Development of SNP genotyping assays for heading date in rice.

IF 2 4区农林科学 Q2 AGRONOMY Breeding Science Pub Date : 2024-06-01 Epub Date: 2024-06-25 DOI:10.1270/jsbbs.23093

Noriyuki Kitazawa, Ayahiko Shomura, Tatsumi Mizubayashi, Tsuyu Ando, Nagao Hayashi, Shiori Yabe, Kazuki Matsubara, Kaworu Ebana, Utako Yamanouchi, Shuichi Fukuoka

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Abstract

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.

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开发针对水稻抽穗期的 SNP 基因分型测定。

发棵期（HD）是水稻（Oryza sativa L.）的一个重要农艺性状，受多个基因位点控制，是一系列地理和季节适应性的条件。因此，在标记辅助育种计划中，杂交亲本的 HD 基因型信息至关重要。在此，我们利用 Fluidigm 96-plex SNP 基因分型平台开发了基因分型测定方法，以确定 41 个 HD 基因座（29 个先前表征的基因和 12 个数量性状基因座 [QTL]，包括一个新检测到的 QTL）上的等位基因。基因分型测定共分辨出 144 个等位基因（根据文献和公开数据库定义）和 QTL。对 377 个栽培品种的基因分型显示，平均每个位点有 3.5 个等位基因，Hd1、Ghd7、PRR37 和 DTH8 的多样性高于其他位点，在 41 个位点中的 30 个位点上，参考基因型（"Nipponbare"）占优势。利用 200 个栽培品种的数据建立的 HD 预测模型显示出良好的相关性（r > 0.69，P

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来源期刊

Breeding Science 农林科学-农艺学

CiteScore

4.90

自引率

4.20%

发文量

审稿时长

1.5 months

期刊介绍： Breeding Science is published by the Japanese Society of Breeding. Breeding Science publishes research papers, notes and reviews related to breeding. Research Papers are standard original articles. Notes report new cultivars, breeding lines, germplasms, genetic stocks, mapping populations, database, software, and techniques significant and useful for breeding. Reviews summarize recent and historical events related breeding. Manuscripts should be submitted by corresponding author. Corresponding author must have obtained permission from all authors prior to submission. Correspondence, proofs, and charges of excess page and color figures should be handled by the corresponding author.