Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase
Abstract Grain weight and size, mostly determined by grain length, width and thickness, are crucial traits affecting grain quality and yield in rice. A quantitative trait locus controlling grain length and width in rice, qGS1-35.2, was previously fine-mapped in a 57.7-kb region on the long arm of ch...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2022-11-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-022-00604-1 |
| _version_ | 1797986641689706496 |
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| author | Shi-Lin Wang Zhen-Hua Zhang Ye-Yang Fan De-Run Huang Yao-Long Yang Jie-Yun Zhuang Yu-Jun Zhu |
| author_facet | Shi-Lin Wang Zhen-Hua Zhang Ye-Yang Fan De-Run Huang Yao-Long Yang Jie-Yun Zhuang Yu-Jun Zhu |
| author_sort | Shi-Lin Wang |
| collection | DOAJ |
| description | Abstract Grain weight and size, mostly determined by grain length, width and thickness, are crucial traits affecting grain quality and yield in rice. A quantitative trait locus controlling grain length and width in rice, qGS1-35.2, was previously fine-mapped in a 57.7-kb region on the long arm of chromosome 1. In this study, OsPUB3, a gene encoding a U-box E3 ubiquitin ligase, was validated as the causal gene for qGS1-35.2. The effects were confirmed firstly by using CRISPR/Cas9-based mutagenesis and then through transgenic complementation of a Cas9-free knock-out (KO) mutant. Two homozygous KO lines were produced, each having a 1-bp insertion in OsPUB3 which caused frameshift mutation and premature termination. Compared with the recipient and a transgenic-negative control, both mutants showed significant decreases in grain weight and size. In transgenic complementation populations derived from four independent T0 plants, grain weight of transgenic-positive plants was significantly higher than transgenic-negative plants, coming with increased grain length and a less significant decrease in grain width. Based on data documented in RiceVarMap V2.0, eight haplotypes were classified according to six single-nucleotide polymorphisms (SNPs) found in the OsPUB3 coding region of 4695 rice accessions. Significant differences on grain size traits were detected between the three major haplotypes, Hap1, Hap2 and Hap3 that jointly occupy 98.6% of the accessions. Hap3 having the largest grain weight and grain length but intermediate grain width exhibits a potential for simultaneously improving grain yield and quality. In another set of 257 indica rice cultivars tested in our study, Hap1 and Hap2 remained to be the two largest groups. Their differences on grain weight and size were significant in the background of non-functional gse5, but non-significant in the background of functional GSE5, indicating a genetic interaction between OsPUB3 and GSE5. Cloning of OsPUB3 provides a new gene resource for investigating the regulation of grain weight and size. |
| first_indexed | 2024-04-11T07:36:22Z |
| format | Article |
| id | doaj.art-58c26664b96a4e57a552e4989e70466d |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-11T07:36:22Z |
| publishDate | 2022-11-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-58c26664b96a4e57a552e4989e70466d2022-12-22T04:36:44ZengSpringerOpenRice1939-84251939-84332022-11-0115111210.1186/s12284-022-00604-1Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin LigaseShi-Lin Wang0Zhen-Hua Zhang1Ye-Yang Fan2De-Run Huang3Yao-Long Yang4Jie-Yun Zhuang5Yu-Jun Zhu6State Key Laboratory of Rice Biology, China National Rice Research InstituteState Key Laboratory of Rice Biology, China National Rice Research InstituteState Key Laboratory of Rice Biology, China National Rice Research InstituteState Key Laboratory of Rice Biology, China National Rice Research InstituteState Key Laboratory of Rice Biology, China National Rice Research InstituteState Key Laboratory of Rice Biology, China National Rice Research InstituteState Key Laboratory of Rice Biology, China National Rice Research InstituteAbstract Grain weight and size, mostly determined by grain length, width and thickness, are crucial traits affecting grain quality and yield in rice. A quantitative trait locus controlling grain length and width in rice, qGS1-35.2, was previously fine-mapped in a 57.7-kb region on the long arm of chromosome 1. In this study, OsPUB3, a gene encoding a U-box E3 ubiquitin ligase, was validated as the causal gene for qGS1-35.2. The effects were confirmed firstly by using CRISPR/Cas9-based mutagenesis and then through transgenic complementation of a Cas9-free knock-out (KO) mutant. Two homozygous KO lines were produced, each having a 1-bp insertion in OsPUB3 which caused frameshift mutation and premature termination. Compared with the recipient and a transgenic-negative control, both mutants showed significant decreases in grain weight and size. In transgenic complementation populations derived from four independent T0 plants, grain weight of transgenic-positive plants was significantly higher than transgenic-negative plants, coming with increased grain length and a less significant decrease in grain width. Based on data documented in RiceVarMap V2.0, eight haplotypes were classified according to six single-nucleotide polymorphisms (SNPs) found in the OsPUB3 coding region of 4695 rice accessions. Significant differences on grain size traits were detected between the three major haplotypes, Hap1, Hap2 and Hap3 that jointly occupy 98.6% of the accessions. Hap3 having the largest grain weight and grain length but intermediate grain width exhibits a potential for simultaneously improving grain yield and quality. In another set of 257 indica rice cultivars tested in our study, Hap1 and Hap2 remained to be the two largest groups. Their differences on grain weight and size were significant in the background of non-functional gse5, but non-significant in the background of functional GSE5, indicating a genetic interaction between OsPUB3 and GSE5. Cloning of OsPUB3 provides a new gene resource for investigating the regulation of grain weight and size.https://doi.org/10.1186/s12284-022-00604-1RiceGrain weightGrain sizeMilling qualityUbiquitin-ligase enzymeU-box domain |
| spellingShingle | Shi-Lin Wang Zhen-Hua Zhang Ye-Yang Fan De-Run Huang Yao-Long Yang Jie-Yun Zhuang Yu-Jun Zhu Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase Rice Rice Grain weight Grain size Milling quality Ubiquitin-ligase enzyme U-box domain |
| title | Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase |
| title_full | Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase |
| title_fullStr | Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase |
| title_full_unstemmed | Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase |
| title_short | Control of Grain Weight and Size in Rice (Oryza sativa L.) by OsPUB3 Encoding a U-Box E3 Ubiquitin Ligase |
| title_sort | control of grain weight and size in rice oryza sativa l by ospub3 encoding a u box e3 ubiquitin ligase |
| topic | Rice Grain weight Grain size Milling quality Ubiquitin-ligase enzyme U-box domain |
| url | https://doi.org/10.1186/s12284-022-00604-1 |
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