Development of genome-wide SNP markers for barley via reference- Based RNA-seq analysis

Tsuyoshi Tanaka, Goro Ishikawa, Eri Ogiso-Tanaka, Takashi Yanagisawa, Kazuhiro Sato

Research output: Contribution to journalArticle

Abstract

Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs.

Original languageEnglish
Article number577
JournalFrontiers in Plant Science
Volume10
DOIs
Publication statusPublished - Apr 16 2019

Fingerprint

barley
RNA
genome
genetic polymorphism
breeding
seedlings
marker-assisted selection
Hordeum vulgare
genotyping
inflorescences
immatures
alleles
flowers
genomics
sampling
loci
genetic markers
shoots
genotype
cultivars

Keywords

  • Amplicon sequencing
  • Barley
  • Genotyping
  • Japanese barley breeding
  • RNA-Seq

ASJC Scopus subject areas

  • Plant Science

Cite this

Development of genome-wide SNP markers for barley via reference- Based RNA-seq analysis. / Tanaka, Tsuyoshi; Ishikawa, Goro; Ogiso-Tanaka, Eri; Yanagisawa, Takashi; Sato, Kazuhiro.

In: Frontiers in Plant Science, Vol. 10, 577, 16.04.2019.

Research output: Contribution to journalArticle

Tanaka, Tsuyoshi ; Ishikawa, Goro ; Ogiso-Tanaka, Eri ; Yanagisawa, Takashi ; Sato, Kazuhiro. / Development of genome-wide SNP markers for barley via reference- Based RNA-seq analysis. In: Frontiers in Plant Science. 2019 ; Vol. 10.
@article{2219673775c944568e9a0a393f82627b,
title = "Development of genome-wide SNP markers for barley via reference- Based RNA-seq analysis",
abstract = "Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85{\%} of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs.",
keywords = "Amplicon sequencing, Barley, Genotyping, Japanese barley breeding, RNA-Seq",
author = "Tsuyoshi Tanaka and Goro Ishikawa and Eri Ogiso-Tanaka and Takashi Yanagisawa and Kazuhiro Sato",
year = "2019",
month = "4",
day = "16",
doi = "10.3389/fpls.2019.00577",
language = "English",
volume = "10",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media S. A.",

}

TY - JOUR

T1 - Development of genome-wide SNP markers for barley via reference- Based RNA-seq analysis

AU - Tanaka, Tsuyoshi

AU - Ishikawa, Goro

AU - Ogiso-Tanaka, Eri

AU - Yanagisawa, Takashi

AU - Sato, Kazuhiro

PY - 2019/4/16

Y1 - 2019/4/16

N2 - Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs.

AB - Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs.

KW - Amplicon sequencing

KW - Barley

KW - Genotyping

KW - Japanese barley breeding

KW - RNA-Seq

UR - http://www.scopus.com/inward/record.url?scp=85067355727&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85067355727&partnerID=8YFLogxK

U2 - 10.3389/fpls.2019.00577

DO - 10.3389/fpls.2019.00577

M3 - Article

AN - SCOPUS:85067355727

VL - 10

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 577

ER -