RRC ID 47944
Author Hisano H, Sakamoto K, Takagi H, Terauchi R, Sato K.
Title Exome QTL-seq maps monogenic locus and QTLs in barley.
Journal BMC Genomics
Abstract BACKGROUND: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.
METHODS: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.
RESULTS: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.
CONCLUSIONS:Exome QTL-seq broadens the utility of NGS-based gene/QTL mapping in organisms with large genomes.
Volume 18(1)
Pages 125
Published 2017-2-2
DOI 10.1186/s12864-017-3511-2
PII 10.1186/s12864-017-3511-2
PMID 28148242
PMC PMC5288901
MeSH Chromosome Mapping* Chromosomes, Plant* Disease Resistance / genetics Exome* Genome, Plant Genomics / methods High-Throughput Nucleotide Sequencing Hordeum / genetics* Plant Diseases / genetics Plant Diseases / microbiology Polymorphism, Single Nucleotide Quantitative Trait Loci* Quantitative Trait, Heritable
IF 3.501
Times Cited 10
WOS Category BIOTECHNOLOGY & APPLIED MICROBIOLOGY GENETICS & HEREDITY
Resource
Barley Haruna Nijo H602