Development of SNP genotyping assays for heading date in rice

• Published in: Breeding Science Vol. 74; no. 3; pp. 274 - 284
• Main Authors: Kitazawa, Noriyuki, Shomura, Ayahiko, Mizubayashi, Tatsumi, Ando, Tsuyu, Hayashi, Nagao, Yabe, Shiori, Matsubara, Kazuki, Ebana, Kaworu, Yamanouchi, Utako, Fukuoka, Shuichi
• Format: Journal Article
• Language: English
• Published: Tokyo Japanese Society of Breeding 01.01.2024; Japan Science and Technology Agency
• Subjects: Alleles; Assaying; Cultivars; functional nucleotide polymorphism; Gene mapping; Genetic diversity; Genotypes; Genotyping; genotyping assay; heading date; Japanese cultivar; Oryza sativa; Plant breeding; Prediction models; Quantitative trait loci; Research Paper; rice; Single-nucleotide polymorphism
• ISSN: 1344-7610; 1347-3735
• DOI: 10.1270/jsbbs.23093

Heading date (HD) is a crucial agronomic trait, controlled by multiple loci, that conditions a range of geographical and seasonal adaptations in rice (Oryza sativa L.). Therefore, information on the HD genotypes of cross parents is essential in marker-assisted breeding programs. Here, we used the Fluidigm 96-plex SNP genotyping platform to develop genotyping assays to determine alleles at 41 HD loci (29 previously characterized genes and 12 quantitative trait loci [QTLs], including a newly detected QTL). The genotyping assays discriminated a total of 144 alleles (defined on the basis of the literature and publicly available databases) and QTLs. Genotyping of 377 cultivars revealed 3.5 alleles per locus on average, a higher diversity of Hd1, Ghd7, PRR37, and DTH8 than that of the other loci, and the predominance of the reference (‘Nipponbare’) genotype at 30 of the 41 loci. HD prediction models using the data from 200 cultivars showed good correlation (r > 0.69, P < 0.001) when tested with 22 cultivars not included in the prediction models. Thus, the developed assays provide genotype information on HD and will enable cost-effective breeding.