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.

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 RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

2020 ◽  
Author(s):  
Toshiyuki Sakai ◽  
Akira Abe ◽  
Motoki Shimizu ◽  
Ryohei Terauchi
Keyword(s):  
Recombinant Inbred ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Gene Interactions ◽  
Rice Seed ◽  
Nucleotide Polymorphisms ◽  
Control Seed ◽  
Seed Hull

SummaryStudying epistatic gene interactions is important in understanding genetic architecture of complex traits in organisms. However, due to an enormous number of gene combinations to be analyzed, detection of epistatic gene-gene interactions has been computationally demanding. Here, we show a simple approach RIL-StEp, specialized to Recombinant Inbred Lines (RILs), to study epistasis using single nucleotide polymorphisms (SNPs) information of the genome. We applied the method to reveal epistasis affecting rice seed hull color phenotype, and successfully identified gene pairs that presumably control seed hull color. This method has a potential to enhancing our understanding of genetic architecture of various traits.

scholarly journals Tightly-linked antagonistic-effect loci underlie polygenic demographic variation in C. elegans

2018 ◽  
Author(s):  
Max R. Bernstein ◽  
Stefan Zdraljevic ◽  
Erik C. Andersen ◽  
Matthew V. Rockman
Keyword(s):  
Recombinant Inbred ◽  
Complex Traits ◽  
Recombinant Inbred Lines ◽  
Empirical Support ◽  
Population Based ◽  
Inbred Lines ◽  
Antagonistic Effect ◽  
Significant Qtls ◽  
C Elegans ◽  
Genomic Regions

AbstractRecent work has provided strong empirical support for the classic polygenic model for trait variation. Population-based findings suggest that most regions of genome harbor variation affecting most traits. This view is hard to reconcile with the experience of researchers who define gene functions using mutagenesis, comparing mutants one at a time to the wild type. Here, we use the approach of experimental genetics to show that indeed, most genomic regions carry variants with detectable effects on complex traits. We used high-throughput phenotyping to characterize demography as a multivariate trait in growing populations of Caenorhabditis elegans sensitized by nickel stress. We show that demography under these conditions is genetically complex in a panel of recombinant inbred lines. We then focused on a 1.4-Mb region of the X chromosome. When we compared two near isogenic lines (NILs) that differ only at this region, they were phenotypically indistinguishable. When we used additional NILs to subdivide the region into fifteen intervals, each encompassing ~0.001 of the genome, we found that eleven of intervals have significant effects. These effects are often similar in magnitude to those of genome-wide significant QTLs mapped in the recombinant inbred lines but are antagonized by the effects of variants in adjacent intervals. Contrary to the expectation of small additive effects, our findings point to large-effect variants whose effects are masked by epistasis or linkage disequilibrium between alleles of opposing effect.

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 Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 745-754 ◽  
Author(s):  
J Xiao ◽  
J Li ◽  
L Yuan ◽  
S D Tanksley
Keyword(s):  
Molecular Markers ◽  
Qtl Analysis ◽  
Recombinant Inbred ◽  
Quantitative Traits ◽  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Rflp Markers ◽  
Major Contributor ◽  
Significant Qtls

Abstract A set of 194 F7 lines derived from a subspecific rice cross showing strong F1 heterosis was backcrossed to the two parents. The materials (388 BC1F7 lines, 194 F8 lines, two parents, F1) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD > or = 2.0) was detected through 141 RFLP markers in the BC1F7 populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC1F7 populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC1F7 populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F8 population having phenotypic values superior to the F1 for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident.

scholarly journals Screening of recombinant inbred lines for salinity tolerance in bread wheat (Triticum aestivum L.)

2011 ◽  
Vol 10 (60) ◽  
pp. 12875-12881 ◽  
Author(s):  
Azadi Amin ◽  
Majidi Hervan Eslam ◽  
Abolghasem Mohammadi Seyed ◽  
Moradi Foad ◽  
Nakhoda Babak ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Salinity Tolerance ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Triticum Aestivum L ◽  
Inbred Lines
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