QTL‐seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

Abstract

SUMMARYThe majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time-consuming and labor-intensive. Here we report the rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines and F 2 populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.

Brachypodium as an emerging model for cereal–pathogen interactions

“…Takagi et al, 2013;Liu et al, 2012; as discussed below) the degree to which this traditional approach is employed may decrease in coming years. In this case, comparative genomic approaches using brachypodium may more frequently involve functional characterization of RGAs and homologues of other classes of genes known to modulate resistance, as exemplified by the work of Schweiger et al (2013) on brachypodium UGTs outlined above.…”

“…Both DNA (e.g. Takagi et al, 2013) and RNA (e.g. Liu et al, 2012) sequencing-based BSA approaches have been developed and applied to the identification of natural allelic variants (e.g.…”

“…Liu et al, 2012) sequencing-based BSA approaches have been developed and applied to the identification of natural allelic variants (e.g. Takagi et al, 2013) and induced mutations (Abe et al, 2012;Nordstrom et al, 2013). Brachypodium's small, diploid genome is particularly amenable to such approaches, and they should therefore facilitate rapid identification of genes involved in brachypodium resistance to cereal pathogens.…”

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

“…The statistical confidence intervals of the ΔSNP index under the null hypothesis of no QTLs were also calculated. For each position, the 95% confidence intervals of the ΔSNP index were obtained following the method described by Takagi et al (2013).…”

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

“…Variants of NGS-based QTL identification methods, such as X-QTL, MutMap, QTL-seq, SHOREmap, and NGM, have been reviewed elsewhere [99]. Among the various NGS-based QTL mapping approaches, QTL-seq, the whole genome re-sequencing-based mapping of QTL [100], can successfully be applied to dissect key quantitative traits underlying biotic and abiotic stresses in major African staple food crops such as cassava, yam, tef, and legumes. One of the essential requirements for QTL-seq is the availability of a quality reference genome and mapping populations.…”