Determinant Of Grain Yield Research Articles

CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice

Enhancing crop productivity and their nutritional quality are the key components and primary focus of crop improvement strategy for fulfilling future food demand and improving human health. Grain filling and endosperm development are the key determinants of grain yield and nutritional quality. GRAIN WIDTH and WEIGHT2 (GW2) gene encodes a RING-type E3 ubiquitin ligase and determines the grain weight in cereal crops. Here we report GW2 knockout (KO) mutants in Indica (var. MTU1010) through CRISPR/Cas9 genome editing. The endosperm of GW2-KO mutant seed displays a thick aleurone layer with enhanced grain protein content. Further the loss of function of OsGW2 results in improved accumulation of essential dietary minerals (Fe, Zn, K, P, Ca) in the endosperm of rice grain. Additionally, the mutants displayed an early growth vigour phenotype with an improved root and shoot architecture. The hull morphology of GW2-KO lines also showed improved, grain filling thereby promoting larger grain architecture. Together, our findings indicate that GW2 may serve as a key regulator of improved grain architecture, grain nutritional quality and an important modulator of plant morphology. The study offers a strategy for the development of improved rice cultivars with enriched nutritional quality and its possible implementation in other cereals as well.

Gibberellins orchestrate panicle architecture mediated by DELLA–KNOX signalling in rice

SummaryPanicle architecture is a key determinant of grain yield in cereals, but the mechanisms governing panicle morphogenesis and organ development remain elusive. Here, we have identified a quantitative trait locus (qPA1) associated with panicle architecture using chromosome segment substitution lines from parents Nipponbare and 9311. The panicle length, branch number and grain number of Nipponbare were significantly higher than CSSL‐9. Through map‐based cloning and complementation tests, we confirmed that qPA1 was identical to SD1 (Semi Dwarf1), which encodes a gibberellin 20‐oxidase enzyme participating in gibberellic acid (GA) biosynthesis. Transcript analysis revealed that SD1 was widely expressed during early panicle development. Analysis of sd1/osga20ox2 and gnp1/ osga20ox1 single and double mutants revealed that the two paralogous enzymes have non‐redundant functions during panicle development, likely due to differences in spatiotemporal expression; GNP1 expression under control of the SD1 promoter could rescue the sd1 phenotype. The DELLA protein SLR1, a component of the GA signalling pathway, accumulated more highly in sd1 plants. We have demonstrated that SLR1 physically interacts with the meristem identity class I KNOTTED1‐LIKE HOMEOBOX (KNOX) protein OSH1 to repress OSH1‐mediated activation of downstream genes related to panicle development, providing a mechanistic link between gibberellin and panicle architecture morphogenesis.

Manipulating assimilate availability provides insight into the genes controlling grain size in sorghum.

Variation in grain size, a major determinant of grain yield and quality in cereal crops, is determined by both the plant's genetic potential and the available assimilate to fill the grain in the absence of stress. This study investigated grain size variation in response to variation in assimilate supply in sorghum using a diversity panel (n=837) and a backcross-nested association mapping population (n=1421) across four experiments. To explore the effects of genetic potential and assimilate availability on grain size, the top half of selected panicles was removed at anthesis. Results showed substantial variation in five grain size parameters with high heritability. Artificial reduction in grain number resulted in a general increase in grain weight, with the extent of the increase varying across genotypes. Genome-wide association studies identified 44 grain size quantitative trait locus (QTL) that were likely to act on assimilate availability and 50 QTL that were likely to act on genetic potential. This finding was further supported by functional enrichment analysis and co-location analysis with known grain number QTL and candidate genes. RNA interference and overexpression experiments were conducted to validate the function of one of the identified gene, SbDEP1, showing that SbDEP1 positively regulates grain number and negatively regulates grain size by controlling primary branching in sorghum. Haplotype analysis of SbDEP1 suggested a possible role in racial differentiation. The enhanced understanding of grain size variation in relation to assimilate availability presented in this study will benefit sorghum improvement and have implications for other cereal crops.

Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner.

Flower development is an important determinant of grain yield in crops. In wheat (Triticum spp.), natural variation for the size of spikelet and floral organs is particularly evident in Triticum turgidum ssp. polonicum (also termed Triticum polonicum), a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT2), which encodes a MADS-box transcription factor belonging to the SHORT VEGETATIVE PHASE family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence rearrangement in intron-1 that results in ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum subspecies-defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across spikelets and within florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can affect agronomic traits in a dosage-dependent manner in polyploid crops.

QTL mapping for grain number per spikelet in wheat using a high-density genetic map

Grain number per spikelet (GNS) is a key determinant of grain yield in wheat. A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained. Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism (SNP) array. A high-density genetic map containing 21,197 SNPs was obtained. These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 cM. Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring. The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations. Based on multi-environment phenotype data and best liner unbiased prediction values, three quantitative trait loci (QTL) for GNS were identified. One of them located on chromosomes 2B and the other two on 2D. Phenotypic variation explained by these loci varied from 3.07% to 26.57%. One of these QTL, QGns.sicau-2D-2, was identified in each of all trials conducted. Based on the best linear unbiased prediction values, this locus explained 19.59%–26.57% of phenotypic variation. A KASP (Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds. The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for marker-assisted selection in wheat breeding programs.

Plant-atmosphere and soil-atmosphere temperature differences and their impact on grain yield of super hybrid rice under different irrigation conditions.

Continued drought during the late growth stage of super hybrid rice (SHR) markedly reduces yield, and management practices that use water more efficiently can contribute greatly to high and stable yields from SHR. The absolute temperature differences (ATDs) between the rice plant and the atmosphere and between the soil and the atmosphere are believed to be important determinants of grain yield. However, it has not previously been determined whether these ATDs have any effect on SHR yields under water-saving cultivation. A two-year field experiment involving two SHR varieties, Liangyoupeijiu (LYPJ) and Y-Liangyou 9000 (YLY900), evaluated the effects of reducing water supply from mid-booting to maturity on grain yield, canopy relative humidity (CRH), leaf area index (LAI), and ATDs between the ambient temperature and the leaf surface, panicles, canopy, and soil. Grain yield increased significantly under shallow water irrigation (SW), by 8.84% (YLY900) and 12.26% (LYPJ), but decreased significantly under mild water stress (MS, -20 to -30 kPa), by 14.36% (YLY900) and 9.47% (LYPJ), as well as severe water stress (SS, -40 to -50 kPa), by 35.06% (YLY900) and 28.74% (LYPJ). As water supply decreased, so did the CRH and the ATDs, with significant decreases under MS and SS. The temperature differences were significantly and positively correlated with grain yield (P < 0.01) in both cultivars. LAI was increased under SW conditions, but was significantly decreased under MS and SS. Our study suggests that the dual goal of saving water while maintaining high yield can be achieved by applying SW irrigation from mid-booting to maturity and by adopting cultivation measures that maintain high CRH and high plant-atmosphere and soil-atmosphere ATDs in order to alleviate water stress. YLY900 has a higher yield potential than LYPJ under SW conditions, suggesting that its wide cultivation may help achieve this dual goal.

Engineering 6-phosphogluconate dehydrogenase improves grain yield in heat-stressed maize

Endosperm starch synthesis is a primary determinant of grain yield and is sensitive to high-temperature stress. The maize chloroplast-localized 6-phosphogluconate dehydrogenase (6PGDH), PGD3, is critical for endosperm starch accumulation. Maize also has two cytosolic isozymes, PGD1 and PGD2, that are not required for kernel development. We found that cytosolic PGD1 and PGD2 isozymes have heat-stable activity, while amyloplast-localized PGD3 activity is labile under heat stress conditions. We targeted heat-stable 6PGDH to endosperm amyloplasts by fusing the Waxy1 chloroplast targeting the peptide coding sequence to the Pgd1 and Pgd2 open reading frames (ORFs). These WPGD1 and WPGD2 fusion proteins import into isolated chloroplasts, demonstrating a functional targeting sequence. Transgenic maize plants expressing WPGD1 and WPGD2 with an endosperm-specific promoter increased 6PGDH activity with enhanced heat stability in vitro. WPGD1 and WPGD2 transgenes complement the pgd3-defective kernel phenotype, indicating the fusion proteins are targeted to the amyloplast. In the field, the WPGD1 and WPGD2 transgenes can mitigate grain yield losses in high-nighttime-temperature conditions by increasing kernel number. These results provide insight into the subcellular distribution of metabolic activities in the endosperm and suggest the amyloplast pentose phosphate pathway is a heat-sensitive step in maize kernel metabolism that contributes to yield loss during heat stress.

Genotypic variation in the grain photosynthetic contribution to grain filling in rice

Grain filling in rice, a staple cereal crop worldwide, is a critical determinant of grain yield and quality. However, there is little available information on the relationship between grain filling and grain photosynthetic capacity in rice. This study evaluated the genetic diversity among six rice cultivars for their grain filling rate (GR0) and the relationships with the grain chlorophyll contents and grain net photosynthetic rate (PN). Significant variations in GR0, PN, and the chlorophyll contents (a, b, and total) in the grains of the cultivars were observed. Approximately 90 % of the variation in GR0 was explained by the grain PN. General linear model regression revealed significant positive correlations between PN/GR0 and the chlorophyll contents (a, b, and total) in the grains. There was also a significant positive correlation between PN and GR0. These positive correlations suggest a direct positive relationship between the grain filling rate and grain chlorophyll contents, which is indicative of the high photosynthetic capacity of the grains during the early grain filling period. These results suggest that the grain chlorophyll contents could be used as a molecular marker in marker-assisted breeding programs for rice cultivars with high grain net photosynthetic capacity during the early period of grain filling to improve grain yield.

Genetic analysis and map‐based delimitation of a major locus qSS3 for seed size in soybean

AbstractSeed size is a major determinant of grain yield in soybean, however their genetic basis remains largely unknown. In order to delimit map‐based position of a major locus qSS3, we evaluated three mapping populations, including RILs, NILs and a sub‐F2 in three environments for six seed size‐related traits. For these traits, the kurtosis and skewness ranged between 0.0 and 1.16, while h2b ranged from 0.75 to 0.96, indicating that this RIL population is suitable for QTL analysis. QTL analysis identified 12 loci which consist of 30 significant QTLs with PVE% and LOD values of 6.6%–26.2% and 2.50–5.61, respectively. Among them, qSS3 was a major and stable locus explaining 7.3%–26.2% of the variation in 5 of the 6 traits, with the respective LOD values falling in the range of 2.72–5.61. Additionally, qSS3 effects were confirmed in NILs and delimited to an interval of ~1,126 kb containing 123 annotated genes. Overall, this study may assist efforts aiming to improve soybean seed traits by identifying valuable genetic resources which can be used in future MAS breeding programmes.

Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size.

Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.

High radiation use efficiency improves yield in the recently developed elite hybrid rice Y-liangyou 900

Yield potential in super hybrid rice has continued to increase in recent decades through morphological improvements and the use of inter-subspecific heterosis. Radiation use efficiency (RUE) has been singled out as an important determinant of grain yield in cereal species. However, it is not known whether yield increases in super hybrid rice breeding programs have involved improvements in RUE. Three-year field experiments evaluated the effects of breeding on grain yield and its physiological determinants, including RUE, intercepted photosynthetically active radiation (IPAR), aboveground biomass production, and harvest index (HI), in three representative super hybrid rice varieties released between 1999 and 2015 and grown under three N regimes (N0: 0 kg ha–1, N1: 210 kg ha−1, N2: 300 kg ha–1). Grain yield in the recently developed super hybrid rice cultivar Y-liangyou 900 (YLY900) increased significantly, relative to Liangyoupeijiu (LYPJ) and Y-liangyou 2 (YLY2), reaching more than 11 t ha–1 in the N2 treatment each year. Yield improvements in YLY900 were primarily due to increased aboveground biomass production resulting from a higher RUE, being 10.6 % (biomass) and 12.1 % (RUE) higher than those in LYPJ and YLY2. Unlike YLY900, aboveground biomass accumulation in LYPJ and YLY2 mostly resulted from increased IPAR. Nitrogen supply significantly increased intercepted radiation and intercepted percentage but not RUE. The N treatments had no effect on HI, within or between varieties. Grain yield had a significant (P < 0.01) positive correlation with both intercepted radiation and RUE in all three cultivars. The multiple regression analysis showed that the higher grain yield in YLY900 was more closely related to RUE, while those in LYPJ and YLY2 were highly dependent on intercepted radiation. Considering that YLY900 had a significant yield advantage, we conclude that RUE plays a more prominent role than HI in yield progress in super hybrid rice. Crop breeders should focus on breeding for improved solar radiation properties as a sustainable means of increasing yields in super hybrid rice.

Genome-wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure.

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co-localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked-down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.

Water and radiation use efficiencies in maize: Breeding effects on single-cross Argentine hybrids released between 1980 and 2012

Water deficit has been signaled as an important determinant of grain yield (GY) gaps between potential and actual GYs. Breeding for improved water as well as solar radiation productivities is a sustainable means to reduce this gap. The aim of this study was to evaluate breeding effects on GY and its physiological determinants, including water (WUE) and radiation (RUE) use efficiencies, of temperate maize hybrids grown under a wide range of environmental conditions in Argentina. We hypothesized that breeding focused on GY performance and broad adaptation produced an increase in crop biomass linked to an increased tolerance to adverse growing conditions, a trend associated with an increase in WUE and/or RUE. For this purpose, hybrids were grown under three stand densities and eight environmental conditions in the main target environment for the production of temperate hybrids in Argentina. Analyzed traits were GY, total shoot biomass (BT) production, harvest index (HI = GY/BT), crop evapotranspiration (ETC), crop radiation interception (IPARC: cumulative amount of intercepted incident photosynthetically active radiation), radiation use efficiency (RUE = BT/IPARC), water use efficiency (WUE) for biomass production (WUEB,ETc= BT/ETC) and WUE for GY production (WUEGY,ETc= GY/ETC). No breeding effect was registered on ETC and IPARC, whereas significant breeding effects (P < 0.05) were detected on GY (0.5 % YOR−1 from 1980 onwards). The latter were due to the improvement of BT (from 1993 onwards) as well as of HI (between 1980 and 1993), with gains of 0.5 % YOR−1 in both cases. Mentioned trends were associated with a significant increase in RUE (0.7 % YOR−1 from 1993 onwards) and consequently in WUEB,ETc (0.6 % YOR−1 from 1993 onwards) and WUEGY,ETc (0.5 % YOR−1 from 1980 onwards). Results demonstrated that breeding efforts, which have been driven almost exclusively by GY improvement, had no evident effect on the crop water use but had clear effects on crop biomass production and its partitioning. These unintended positive effects of breeding on RUE and WUEs are welcome on a global scale, considering that predicted trends of increasing human demand for water will require increased water productivity rather than increased water use by crops.

Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

BackgroundCarbon (C) and nitrogen (N) are two fundamental components of starch and protein, which are important determinants of grain yield and quality. The food preferences of consumers and the expected end-use of grains in different rice-growing regions require diverse varieties that differ in terms of the grain N content (GNC) and grain C content (GCC) of milled rice. Thus, it is important that quantitative trait loci (QTLs)/genes with large effects on the variation of GNC and GCC are identified in breeding programs.ResultsTo dissect the genetic basis of the variation of GNC and GCC in rice, the Dumas combustion method was used to analyze 751 diverse accessions regarding the GNC, GCC, and C/N ratio of the milled grains. The GCC and GNC differed significantly among the rice subgroups, especially between Xian/Indica (XI) and Geng/Japonica (GJ). Interestingly, in the GJ subgroup, the GNC was significantly lower in modern varieties (MV) than in landraces (LAN). In the XI subgroup, the GCC was significantly higher in MV than in LAN. One, six, and nine QTLs, with 55 suggestively associated single nucleotide polymorphisms, were detected for the GNC, GCC, and C/N ratio in three panels during a single-locus genome-wide association study (GWAS). Three of these QTLs were also identified in a multi-locus GWAS. We screened 113 candidate genes in the 16 QTLs in gene-based haplotype analyses. Among these candidate genes, LOC_Os01g06240 at qNC-1.1, LOC_Os05g33300 at qCC-5.1, LOC_Os01g04360 at qCN-1.1, and LOC_Os05g43880 at qCN-5.2 may partially explain the significant differences between the LAN and MV. These candidate genes should be cloned and may be useful for molecular breeding to rapidly improve the GNC, GCC, and C/N ratio of rice.ConclusionsOur findings represent valuable information regarding the genetic basis of the GNC and GCC and may be relevant for enhancing the application of favorable haplotypes of candidate genes for the molecular breeding of new rice varieties with specific grain N and C contents.

Sucrose Synthase Enhances Hull Size and Grain Weight by Regulating Cell Division and Starch Accumulation in Transgenic Rice.

Grain size and weight are two important determinants of grain yield in rice. Although overexpression of sucrose synthase (SUS) genes has led to several improvements on cellulose and starch-based traits in transgenic crops, little is reported about SUS enhancement of hull size and grain weight in rice. In this study, we selected transgenic rice plants that overexpressed OsSUS1-6 genes driven with the maize Ubi promoter. Compared to the controls (wild type and empty vector line), all independent OsSUS homozygous transgenic lines exhibited considerably increased grain yield and grain weights. Using the representative OsSUS3 overexpressed transgenic plants, four independent homozygous lines showed much raised cell numbers for larger hull sizes, consistent with their enhanced primary cell wall cellulose biosynthesis and postponed secondary wall synthesis. Accordingly, the OsSUS3 transgenic lines contained much larger endosperm volume and higher starch levels than those of the controls in the mature grains, leading to increased brown grain weights by 15–19%. Hence, the results have demonstrated that OsSUS overexpression could significantly improve hull size and grain weight by dynamically regulating cell division and starch accumulation in the transgenic rice.

Contrasting change in biomass translocation with environment in two rice hybrids.

Translocation of biomass produced during pre-heading to grains is a determinant of grain yield, but also plays an important role in adaptation to unfavorable environments during post-heading in rice. In this study, field experiments were conducted to determine the critical factors that regulate biomass translocation in rice. Biomass translocation and production characteristics of two rice hybrids (Guiliangyou 2 and Y-liangyou 1) were compared between two site-year environments (Naning-2014 and Yongan-2018). Results showed that biomass translocation parameters (biomass translocation amount and rate and contribution of biomass translocation to filled grain weight) and ratio of biomass production during pre-heading to post-heading (BPpre/BPpost ratio) decreased in Guiliangyou 2 but increased in Y-liangyou 1 with the environment change from Nanning-2014 to Yongan-2018. The decreased BPpre/BPpost in Guiliangyou 2 was attributable to increased biomass production during post-heading (BPpost), while the increased BPpre/BPpost ratio in Y-liangyou 1 was due to increased biomass production during pre-heading (BPpre). Higher cumulative incident solar radiation and larger diurnal temperature variation were responsible for the increased BPpost in Guiliangyou 2 and the increased BPpre in Y-liangyou 1 grown in Yongan in 2018 compared to in Nanning in 2014. The results of this study indicate that changes in biomass translocation and production with environment (climate) in rice are dependent on genotype and that the BPpre/BPpost ratio is an important factor regulating biomass translocation in rice.

OsPEX5 regulates rice spikelet development through modulating jasmonic acid biosynthesis.

Spikelet is the primary reproductive structure and a critical determinant of grain yield in rice. The molecular mechanisms regulating rice spikelet development still remain largely unclear. Here, we report that mutations in OsPEX5, which encodes a peroxisomal targeting sequence 1 (PTS1) receptor protein, cause abnormal spikelet morphology. We show that OsPEX5 can physically interact with OsOPR7, an enzyme involved in jasmonic acid (JA) biosynthesis and is required for its import into peroxisome. Similar to Ospex5 mutant, the knockout mutant of OsOPR7 generated via CRISPR-Cas9 technology has reduced levels of endogenous JA and also displays an abnormal spikelet phenotype. Application of exogenous JA can partially rescue the abnormal spikelet phenotype of Ospex5 and Osopr7. Furthermore, we show that OsMYC2 directly binds to the promoters of OsMADS1, OsMADS7 and OsMADS14 to activate their expression, and subsequently regulate spikelet development. Our results suggest that OsPEX5 plays a critical role in regulating spikelet development through mediating peroxisomal import of OsOPR7, therefore providing new insights into regulation of JA biosynthesis in plants and expanding our understanding of the biological role of JA in regulating rice reproduction.

A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population.

Increasing agricultural productivity is one of the most important goals of plant science research and imperative to meet the needs of a rapidly growing population. Rice (Oryza sativa L.) is one of the most important staple crops worldwide. Grain size is both a major determinant of grain yield in rice and a target trait for domestication and artificial breeding. Here, a genome-wide association study of grain length and grain width was performed using 996,722 SNP markers in 270 rice accessions. Five and four quantitative trait loci were identified for grain length and grain width, respectively. In particular, the novel grain size gene OsSNB was identified from qGW7, and further results showed that OsSNB negatively regulated grain size. Most notably, knockout mutant plants by CRISPR/Cas9 technology showed increased grain length, width, and weight, while overexpression of OsSNB yielded the opposite. Sequencing of this gene from the promoter to the 3’-untranslated region in 168 rice accessions from a wide geographic range identified eight haplotypes. Furthermore, Hap 3 has the highest grain width discovered in japonica subspecies. Compared to other haplotypes, Hap 3 has a 225 bp insertion in the promoter. Based on the difference between Hap 3 and other haplotypes, OsSNB_Indel2 was designed as a functional marker for the improvement of rice grain width. This could be directly used to assist selection toward an improvement of grain width. These findings suggest OsSNB as useful for further improvements in yield characteristics in most cultivars.

The PLATZ Transcription Factor GL6 Affects Grain Length and Number in Rice.

Grain size is one of the key determinants of grain yield. Although a number of genes that control grain size in rice (Oryza sativa) have been identified, the overall regulatory networks behind this process remain poorly understood. Here, we report the map-based cloning and functional characterization of the quantitative trait locus GL6, which encodes a plant-specific plant AT-rich sequence- and zinc-binding transcription factor that regulates rice grain length and spikelet number. GL6 positively controls grain length by promoting cell proliferation in young panicles and grains. The null gl6 mutant possesses short grains, whereas overexpression of GL6 results in large grains and decreased grain number per panicle. We demonstrate that GL6 participates in RNA polymerase III transcription machinery by interacting with RNA polymerase III subunit C53 and transcription factor class C1 to regulate the expression of genes involved in rice grain development. Our findings reveal a further player involved in the regulation of rice grain size that may be exploited in future rice breeding.

Fine mapping of qTGW10-20.8, a QTL having important contribution to grain weight variation in rice

Grain weight is one of the most important determinants of grain yield in rice. In this study, QTL analysis for grain weight, grain length, and grain width was performed using populations derived from crosses between major parental lines of three-line indica hybrid rice. A total of 27 QTL for grain weight were detected using three recombinant inbred line populations derived from the crosses Teqing/IRBB lines, Zhenshan 97/Milyang 46, and Xieqingzao/Milyang 46. Of these, 10 were found in only a single population and the other 17 in two or all three populations. Nine of the 17 common QTL were located in regions where no QTL associated with grain weight have been cloned and one was selected for fine-mapping. Eight populations segregating in an isogenic background were derived from one F7 residual heterozygote of Teqing/IRBB52. The target QTL, qTGW10-20.8 controlling grain weight, grain length, and grain width, was localized to a 70.7-kb region flanked by InDel markers Te20811 and Te20882 on the long arm of chromosome 10. The QTL region contains seven annotated genes, of which six encode proteins with known functional domains and one encodes a hypothetical protein. One of the genes, Os10g0536100 encoding the MIKC-type MADS-box protein OsMADS56, is the most likely candidate for qTGW10-20.8. These results provide a basis for cloning qTGW10-20.8, which has an important contribution to grain weight variation in rice.