Complex traits such as crop performance and human diseases are controlled by multiple genetic loci, many of which have small effects and often go undetected by traditional quantitative trait locus (QTL) mapping. Recently, bulked segregant analysis with large F2 pools and genome-level markers (named extreme-QTL or X-QTL mapping) has been used to identify many QTLs. To estimate parameters impacting QTL detection for X-QTL mapping, we simulated the effects of population size, marker density, and sequencing depth of markers on QTL detectability for traits with differing heritabilities. These simulations indicate that a high (>90%) chance of detecting QTLs with at least 5% effect requires 5,000X sequencing depth for a trait with heritability of 0.4 - 0.7. For most eukaryotic organisms, whole genome sequencing at this depth is not economically feasible. Therefore, we tested and confirmed the feasibility of applying deep sequencing of target-enriched markers for X-QTL mapping. We used two traits in Arabidopsis thaliana with different heritabilities: seed size (H2 = 0.61) and seedling greening in response to salt (H2 = 0.94). We use a modified G test to identify QTL regions and developed a model-based statistical framework to resolve individual peaks by incorporating recombination rates. Multiple QTLs were identified for both traits, including previously undiscovered QTLs. We call our method target-enriched X-QTL (TEX-QTL) mapping. TEX-QTL mapping is not limited by the genome size or the availability of recombinant inbred populations, and should be applicable to many 47 organisms and traits.
- Arabidopsis thaliana
- bulked segregant analysis
- salt tolerance
- seed size
- target-enriched extreme quantitative trait locus mapping
- Received August 17, 2015.
- Accepted October 28, 2015.
- Copyright © 2015 Author et al.
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