Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato

Rumi Sasai, Hiroaki Tabuchi, Kenta Shirasawa, Kazuki Kishimoto, Shusei Sato, Yoshihiro Okada, Akihide Kuramoto, Akira Kobayashi, Sachiko Isobe, Makoto Tahara, Yuki Monden

Research output: Contribution to journalArticle

Abstract

The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.

Original languageEnglish
Pages (from-to)399-409
Number of pages11
JournalDNA research : an international journal for rapid publication of reports on genes and genomes
Volume26
Issue number5
DOIs
Publication statusPublished - Oct 1 2019

Fingerprint

Tylenchoidea
Quantitative Trait Loci
Genome-Wide Association Study
Single Nucleotide Polymorphism
Ipomoea batatas
Retroelements
Genetic Linkage
Genetic Markers
Microsatellite Repeats
Genotype
Genome
Polymerase Chain Reaction

Keywords

  • GWAS
  • marker-assisted breeding
  • polyploids
  • QTL mapping
  • sweetpotato

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. / Sasai, Rumi; Tabuchi, Hiroaki; Shirasawa, Kenta; Kishimoto, Kazuki; Sato, Shusei; Okada, Yoshihiro; Kuramoto, Akihide; Kobayashi, Akira; Isobe, Sachiko; Tahara, Makoto; Monden, Yuki.

In: DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 26, No. 5, 01.10.2019, p. 399-409.

Research output: Contribution to journalArticle

Sasai, Rumi ; Tabuchi, Hiroaki ; Shirasawa, Kenta ; Kishimoto, Kazuki ; Sato, Shusei ; Okada, Yoshihiro ; Kuramoto, Akihide ; Kobayashi, Akira ; Isobe, Sachiko ; Tahara, Makoto ; Monden, Yuki. / Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. In: DNA research : an international journal for rapid publication of reports on genes and genomes. 2019 ; Vol. 26, No. 5. pp. 399-409.
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