Genetic Performance of the Semidwarfing Allele sd1 Derived from a Japonica Rice Cultivar and Minimum Requirements to Detect Its Single-Nucleotide Polymorphism by MiSeq Whole-Genome Sequencing.

Motonori Tomita,Kazuo Ishii

doi:10.1155/2018/4241725

Motonori Tomita, Kazuo Ishii

Open Access

https://doi.org/10.1155/2018/4241725

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Abstract

The influence of the semidwarfing gene sd1 derived from the rice cultivar Jukkoku (Jukkoku_sd1) and IR8 (IR8_sd1), which contributed to the Green Revolution, d60 from Hokuriku 100, as well as the combination of sd1 and d60 (Jukkoku_sd1 plus d60 and IR8_sd1 plus d60), was investigated using isogenic lines raised by backcrossing with the cultivar Koshihikari. The isogenic lines carrying Jukkoku_sd1, IR8_sd1, d60, Jukkoku_sd1 plus d60, and IR8_sd1 plus d60 had considerably shorter culm lengths than Koshihikari by 19.2%, 22.8%, 26.0%, 45.1%, and 43.4%, respectively. The sd1 plus d60 lines showed additively reduced culms, indicating that the function of d60 was different from sd1. In contrast to the culm reduction, Jukkoku_sd1 showed productive merit with a panicle length of 2.5% greater than the origin. MiSeq next-generation sequencer was used to optimize a minimum scale to detect Jukkoku_sd1 in practical breeding. Mapping with the reference genome of Nipponbare gained the average depths of Koshihikari Jukkoku_sd1 and Koshihikari being 9.17 and 7.29, respectively. Comparing the vcf files of the entire genomes of Koshihikari Jukkoku_sd1 and the virtual Koshihikari revealed a G to T SNP at position 38,382,746 in the sd1 locus on chromosome 1 of Koshihikari, causing a loss-of-function mutation of GA20-oxidase.

Highlights

IntroductionSemidwarfism of rice improves phenotype (light-interception properties and harvest index), nitrogen responsiveness, and lodging resistance and is an important trait worldwide
Semidwarfism of rice improves phenotype, nitrogen responsiveness, and lodging resistance and is an important trait worldwide
The results of this study showed that all tested semidwarf lines had shorter culm lengths than Koshihikari, indicating improved lodging resistance

Summary

Introduction

Semidwarfism of rice improves phenotype (light-interception properties and harvest index), nitrogen responsiveness, and lodging resistance and is an important trait worldwide. The International Rice Research Institute produced a cross between Peta, a tall indica variety (culm length, 150–180 cm), characterized by abundant, long hanging leaves, commonly grown in tropical Asia, and Dee-geo-woo-gen (DGWG), a Taiwanese indigenous semidwarf variety, to improve its lodging resistance and light-interception properties. The resulting semidwarf rice variety IR8 (culm length, 90–100 cm), developed in 1966, has dramatically improved rice yields and brought the Green Revolution to tropical Asia [1]. The semidwarf trait has been introduced into rice cultivars grown in other countries. A series of cultivars, such as Akihikari and Niigata Wase, were developed in the 1970s in the Tohoku region using the semidwarf cultivar Reimei, which was induced by gammaray irradiation of Fujiminori [3]. In Korea, d47 derived from IR8 was introduced into Tongil by japonica-indica hybridization [7]

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