Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield

Ishimaru, Ken; Hirotsu, Naoki; Madoka, Yuka; Murakami, Naomi; Hara, Nao; Onodera, Hidehiro; Kashiwagi, Takayuki; Ujiie, Kazuhiro; Shimizu, Bun-ichi; Onishi, Atsuko; Miyagawa, Hisashi; Katoh, Etsuko

doi:10.1038/ng.2612

Cited by 503 publications

(393 citation statements)

References 42 publications

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“…This finding suggested that numerous rare alleles might not be captured in the core collection. In recent decades, many elite genes or alleles have been discovered from landraces and utilized in rice breeding, including the semi-dwarf genes (Monna et al, 2002;Sasaki et al, 2002), resistant/tolerant genes to diseases and pests, and genes for improving grain yield and quality (Fukuoka et al, 2009;Ishimaru et al, 2013). It is likely, therefore, that three minor groups of rice germplasm (aus, aromatic and rayada) that have a limited presence in Chinese germplasm may be important genetic resources for future rice genetics and breeding in China given their unique genetic and phenotypic characteristics (Glaszmann, 1987;Khush, 1997).…”

Section: Diversity and Differentiation Of Chinese Rice Cultivarsmentioning

confidence: 99%

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

et al. 2013

Heredity

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Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of modelbased grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.

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Section: Diversity and Differentiation Of Chinese Rice Cultivarsmentioning

confidence: 99%

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

et al. 2013

Heredity

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“…Higher expression of these two genes contributed to larger grain size through their effects on the cell-cycle machinery. Additionally, the GIF1 gene encodes a cell-wall invertase required for carbon partitioning during early grain filling (Wang et al 2008), and TGW6 encodes an indole-3-acetic acid-glucose hydrolase affecting the transition from the syncytial to the cellular phase of the endosperm (Ishimaru et al 2013). GIF1 and TGW6 directly affect the endosperm size and consequently regulate grain size and weight.…”

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confidence: 99%

Natural Variations in SLG7 Regulate Grain Shape in Rice

Zhou

Peng

et al. 2015

Genetics

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Rice (Oryza sativa) grain shape, which is controlled by quantitative trait loci (QTL), has a strong effect on yield production and quality. However, the molecular basis for grain development remains largely unknown. In this study, we identified a novel QTL, Slender grain on chromosome 7 (SLG7), that is responsible for grain shape, using backcross introgression lines derived from 9311 and Azucena. The SLG7 allele from Azucena produces longer and thinner grains, although it has no influence on grain weight and yield production. SLG7 encodes a protein homologous to LONGIFOLIA 1 and LONGIFOLIA 2, both of which increase organ length in Arabidopsis. SLG7 is constitutively expressed in various tissues in rice, and the SLG7 protein is located in plasma membrane. Morphological and cellular analyses suggested that SLG7 produces slender grains by longitudinally increasing cell length, while transversely decreasing cell width, which is independent from cell division. Our findings show that the functions of SLG7 family members are conserved across monocots and dicots and that the SLG7 allele could be applied in breeding to modify rice grain appearance.KEYWORDS rice; quantitative trait loci; grain shape; cell elongation R ICE (Oryza sativa L.) is a staple food for half of the world's population (Khush 2001). Three major components, panicle number per plant, grain number per panicle, and grain weight, determine rice yield production. Grain weight is associated with grain size and shape, which are defined as grain length, grain width, and grain thickness (Duan et al. 2014). There is a striking diversity of grain size among the rice species worldwide. The grains of domesticated rice range from 3 to 11 mm in length and from 1.2 to 3.8 mm in width (Fitzgerald et al. 2009). Despite the influence of several environmental factors on plant growth and development, such as water supply and fertilizer level, the final grain size of rice is reasonably constant within a given species.Rice grain traits are quantitatively inherited. In the past decade, several quantitative trait loci (QTL) controlling grain size and shape have been cloned. GS3, encoding a transmembrane protein containing four putative domains, was the first characterized QTL that regulates grain length (Fan et al. 2006). qGL3 encodes a putative protein phosphatase with a Kelch-like repeat domain, and an aspartate-to-glutamate transition in the second Kelch domain leads to a long-grain phenotype (Zhang et al. 2012). GW6 encodes a GNAT-like protein that harbors intrinsic histone acetyltransferase activity, and an elevated expression enhances grain length and weight by enlarging spikelet hulls and accelerating grain filling (Song et al. 2015). GW2, GW5/qSW5, GS5, and GW8 were identified as regulators of rice grain width. GW2 encodes a previously unknown RING-type protein with E3 ubiquitin ligase, which negatively regulates cell division by degrading its substrate(s) through the ubiquitin-proteasome pathway (Song et al. 2007). GW5/qSW5 encodes a nuclearlocated protein t...

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“…In recent years, substantial research progress has been made regarding genes associated with grain size, particularly research focused on GS3, qSW5, GW2, GS3, GS5, and TGW6 haplotypes (Weng et al, 2008;Fan et al, 2009;Takano-Kai et al, 2009;Mao et al, 2010;Li et al, 2011;Dixit et al, 2013;Ishimaru et al, 2013;Lu et al, 2013;Xu et al, 2015). Zhang et al (2012) found that only SNP1 in the qGL3 region in 94 germplasms (the same SNP that was found in TD70) contributed highly to grain length, whereas other polymorphic sites had no significant contributions to grain length.…”

Section: Haplotypes Of Genes Associated With Grain Sizementioning

confidence: 99%

“…Grain shape, as the major determinant of grain weight, is characterized by a combination of four parameters: grain length, grain width, grain thickness, and filling degree (Xing and Zhang, 2010;Huang et al, 2013;Ikeda et al, 2013;Zuo and Li, 2014). In recent years, several key genes that regulate grain shape were identified (Fan et al, 2006;Shomura et al, 2008;Weng et al, 2008;Li et al, 2011;Zhang et al, 2012;Ishimaru et al, 2013;Song et al, 2007Song et al, , 2015Wang et al, 2012Wang et al, , 2015a. For instance, qGL3/qGL3.1 is a newly identified QTL associated with grain length, which exhibited the highest logarithm of the odds value and the greatest phenotypic variation compared to other markers, and it also significantly contributed to grain thickness and grain width (Hu et al, 2012;Qi et al, 2012;Zhang et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Haplotypes of qGL3 and their roles in grain size regulation with GS3 alleles in rice

Zhang¹,

Zhu²,

QingYong³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Grain size is an important trait that directly influences rice yield. The qGL3 and GS3 genes are two putative regulators that play a role in grain size determination. A single rare nucleotide substitution (C→A) at position 1092 in exon 10 of qGL3 might be responsible for variations in grain size. However, little is known about the haplotype variations of qGL3 and their interactions with GS3 during the regulation of grain length and grain weight. In this study, qGL3 haplotype variations were examined in 61 Indica varieties, and the effects of qGL3 and GS3 on grain trait variation in 110 lines were evaluated. Six qGL3 haplotypes were identified, and qGL3-2 was a major haplotype in Indica varieties. Moreover, qGL3-6, a reported key single nucleotide polymorphism, was validated. Our results showed that the mutants qgl3 and gs3 (loss-of-function mutation types of qGL3 and GS3, respectively) had significant effects on grain length and grain weight. However, no significant effects associated with differences in the regulation of grain thickness were observed. The genetic effects of qgl3 on grain phenotypes were stronger than those of gs3. In addition to increased grain length, qgl3 had an evident role in grain width increases. In contrast, gs3 played an opposite role in grain width regulation. These results provided novel insights into grain size control and the functions of qgl3 and gs3 in rice yield improvement.

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Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield

Cited by 503 publications

References 42 publications

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Natural Variations in SLG7 Regulate Grain Shape in Rice

Haplotypes of qGL3 and their roles in grain size regulation with GS3 alleles in rice

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