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

doi:10.1016/j.plantsci.2015.09.008

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

Plant Sci. 2016 Jan:242:131-139. doi: 10.1016/j.plantsci.2015.09.008. Epub 2015 Sep 10.

Affiliations

¹ Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
² Wonder Rice Initiative for Food Security and Health (WISH) project, Japan International Cooperation Agency (JICA), Japan; Science and Technology Research Partnership for Sustainable Development (SATREPS) project, Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA), Japan; Plant Breeding Laboratory, Kyushu University, 6-10-1Hakozaki, Higashi, Fukuoka 812-8581, Japan.
³ Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan; Novel Gene Resources Laboratory, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines; Wonder Rice Initiative for Food Security and Health (WISH) project, Japan International Cooperation Agency (JICA), Japan.
⁴ Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
⁵ Novel Gene Resources Laboratory, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
⁶ Science and Technology Research Partnership for Sustainable Development (SATREPS) project, Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA), Japan; Plant Breeding Laboratory, Kyushu University, 6-10-1Hakozaki, Higashi, Fukuoka 812-8581, Japan.
⁷ Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan; Wonder Rice Initiative for Food Security and Health (WISH) project, Japan International Cooperation Agency (JICA), Japan; Science and Technology Research Partnership for Sustainable Development (SATREPS) project, Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA), Japan.
⁸ Wonder Rice Initiative for Food Security and Health (WISH) project, Japan International Cooperation Agency (JICA), Japan; Science and Technology Research Partnership for Sustainable Development (SATREPS) project, Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA), Japan; Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan. Electronic address: kdoi@agr.nagoya-u.ac.jp.

PMID: 26566831
DOI: 10.1016/j.plantsci.2015.09.008

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.

Keywords: Gene pyramiding; MAS; QTL; Rice breeding; SNP.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Gene Frequency
Genes, Plant / genetics*
Genetics, Population / methods
Genome, Plant / genetics
Genotype
Genotyping Techniques / methods
Haplotypes*
Microarray Analysis / methods
Molecular Sequence Data
Oryza / classification
Oryza / genetics*
Plant Breeding / methods
Polymorphism, Single Nucleotide*
Reproducibility of Results
Selective Breeding
Sequence Homology, Nucleic Acid