Exome QTL-seq maps monogenic locus and QTLs in barley.
QTL-seq, in combination with bulked segregant analysis and next-generation sequencing (NGS), is used to identify loci in small plant genomes, but is technically challenging to perform in species with large genomes, such as barley. A combination of exome sequencing and QTL-seq (exome QTL-seq) was used to map the mono-factorial Mendelian locus black lemma and pericarp (Blp) and QTLs for resistance to net blotch disease, a common disease of barley caused by the fungus Pyrenophora teres, which segregated in a population of 100 doubled haploid barley lines.



The provisional exome sequences were prepared by ordering the loci of expressed genes based on the genome information and concatenating genes with intervals of 200-bp spacer "N" for each chromosome. The QTL-seq pipeline was used to analyze short reads from the exome-captured library.



In this study, short NGS reads of bulked total DNA samples from segregants with extreme trait values were subjected to exome capture, and the resulting exome sequences were aligned to the reference genome. SNP allele frequencies were compared to identify the locations of genes/QTLs responsible for the trait value differences between lines. For both objective traits examined, exome QTL-seq identified the monogenic Mendelian locus and associated QTLs. These findings were validated using conventional mapping approaches.



Exome QTL-seq broadens the utility of NGS-based gene/QTL mapping in organisms with large genomes.
Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
Hiroshi
H
Hisano
Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
Kazuki
K
Sakamoto
Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
Hiroki
H
Takagi
Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
Ryohei
R
Terauchi
Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan. kazsato@rib.okayama-u.ac.jp.
Kazuhiro
0000-0001-8818-5203
K
Sato
D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D060467:Disease Resistance / Q000235:genetics; D059472:Exome; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000235:genetics*; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
Exome sequencing; Hordeum vulgare; Kernel color; Mapping; Net blotch; QTL-seq