Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 9/9/2014
Publication Date: 3/13/2015
Citation: Jamann, T., Balint Kurti, P.J., Holland, J.B. 2015. QTL mapping using high-throughput sequencing. In: Alonso, J., Stepanova, A.N., editors. Methods in Molecular Biology: Plant Functional Genomics: Methods and Protocols. New York, NY: Springer. p. 257-285.
Interpretive Summary: Many important agricultural traits are quantitative in nature, and controlled by many genes sometimes with small effects. This makes it difficult to identify the particular genes that control important complex traits. We review in this chapter methods and protocols to identify specific genes controlling complex traits using a combination of high throughput DNA sequencing and careful field measurements of important traits.
Technical Abstract: Quantitative trait locus (QTL) mapping in plants dates to the 1980’s, but earlier studies were often hindered by the expense and time required to identify large numbers of polymorphic genetic markers that differentiated the parental genotypes and then to genotype them on large segregating mapping populations. High-throughput sequencing has provided an efficient means to discover single nucleotide polymorphisms (SNPs), which can then be assayed rapidly on large populations with array-based techniques. Alternatively, high-throughput sequencing methods such as restriction site-associated DNA sequencing (RAD-Seq) and genotyping-by-sequencing (GBS) can be used to identify and genotype polymorphic markers directly. Linkage disequilibrium (LD) between markers and causal variants is needed to detect QTL. The earliest QTL mapping methods used backcross and F2 generations of crosses between inbred lines, which have high levels of linkage disequilibrium (dependent entirely on the recombination frequency between chromosomal positions), to ensure that QTL would have sufficiently high linkage disequilibrium with one or more markers on sparse genetic linkage maps. The downside of this approach is that resolution of QTL positions is poor. The sequencing technology revolution, by facilitating genotyping of vastly more markers than was previously feasible, has allowed researchers to map QTL in situations of lower linkage disequilibrium, and consequently, at higher resolution. We provide a review of methods to identify QTL with higher precision than was previously possible with lower density marker analyses. We discuss modifications of the traditional biparental mapping population that provide higher resolution of QTL positions, QTL fine-mapping procedures, and genome-wide association studies, all of which are greatly facilitated by high-throughput sequencing methods. Each of these procedures has many variants, and consequently many details to consider; we focus our chapter on the consequences of practical decisions that researchers make when designing QTL mapping studies and when analyzing the resulting data. The ultimate goal of many of these studies is to resolve a QTL to its causal sequence variation.