Natural variations in grain length 10 (GL10) regulate rice grain size

Zhan, Penglin; Ma, Shuaipeng; Xiao, Zhili; Li, Fangping; Xin, Wei; Lin, Shaojun; Wang, Xiaoling; Ji, Zhe; Fu, Yu; Pan, Jiahao; Zhou, Mingfei; Liu, Yue; Chang, Zengyuan; Li, Lü; Bu, Suhong; Liu, Zupei; Zhu, Haitao; Liu, Guifu; Zhang, Guiquan; Wang, Shaokui

doi:10.1016/j.jgg.2022.01.008

Cited by 43 publications

(22 citation statements)

References 55 publications

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“…With the advancement of genomic and genetic technologies, great progress has been made in resolving the genetic basis of grain shape. At present, twenty genes have been reported to control grain shape in rice, including GL1 (Zhang et al 2021b ) , GW2 (Song et al 2007 ) , GS2 (Duan et al 2015 ; Hu et al 2015 ) , GS3 (Fan et al 2006 ; Zhang et al 2021b ) , qGL3/GL3.1 (Qi et al 2012 ; Zhang et al 2012 ) , TGW3/qTGW3/GL3.3 (Hu et al 2018 ; Xia et al 2018 ; Ying et al 2018 ), LGY3 (Liu et al 2018 ), GW5/GSE5/qSW5 (Shomura et al 2008 ; Weng et al 2008 ; Duan et al 2017 ; Liu et al 2017 ) , GS5 (Li et al 2011 ) , GW5.1 (Zhang et al 2021b ) , GS6 (Sun et al 2013 ) , TGW6 (Ishimaru et al 2013 ) , GW6a (Song et al 2015 ) , GW6 (Shi et al 2020 ; Tang et al 2021 ), GLW7 (Si et al 2016 ) , GW7/GL7 (Wang et al 2015a , b ) , GW8 (Wang et al 2012 ) , GS9/GL9 (Zhao et al 2018 ; Lin et al 2022 ) , GW10 (Zhan et al 2021 ) and GL10 (Zhan et al 2022 ). However, although many QTLs and genes controlling grain shape in rice have been identified, how different combinations of the alleles of these genes affect grain shape and are selected during the breeding process to acquire desired grain shapes is largely unknown.…”

Section: Introductionmentioning

confidence: 99%

Artificially Selected Grain Shape Gene Combinations in Guangdong Simiao Varieties of Rice (Oryza sativa L.)

Yang

et al. 2023

Rice

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Background Grain shape is a key trait in rice breeding. Although many QTLs and genes of grain shape have been identified, how different combinations of alleles of these genes affect grain shape is largely unknown. It is important to understand the effects of grain shape gene combinations for breeding by design. In the present study, we performed genetic dissection of the grain shapes in Guangdong Simiao varieties, a popular kind of rice in South China, to identify the effective alleles and their combination for breeding. Results We selected two hundred nineteen indica accessions with diverse grain shapes and fifty-two Guangdong Simiao varieties with long and slender grain shapes for genome-wide selection analysis. The results showed that four (GS3, GS5, GW5 and GL7) of the twenty grain shape genes fall into the regions selected for in Guangdong Simiao varieties. Allele analysis and frequency distribution of these four genes showed that GS3allele3 and GW5allele2 accounted for 96.2%, and GL7allele2 and GS5allele2 accounted for 76.9% and 74.5% of the Simiao varieties, respectively. Further analysis of the allelic combinations showed that 30 allelic combinations were identified in the whole panel, with 28 allelic combinations found in the international indica accessions and 6 allelic combinations found in Guangdong Simiao varieties. There were mainly three combinations (combinations 17, 18 and 19) in the Guangdong Simiao varieties, with combination 19 (GS3allele3 + GW5allele2 + GL7allele2 + GS5allele2) having the highest percentage (51.9%). All three combinations carried GS3allele3 + GW5allele2, while combinations 17 (GL7allele1) and 19 (GL7allele2) showed significant differences in both grain length and length/width ratio due to differences in GL7 alleles. Pedigree analysis of Guang8B, the maintainer of the first released Simiao male sterile line Guang8A, showed that the parent lines and Guang8B carried GS3allele3 + GW5allele2 + GS5allele2, while the GL7 allele differed, resulting in significant differences in grain size. Conclusion The results suggest that specific alleles of GS3, GS5, GW5 and GL7 are the key grain shape genes used in the Guangdong Simiao varieties and selected for grain shape improvement. Combination 19 is the predominant allelic combination in the Guangdong Simiao varieties. Our current study is the first to dissect the genetics of grain shape in Guangdong Simiao varieties, and the results will facilitate molecular breeding of Guangdong Simiao varieties.

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Section: Introductionmentioning

confidence: 99%

Artificially Selected Grain Shape Gene Combinations in Guangdong Simiao Varieties of Rice (Oryza sativa L.)

Yang

et al. 2023

Rice

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“…We have developed an SSSL library, which includes 2,360 SSSLs derived from 43 donors of 7 species of rice AA genome in the Huajingxian 74 (HJX74) genetic background (Zhang et al, 2004 ; Xi et al, 2006 ; Zhang, 2021 ). The HJX74-SSSLs were widely used to detect QTLs for traits of agronomic importance (Zhang et al, 2012 ; Zhu et al, 2014 , 2018 ; Yang et al, 2016 , 2021a , b ; Zhou et al, 2017b ; Pan et al, 2021 ; Zhan et al, 2021 ; Fu et al, 2022 ), to clone genes of functional importance, and to mine alleles of functional variants (Zeng et al, 2006 ; Teng et al, 2012 ; Wang et al, 2012 ; Fang et al, 2019 ; Sui et al, 2019 ; Gao et al, 2021 ; Zhan et al, 2022 ). Using the HJX74-SSSL library as a platform for rice design, a series of cytoplasmic male sterility (CMS), maintainer and restorer lines, and wide-compatible indica lines (WCILs) were developed (Dai et al, 2015 , 2016 ; Luan et al, 2019 ; Guo et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs

Tan

Chen

et al. 2022

Front. Plant Sci.

Self Cite

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Asian cultivated rice is a self-pollinating crop, which has already lost some traits of natural outcrossing in the process of domestication. However, male sterility lines (MSLs) need to have a strong outcrossing ability to produce hybrid seeds by outcrossing with restorer lines of male parents in hybrid rice seed production. Stigma exsertion rate (SER) is a trait related to outcrossing ability. Reconstruction of the high-SER trait is essential in the MSL breeding of rice. In previous studies, we detected eighteen quantitative trait loci (QTLs) for SER from Oryza sativa, Oryza glaberrima, and Oryza glumaepatula using single-segment substitution lines (SSSLs) in the genetic background of Huajingxian 74 (HJX74). In this study, eleven of the QTLs were used to develop pyramiding lines. A total of 29 pyramiding lines with 2–6 QTLs were developed from 10 SSSLs carrying QTLs for SER in the HJX74 genetic background. The results showed that the SER increased with increasing QTLs in the pyramiding lines. The SER in the lines with 5–6 QTLs was as high as wild rice with strong outcrossing ability. The epistasis of additive by additive interaction between QTLs in the pyramiding lines was less-than-additive or negative effect. One QTL, qSER3a-sat, showed minor-effect epistasis and increased higher SER than other QTLs in pyramiding lines. The detection of epistasis of QTLs on SER uncovered the genetic architecture of SER, which provides a basis for using these QTLs to improve SER levels in MSL breeding. The reconstruction of the high-SER trait will help to develop the MSLs with strong outcrossing ability in rice.

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“…At least 25 QTLs for grain shape and size in rice have been cloned. Fifteen of them mainly regulated grain length, including qTGW1.2b [ 5 ], GS2 / GL2 [ 6 , 7 ], OsLG3 [ 8 ], OsLG3b / qLGY3 [ 9 , 10 ], GS3.1 [ 11 ], GS3 [ 12 ], SG3 [ 13 ], GL3.1 / qGL3 [ 14 , 15 ], qTGW3 [ 16 ], qGL5 [ 17 ], TGW6 [ 18 ], GW6a [ 19 ], GL6 [ 20 ], GLW7 [ 21 ] and GL10 / OsMADS56 [ 22 , 23 ]. Seven other QTLs mainly regulated grain width, including GW2 [ 24 ], TGW2 [ 25 ], GS5 [ 26 ], GSE5 [ 27 ], GW6 [ 28 ], GW8 [ 29 ] and GW10 [ 30 ].…”

Section: Introductionmentioning

confidence: 99%

Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background

Wang

Yingguo

et al. 2022

Plants

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Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). One annotated gene, OsPUB3, was found to be the most likely candidate gene. Here, knockout and overexpression experiments were performed to investigate the effects of OsPUB3 on grain shape and size. Four traits were tested, including grain length, grain width, grain weight, and the ratio of grain length to width. Knockout of OsPUB3 in NILZS97, NILMY46, and another rice cultivar carrying the OsPUB3MY46 allele all caused decreases in grain width and weight and increases in the ratio of grain length to width. Results also showed that the magnitude of the mutational effects varied depending on the target allele and the genetic background. Moreover, it was found that NILZS97 and NILMY46 carried different functional alleles of OsPUB3, causing differences in grain shape rather than grain weight. In the overexpression experiment, significant differences between transgenic-positive and transgenic-negative plants were detected in all four traits. These results indicate that OsPUB3 regulates grain shape and size through a complex mechanism and is a good target for deciphering the regulatory network of grain shape. This gene could be used to improve grain appearance quality through molecular breeding as well.

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Natural variations in grain length 10 (GL10) regulate rice grain size

Cited by 43 publications

References 55 publications

Artificially Selected Grain Shape Gene Combinations in Guangdong Simiao Varieties of Rice (Oryza sativa L.)

Artificially Selected Grain Shape Gene Combinations in Guangdong Simiao Varieties of Rice (Oryza sativa L.)

Reconstruction of the High Stigma Exsertion Rate Trait in Rice by Pyramiding Multiple QTLs

Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background

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