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Open AccessArticle

Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2

1
Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka 422-8529, Japan
2
Faculty of Agriculture, Tottori University, 4-101 Koyama Minami, Tottori 680-8550, Japan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(21), 5442; https://doi.org/10.3390/ijms20215442
Received: 19 September 2019 / Revised: 18 October 2019 / Accepted: 18 October 2019 / Published: 31 October 2019
(This article belongs to the Special Issue Plant Genomics 2019)
Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F3 plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F2 and all BCnF2 generations, large, medium, and small grain segregated in a 1:2:1 ratio, indicating that the large grain is controlled by a single allele. Mapping by using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers with small grain homozygous segregants in the F2 of Nipponbare × Inochinoichi, revealed linkage with around 7.7 Mb markers from the distal end of the short arm of chromosome 2. Whole-genome sequencing on a large grain isogenic Koshihikari (BC4F2) using next-generation sequencing (NGS) identified a single nucleotide deletion in GW2 gene, which is located 8.1 Mb from the end of chromosome 2, encoding a RING protein with E3 ubiquitin ligase activity. The GW2-integrated isogenic Koshihikari showed a 34% increase in thousand kernel weight compared to Koshihikari, while retaining a taste score of 80. We further developed a large grain/semi-dwarf isogenic Koshihikari integrated with GW2 and the semidwarfing gene d60, which was found to be localized on chromosome 2. The combined genotype secured high yielding while providing robustness to withstand climate change, which can contribute to the New Green Revolution. View Full-Text
Keywords: rice; large grain gene; large grain-isogenic Koshihikari; fine mapping; NGS; GW2; co-integration; gene recombination; semidwarf gene; d60; linkage; chromosome 2 rice; large grain gene; large grain-isogenic Koshihikari; fine mapping; NGS; GW2; co-integration; gene recombination; semidwarf gene; d60; linkage; chromosome 2
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Tomita, M.; Yazawa, S.; Uenishi, Y. Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2. Int. J. Mol. Sci. 2019, 20, 5442.

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