Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice

Song, Xian Jun; Kuroha, Takeshi; Ayano, Madoka; Furuta, Tomohisa; Nagai, Keisuke; Komeda, Norio; Segami, Shuhei; Miura, Kotaro; Ogawa, Daisuke; Kamura, Takumi; Suzuki, Takamasa; Higashiyama, Tetsuya; Yamasaki, Mariko; Mori, Hitoshi; Inukai, Yoshiaki; Wu, Jianzhong; Kitano, Hidemi; Sakakibara, Hitoshi; Jacobsen, Steven E.; Ashikari, Motoyuki

doi:10.1073/pnas.1421127112

Cited by 251 publications

(169 citation statements)

References 30 publications

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“…Since lateral florets were strongly suppressed at the awn primordium stage, the up-regulation of histone genes would be a central spikelet event and an indirect effect through the suppression of lateral floret development. In rice, higher expression of GW6a enhances grain weight and yield by increasing acetylation levels of histone H4 and the up-regulation of cell cycle genes (Song et al, 2015). Interestingly, the rare allele elevating GW6a expression has escaped human selection during rice domestication and modern breeding.…”

Section: Higher Yield Potential Of Deficiens Barleymentioning

confidence: 99%

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Sakuma

Lundqvist²,

Kakei

et al. 2017

Plant Physiol.

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Increasing grain yield is an endless challenge for cereal crop breeding. In barley (Hordeum vulgare), grain number is controlled mainly by Six-rowed spike 1 (Vrs1), which encodes a homeodomain leucine zipper class I transcription factor. However, little is known about the genetic basis of grain size. Here, we show that extreme suppression of lateral florets contributes to enlarged grains in deficiens barley. Through a combination of fine-mapping and resequencing of deficiens mutants, we have identified that a single amino acid substitution at a putative phosphorylation site in VRS1 is responsible for the deficiens phenotype. deficiens mutant alleles confer an increase in grain size, a reduction in plant height, and a significant increase in thousand grain weight in contemporary cultivated germplasm. Haplotype analysis revealed that barley carrying the deficiens allele (Vrs1.t1) originated from two-rowed types carrying the Vrs1.b2 allele, predominantly found in germplasm from northern Africa. In situ hybridization of histone H4, a marker for cell cycle or proliferation, showed weaker expression in the lateral spikelets compared with central spikelets in deficiens. Transcriptome analysis revealed that a number of histone superfamily genes were up-regulated in the deficiens mutant, suggesting that enhanced cell proliferation in the central spikelet may contribute to larger grains. Our data suggest that grain yield can be improved by suppressing the development of specific organs that are not positively involved in sink/source relationships.

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Section: Higher Yield Potential Of Deficiens Barleymentioning

confidence: 99%

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Sakuma

Lundqvist²,

Kakei

et al. 2017

Plant Physiol.

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“…The GW1-1 and GW1-2 [5], qGRL1.1 [6], GS2 [7], GW3 and GW6 [8], qGL-4b [9], qPGWC-7 [10] qGL-7 [11], qGRL7.1 [6], gw8.1 [12], gw9.1 [13], tgw11 [14] have been fine mapped. The GW2 [15], GS3 [16], qGL-3 [17], qSW5 [18], GS5 [19], Chalk5 [20], TGW6 [21], GW6a [22], SRS1 [23], GL7/GW7 [24,25], GW8 [26] and CycT1;3 [27] have been cloned. The usefulness of some of the well characterized genes/QTL was proven in an indica population of diverse breeding lines [4].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Fang¹,

Yingguo²,

Wu³

et al. 2018

Acta Agronomica Sinica

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Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.

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“…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.…”

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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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Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice

Cited by 251 publications

References 30 publications

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Natural Variations in SLG7 Regulate Grain Shape in Rice

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