QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines

Sureshkumar Balasubramanian*, Christopher Schwartz, Anandita Singh, Norman Warthmann, Min Chul Kim, Julin N. Maloof, Olivier Loudet, Gabriel T. Trainer, Tsegaye Dabi, Justin O. Borevitz, Joanne Chory, Detlef Weigel

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

89 Citations (Scopus)


Background: Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs). Methodology/Principal Findings: We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F2 population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions. Conclusions/Significance: The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.

Original languageEnglish
Article numbere4318
JournalPLoS ONE
Issue number2
Publication statusPublished - 2 Feb 2009
Externally publishedYes


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