Construction of a versatile SNP array for pyramiding useful genes of rice

Yusuke Kurokawa, Tomonori Noda, Yoshiyuki Yamagata, Rosalyn Angeles-Shim, Hidehiko Sunohara, Kanako Uehara, Tomoyuki Furuta, Keisuke Nagai, Kshirod Kumar Jena, Hideshi Yasui, Atsushi Yoshimura, Motoyuki Ashikari, Kazuyuki Doi

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed.

Original languageEnglish
Pages (from-to)131-139
Number of pages9
JournalPlant Science
Volume242
DOIs
Publication statusPublished - Jan 1 2016
Externally publishedYes

Fingerprint

single nucleotide polymorphism
Single Nucleotide Polymorphism
rice
Haplotypes
Genes
haplotypes
genes
marker-assisted selection
genotyping
biotic stress
Genetic Markers
stress tolerance
Breeding
Oryza
Alleles
Genotype
genetic polymorphism
Genome
alleles
genetic markers

Keywords

  • Gene pyramiding
  • MAS
  • QTL
  • Rice breeding
  • SNP

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

Kurokawa, Y., Noda, T., Yamagata, Y., Angeles-Shim, R., Sunohara, H., Uehara, K., ... Doi, K. (2016). Construction of a versatile SNP array for pyramiding useful genes of rice. Plant Science, 242, 131-139. https://doi.org/10.1016/j.plantsci.2015.09.008

Construction of a versatile SNP array for pyramiding useful genes of rice. / Kurokawa, Yusuke; Noda, Tomonori; Yamagata, Yoshiyuki; Angeles-Shim, Rosalyn; Sunohara, Hidehiko; Uehara, Kanako; Furuta, Tomoyuki; Nagai, Keisuke; Jena, Kshirod Kumar; Yasui, Hideshi; Yoshimura, Atsushi; Ashikari, Motoyuki; Doi, Kazuyuki.

In: Plant Science, Vol. 242, 01.01.2016, p. 131-139.

Research output: Contribution to journalArticle

Kurokawa, Y, Noda, T, Yamagata, Y, Angeles-Shim, R, Sunohara, H, Uehara, K, Furuta, T, Nagai, K, Jena, KK, Yasui, H, Yoshimura, A, Ashikari, M & Doi, K 2016, 'Construction of a versatile SNP array for pyramiding useful genes of rice', Plant Science, vol. 242, pp. 131-139. https://doi.org/10.1016/j.plantsci.2015.09.008
Kurokawa Y, Noda T, Yamagata Y, Angeles-Shim R, Sunohara H, Uehara K et al. Construction of a versatile SNP array for pyramiding useful genes of rice. Plant Science. 2016 Jan 1;242:131-139. https://doi.org/10.1016/j.plantsci.2015.09.008
Kurokawa, Yusuke ; Noda, Tomonori ; Yamagata, Yoshiyuki ; Angeles-Shim, Rosalyn ; Sunohara, Hidehiko ; Uehara, Kanako ; Furuta, Tomoyuki ; Nagai, Keisuke ; Jena, Kshirod Kumar ; Yasui, Hideshi ; Yoshimura, Atsushi ; Ashikari, Motoyuki ; Doi, Kazuyuki. / Construction of a versatile SNP array for pyramiding useful genes of rice. In: Plant Science. 2016 ; Vol. 242. pp. 131-139.
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