Natural variation in Arabidopsis, the MAGIC way

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Published on: November 24, 2014

The research: Finding the causes 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. Lead author Paula Kover and her team investigated the genetic basis of variation in seed size and number.

All 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 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.

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. 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.

Based on QTL analysis, Kover et al. 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.


The tool: MAGIC Arabidopsis lines

All the above work was carried out using Mulitparent Advanced Generation Inter-Cross (MAGIC) Arabidopsis lines. Kover and others developed these lines to improve methods of identifying natural allelic variation that underlies variable phenotypic traits. The lines are recombinant, inbred over 6 generations, that originate from an intermated hereogenous stock. This pedigree means they represent a large diversity of genes in mostly homozygous lines; ideal for accurate QTL mapping. The original MAGIC paper from 2009 paper states ‘MAGIC lines occupy an intermediate niche between naturally occurring accessions and existing synthetic populations.’

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. All lines in the 2009 paper are available from NASC. 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.


Highlighted paper: Gnan, Priest and Kover. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Genetics, 2014. 10.1534/genetics.114.170746

Also cited: Kover et al. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLOS Genetics, 2009. DOI: 10.1371/journal.pgen.1000551

For a comparison of resources for studying natural variation, see Weigel, Plant Phys, 2012 158:2-22

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