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

Takagi, H. and Abe, A. and Yoshida, K. and et al, . (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. The Plant Journal, 74. pp. 174-183.

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The 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 F2 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.

Item Type: Article
Additional Information: This study was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN), the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics for Agricultural Innovation PMI-0010) and Grant-in-aid for Scientific Research from the Ministry of Education, Cultures, Sports and Technology, Japan to HK and RT (Grant-in-Aid for Scientific Research on Innovative Areas 23113009) and JSPS KAKENHI to RT (Grant No. 24248004) .
Uncontrolled Keywords: quantitative trait loci, breeding, whole genome sequencing, next generation sequencer, selective sweep, technical advance.
Author Affiliation: Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan
Subjects: Crop Improvement > Genetics/Genomics
Divisions: Other Crops
Depositing User: Mr Siva Shankar
Date Deposited: 04 Apr 2013 08:03
Last Modified: 08 Aug 2013 05:07
Official URL: http://dx.doi.org/10.1111/tpj.12105
URI: http://eprints.icrisat.ac.in/id/eprint/10196

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