45 MAGIC populations in different crops being reported here. Though cereals are by far the crop group where more MAGIC populations have been developed, MAGIC populations have also started to become available in other crop groups. The results obtained so far demonstrate that MAGIC populations are a very powerful tool for the dissection of complex traits, as well as a resource for the selection of recombinant elite breeding material and cultivars. In addition, some new MAGIC approaches that can make significant contributions to breeding, such as the development of inter-specific MAGIC populations, the development of MAGIC-like populations in crops where pure lines are not available, and the establishment of strategies for the straightforward incorporation of MAGIC materials in breeding pipelines, have barely been explored. The evidence that is already available indicates that MAGIC populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of dramatically improved cultivars.

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“…Although high throughput sequencing techniques are being developed nowadays, the use of variable markers present in candidate genes is still an interesting alternative for association studies. An approach known as intron length polymorphism (ILP), based on the alignment of EST cDNA sequences against known genomic sequences, has been applied to a range of crop species for genetic diversity, evolutionary and association genetic studies [ 15 , 16 , 17 , 18 , 19 , 20 , 21 ]. As ILP markers are gene-based, co-dominant, neutral, convenient, reliable and cost effective, and can play a vital role in regulation of gene expression [ 22 ], this is a promising approach to genetic studies such as candidate gene association mapping, which seeks to identify allelic variation in the genes that influence girth growth.…”

Section: Introductionmentioning

confidence: 99%

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

Bhusudsawang

Rattanawong²,

Phumichai³

et al. 2021

Plants

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Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

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

Cited by 10 publications

References 79 publications

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material

Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

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