Whole-Genome Sequencing Revealed a Late-Maturing Isogenic Rice Koshihikari Integrated with Hd16 Gene Derived from an Ise Shrine Mutant

Motonori Tomita,Vijay Gahlaut,Kazuo Ishii,Ryotaro Tokuyama,Shosuke Matsumoto

doi:10.1155/2022/4565977

Motonori Tomita, Vijay Gahlaut

Open Access

https://doi.org/10.1155/2022/4565977

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Abstract

We identified the key genes controlling the late maturation of the Japonica cultivar Isehikari, which was found at Ise Jingu Shrine and matures 6 days later than Koshihikari. We conducted a genetics-based approach through this study. First, the latest mature plants, which flowered later than Isehikari, were segregated in the F2 and F3 generations of Koshihikari×Isehikari. Next, the linkage relationship of a single late-maturing gene with the SSR markers on the long arm of chromosome 3 was inferred by using late-maturing homozygous F2 segregants. Moreover, genetic analyses of late maturity were conducted through the process of six times of continuous backcross with Koshihikari as a recurrent parent by using the late-maturing homozygous F3 line as a nonrecurrent parent, thus developing a late-maturing isogenic Koshihikari (BC6F2). As a result, we elucidated a single late-maturing gene with incomplete dominance that caused the 14-day maturation delay of Koshihikari. The whole-genome sequencing was conducted on both of Koshihikari and the late-maturing isogenic Koshihikari. Then, the SNP call was conducted as the reference genome of Koshihikari. Finally, a single SNP was identified in the key gene Hd16 of the late-maturing isogenic Koshihikari.

Highlights

Rice is cultivated worldwide, in Asia, and is one of the world’s top three grains with an annual yield of 680 million tons, alongside corn (1.73 billion tons) and wheat (680 million tons) [1]; stable production is crucial
The white immature grain occurs when warm nights lead to increased respiration, causing a reduction in nitrogen content, and reducing the transportation of photosynthetic products, which serve as a substrate for starch, to the panicles; it results in an imbalance in nutrient supply and demand [7,8,9]
Twenty-three F3 lines were fixed in late-maturation headings between 8/31 and 9/8, which derived from late-maturing F2 plants that head from 8/23 to 9/2

Summary

Introduction

In Asia, and is one of the world’s top three grains with an annual yield of 680 million tons, alongside corn (1.73 billion tons) and wheat (680 million tons) [1]; stable production is crucial. In the IPCC’s 6th evaluation report, global warming is expected to bring about an increase in the frequency of strong tropical cyclones, and there are concerns that damage from heavy rains will be magnified [3, 4]. Rice has suffered from lodging damage, yield reduction, lowered grain quality by ear germination, and lowered production efficiency, which are brought by serious strong winds and rain [5]. If the average daily temperature exceeds 23°C–24°C during the 20 days after heading, a white immature grain arises [6]. The white immature grain occurs when warm nights lead to increased respiration, causing a reduction in nitrogen content, and reducing the transportation of photosynthetic products (sugars), which serve as a substrate for starch, to the panicles; it results in an imbalance in nutrient supply and demand [7,8,9]. In 2011, 170,000 tons of rice, or 21% of the total

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