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

Tomita, Motonori; Yazawa, Shiho; Uenishi, Yoshimasa

doi:10.3390/ijms20215442

Cited by 4 publications

(5 citation statements)

References 15 publications

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“…Furthermore, the double dwarfness by combining d60 and d30 was obtained in F 3 via recombination breaking repulsion-phase linkage on rice chromosome 2 (Tomita and Tanaka 2019). d60 was also linked with a large grain gene GW2 on chromosome 2 (Tomita et al 2019). Next, the Koshihikari d60 line was crossed with a chromosome segment substitution line that carried a segment of chromosome 2 derived from Indica cultivar ‘Kasalath’ in the background of the japonica cultivar ‘Koshihikari’.…”

Section: Discussionmentioning

confidence: 99%

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Rice novel useful semidwarf gened60on chromosome 2 causing pleiotropically gamete abortion

Tomita,

Kamiya,

Okawa

et al. 2024

Preprint

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Rice semidwarf gened60is inherited according to a unique mode because it causes pleiotropically gamete abortion in the case of coexistence with the gamete lethal genegal. Namely, F2progenies of Koshihikari (D60D60galgal, long stem) × Hokuriku 100 (d60d60GalGal, short stem) segregated in the ratio of 1 semidwarf (1d60d60GalGal):2 tall and quarter sterile (2D60d60Galgal):6 tall (2D60d60GalGal:1D60D60GalGal:2D60D60Galgal:1D60D60galgal), which is skewed from the Mendelian 1 semidwarf:3 tall ratio. Firstly, genetic linkage was tested on the basis that the segregation ratios of the phenotypic marker genes linked tod60do not fit Mendelian ratio. F2of Koshihikari d60 line (d60d60GalGal)× lines carryingd30orgh2on chromosome 2, the segregation ratios of these alleles were deviated from 1:3 but well fitted to 5:4 whend30 and gh2were closely linked toD60. We then conducted molecular fine mapping ofd60by using DNA polymorphisms in F2of Koshihikari d60 line × line carrying the indica chromosome 2 segment in Koshihikari. As a result,d60was tightly linked with RM12970 by a recombination value 0.0 at the region 10.3 Mb away from the distal end of the short arm of chromosome 2. Whole genome sequencing of Koshihikari d60 revealed no SNPs and Indels around the 10.3 Mb region. RT-qPCR for ent-copalyl diphosphate synthase-like gene on 10.3 Mb indicated its transcription was reduced compared to that of Koshihikari.

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Section: Discussionmentioning

confidence: 99%

“…d60 confers a good semidwarf phenotype without detrimental effects on grain yield (Tomita & Ishimoto 2019). Furthermore, a semidwarf and large grain isogenic Koshihikari was developed by integrated with d60 and GW2 (Tomita et al 2019). Therefore, d60 is a useful gene source to diversify semidwarf rice varieties.…”

Section: Discussionmentioning

confidence: 99%

Rice novel useful semidwarf gened60on chromosome 2 causing pleiotropically gamete abortion

Tomita,

Kamiya,

Okawa

et al. 2024

Preprint

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“…However, the genes that control its large grain size, approximately 1.5 times that of Koshihikari, have not been elucidated; hence, the production of "Inochinoichi" is limited to the area around Gifu Prefecture. In a previous study, we identified the gene GW2 responsible for the large grain size of Inochinoichi, an unused and buried genetic resource, and then applied the gene to develop a large-grain isogenic line of Koshihikari (Koshihikari GW2) [27]. Furthermore, in this study, we developed a large-grain/semidwarf isogenic line (Koshihikari sd1GW2) that incorporates both the large-grain gene GW2 and semidwarf gene sd1, which we believe is a large-grain rice cultivar with enhanced resistance to lodging.…”

Section: Discussionmentioning

confidence: 99%

“…It has since been clarified that sd1 is a deletion mutation of the GA20 oxidase gene in the gibberellin (GA) biosynthesis pathway (GA 20-oxidase, OsGA20ox2) [10][11][12] localized on A Japanese leading rice variety, Koshishikri, was used as a recurrent parent to develop isogenic lines based on Koshishikri. The Japanese rice variety Inochinoichi was used as a source of the large-grain gene GW2, which was identified in a previous study [27].…”

Section: Introductionmentioning

confidence: 99%

Large-Grain and Semidwarf Isogenic Rice Koshihikari Integrated with GW2 and sd1

2022

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Intending to contribute to sustainable agriculture by “New Green Revolution,” we developed a large-grain/semidwarf isogenic line “Koshihikari sd1GW2” that incorporates both the large-grain gene GW2 and semidwarf gene sd1. GW2 homozygous B3F2 plant with the genomic background of Koshihikari was backcrossed twice with “Koshihikari sd1.” Koshihikari sd1GW2 fixed in BC5F3 was found to be 12.6 cm shorter than Koshihikari. Whole-genome sequencing proved one deletion in GW2 at 8,147,416 bp on chromosome 2 and the SNPs in sd1 at 38,267,510 bp on chromosome 1. The size of the DNA fragments integrated with each gene was determined as the distance between both ends of SNP clusters. Through the backcrossing from BC4 to BC5, the DNA fragment integrated with GW2 decreased by 148,139 bp. The thousand-grain weight of Koshihikari sd1GW2 (27.8 g) was 18% greater than that of Koshihikari (23.6 g), and the grain yield of Koshihikari sd1GW2 (42.6 kg/a) was 0.5% higher than that of Koshihikari (42.4 kg/a). Our results suggested that Koshihikari sd1GW2 will be less susceptible to lodging by typhoons, cyclones, and heavy rainfall, ordinarily a concern in heavier panicle weight cultivars. We successfully integrated GW2 with sd1 for the first time, specifically in the genome of the leading, globally produced Japonica cultivar Koshihikari.

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“…To date, more than four genes linked to grain shape have been cloned in rice [ 7 , 8 , 9 ]. GW2 , the first major quantitative traits loci (QTL) isolated through map-based cloning, controls the width and weight of rice grains [ 10 ]. Similarly, the GS3 locus controls GL, TGW, GW, and grain plumpness [ 9 ], while GW8/OsSPL16 and GW7/OsSPL16 are determinants of GW and grain quality [ 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1

et al. 2022

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Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient’s genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.

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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

Cited by 4 publications

References 15 publications

Rice novel useful semidwarf gened60on chromosome 2 causing pleiotropically gamete abortion

Rice novel useful semidwarf gened60on chromosome 2 causing pleiotropically gamete abortion

Large-Grain and Semidwarf Isogenic Rice Koshihikari Integrated with GW2 and sd1

Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1

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