Natural variation in GS5 plays an important role in regulating grain size and yield in rice

Li, Yibo; Fan, Chuchuan; Xing, Yongzhong; Jiang, Yunhe; Luo, Lijun; Sun, Liang; Shao, Di; Xu, Chunjue; Li, Xianghua; Xiao, Jinghua; He, Yuqing; Zhang, Qifa

doi:10.1038/ng.977

Cited by 779 publications

(628 citation statements)

References 36 publications

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“…By contrast, GW7 was reported to influence cell proliferation, rather than cell expansion (S. . We compared the expression levels of 25 genes, including 14 putatively involved in the G 1 /S and 11 in the G 2 /M phase, as shown in a previous report (Li et al 2011). None of them showed more than a twofold change in transcript levels between NIL-SLG7 and NIL-slg7 inflorescences ( Figure S4A).…”

Section: Discussionmentioning

confidence: 99%

“…Loss of function of GW5/qSW5 leads to a significant increase in sink size, reflecting an increase in cell number in the outer glume of the rice flower (Shomura et al 2008;Weng et al 2008). GS5 encodes a putative serine carboxypeptidase (Li et al 2011), and GW8 encodes squamosa promoter-binding protein-like 16, which belongs to the SBP domain family of transcription factors . Both are positive regulators of grain width.…”

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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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Section: Discussionmentioning

confidence: 99%

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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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“…To improve the sensitivity of evolutionary inferences and study sequence evolution of the six Oryza AA-genome diploid species that diverged over a relatively short time frame, we analyzed a total of 100 orthologous genomic segments across all species on a finer scale (SI Appendix) and present two representative examples: one highly conserved, grain size 5 (GS5) (30), and one rapidly evolving, prostrate growth 1 (PROG1) (31,32). Sequence alignment and annotation showed, to a variable extent, highly conserved gene colinearity and genomic structure across both GS5-and PROG1-orthologous regions ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Zhang

Zhu

Xia

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

134

142

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Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.comparative genomics | full-genome sequencing | genomic variation | positive selection | Oryza D rawing the landscape of genomic divergence among multiple lineages is fundamental to understanding plant gene and genome evolution (1, 2). The comprehensive comparison of closely related genomes in different chronologically ordered stages under a well-resolved phylogenetic framework could dramatically improve the inference precision and sensitivity of gene evolution studies and should allow more robust results for investigating broad-scale patterns of genomic architecture in the course of the speciation process compared with analyses of single genomes (3, 4). For instance, studies of yeast, Drosophila, and human genomes have demonstrated how comparisons of closely related genome sequences can reveal mechanisms of gene and genome evolution in fungi and animals (5-7). In plants, however, we know little about broad-scale patterns of evolutionary dynamics, differentiation, and consequences. Studies are needed of very closely related plant species that span the speciation continuum and have well-characterized biogeographic histories.The genus Oryza, consisting of 24 species, provides a uniquely powerful system for studying comparative genomics and evolutionary biology, and can contribute to the improvement of rice, which is of pivotal significance in worldwide food production and security (8-10). Many genes involved in rice improvement are derived from wild AA-genome species, and broadening the gene pool of cultivated rice through i...

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“…Several of the resolved loci alter the encoded protein sequence, thus, either the protein is functionally altered, or it becomes non-functional, and the resulting allelic polymorphisms can explain the origin of natural variation [34][35][36][37][38][39][40][41] . Nonetheless, substantial natural variation exists in gene expression within and among natural populations, and this quantitative variation is also important in the evolution of natural variation 36,42 . We comprehensively evaluated the role of the POS1 sequence variation in the observed variations of reproductive organ size.…”

Section: Article Nature Communications | Doi: 101038/ncomms5271mentioning

confidence: 99%

“…Grain size-regulating genes (GS), such as GS3 and GS5 that cause a large difference in grain size were characterized in rice 36,[45][46][47] . GS3 and GS5 are strongly R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R (58) R2 (59) R2 (59) R2 (59) R3 (59) R3 (59) R (58) R (58) R (58) R (58) CS58 CS59 pro58 pro58 pro58 pro58 pro58 pro58 pro58 pro58 pro58 pro58 R1 (59) R1 (59) R1 (59) R1 (59) R2 (59) R2 (59) R2 (59) R2 (59) R3 (59) R3 (59) R3 (59 R1 (64) R1 (59) R1 (106) R2 (106) R2 (59) R2 ( associated with natural variation of grain size 36,45 . In Solanum, FW2.2, FAS and LC, as negative regulators, account for 480% of the berry s...…”

Section: Articlementioning

confidence: 99%

Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size

Wang

et al. 2014

Nat Commun

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The genetic basis of size variation in the reproductive organs of tomatillo (Physalis philadelphica) is unknown. Here we report that the expression levels of the gene Physalis Organ Size 1 (POS1) are positively associated with size variation in P. philadelphica reproductive organs such flowers, berries and seeds. POS1 knockdown results in smaller flowers and berries with smaller cells as compared with their wild-type counterparts. Conversely, POS1 overexpression promotes organ size without increasing the cell number. The first introns of the POS1 alleles from the large, intermediate and small tomatillo groups contain one, two and three 37-bp repeats, respectively. Furthermore, our results show that copy variation of repeats in the first intron of POS1 alleles results in differential expression of this gene. Thus, co-variation in tomatillo reproductive organ sizes can be attributed to the novel regulatory variation in POS1.

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Natural variation in GS5 plays an important role in regulating grain size and yield in rice

Cited by 779 publications

References 36 publications

Natural Variations in SLG7 Regulate Grain Shape in Rice

Natural Variations in SLG7 Regulate Grain Shape in Rice

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size

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