title: Construction of a versatile SNP array for pyramiding useful genes of rice.
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.
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kurokawa
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Tomonori
authors.initials: T
authors.lastname: Noda
authors.affiliation: 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.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Yamagata
authors.affiliation: 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.
authors.forename: Rosalyn
authors.initials: R
authors.lastname: Angeles-Shim
authors.affiliation: Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Hidehiko
authors.initials: H
authors.lastname: Sunohara
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Kanako
authors.initials: K
authors.lastname: Uehara
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Furuta
authors.affiliation: Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Nagai
authors.affiliation: Novel Gene Resources Laboratory, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
authors.forename: Kshirod Kumar
authors.initials: KK
authors.lastname: Jena
authors.affiliation: 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.
authors.forename: Hideshi
authors.initials: H
authors.lastname: Yasui
authors.affiliation: 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.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yoshimura
authors.affiliation: 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.
authors.forename: Motoyuki
authors.initials: M
authors.lastname: Ashikari
authors.affiliation: 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.
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Doi
mesh_terms: D001483:Base Sequence; D005787:Gene Frequency; D017343:Genes, Plant / Q000235:genetics*; D005828:Genetics, Population / Q000379:methods; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D006239:Haplotypes; D046228:Microarray Analysis / Q000379:methods; D008969:Molecular Sequence Data; D012275:Oryza / Q000145:classification / Q000235:genetics*; D000069600:Plant Breeding / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D000068618:Selective Breeding; D012689:Sequence Homology, Nucleic Acid
keywords: Gene pyramiding; MAS; QTL; Rice breeding; SNP