I hope to soon implement some functions to convert the MAGIC genotypes to R/qtl2 format. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. In the long term, a better way to carry out these tests is using the R/qtl2 package, which is under development, but now supports analysis of the Arabidopsis MAGIC lines (see here). The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Highlighted paper: Gnan, Priest and Kover.
#ARABIDOPSIS MAGIC LINES SOFTWARE#
A set of digital tools, hosted at the Wellcome Trust Centre for Human Genetics, contains the (open source) software needed to run the QTL analysis and the data files associated with the lines. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Yet, extensive natural variation within species is observed for these traits. All lines in the 2009 paper are available from NASC. Offspring number and size are key traits determining an individual’s fitness and a crop’s yield. The genomes of the produced inbred lines are fine-grained random mosaics of the founder genomes. The MAGIC lines are an incredible open resource for studying natural variation in Arabidopsis: they enable a researcher to map a trait to within 300kb. Examples of such populations are Collaborative Cross (CC) in mice and Multiparent Advanced Generation Inter-Cross (MAGIC) lines in Arabidopsis. thaliana world-wide accessions provided by Andrea Schrader (NASC, Table S2), 164 lines of the Can × Col-0 population (Core-Pop) (Simon et al. 2009, Supporting Information Table S1), seeds from a selected set of 66 parallel and randomized grown A. The original MAGIC paper from 2009 paper states ‘MAGIC lines occupy an intermediate niche between naturally occurring accessions and existing synthetic populations.’ The following Arabidopsis lines were used in this study: The MAGIC population (Kover et al. This pedigree means they represent a large diversity of genes in mostly homozygous lines ideal for accurate QTL mapping. The lines are recombinant, inbred over 6 generations, that originate from an intermated hereogenous stock.
Kover and others developed these lines to improve methods of identifying natural allelic variation that underlies variable phenotypic traits. identify five potential genes that underlie quantitative variation in seed size and number: AAP1 (AT1G58360) and KLUH (AT1G13710) on chromosome 1 and JAGGED LATERAL ORGANS (AT4G00220), YABBY 3 (AT4G00180), and BEL1 (AT5G41410) on chromosomes 4 and 5.Īll the above work was carried out using Mulitparent Advanced Generation Inter-Cross (MAGIC) Arabidopsis lines. Here too there was only 1 QTL overlapping between the two traits, suggesting that any correlation is not inherent and may vary according to environmental or internal factors.īased on QTL analysis, Kover et al. There is enough of a positive correlation between seed number and fruit length that fruit length is sometimes used to estimate seed number – though the correlation is not strong. The strong negative correlation seen in size and number is logically due to resource use efficiency, but these data suggest that this is not determined genetically. Īll plants negotiate a trade-off between the number and size of their seeds, so it was a surprise to learn that of 9 QTL for seed number and 8 for seed size, there was only 1 overlapping QTL. The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines. Lead author Paula Kover and her team investigated the genetic basis of variation in seed size and number. In the Arabidopsis Research Round-up a few weeks ago, Lisa highlighted a paper from a team at the University of Bath about natural variation in Arabidopsis seeds. The research: Finding the causes of variation in seed size and number An improvement in one trait will not affect the other trait.įurther details of the study can be read at: and. It is then possible to independently control seed size and seed number. This result implies that the genetic factors involve with the two seed traits are located differently in the genome. A QTL mapping was conducted on the seeds and showed that there is a non-overlapping QTL between seed size and seed number. With this plant lines, the precise location of gene chromosomes associated with seed size and number can be identified.
With this, the researchers observed the genetic basis of natural variation in seed size and number to identify the factors associated with them.Ī multiparent advanced generation intercross (MAGIC) lines of Arabidopsis thaliana plant was used.
This scenario occurs due to trade-offs associated with the two traits.
Typically, a small seed size will yield high seed number while a large seed size will then give off small seed number. Researchers from University of Bath studied the two main traits in seeds, seed size and seed number, which are necessary for improving crop yields.