OsDA1 positively regulates grain width in rice

The size and shape of rice grains influence their yield and commercial value.We investigated the role of OsDA1,a rice homolog of the Arabidopsis DA1 gene,in regulating grain size and shape.OsDA1 was highly expressed in young spikelets and glumes.Its overexpression led to enlarged seeds with increased width and decreased length/width ratio(LWR)and knocking out OsDA1 reduced grain width and increased grain length and LWR.A R310K point mutation in the DA1-like domain is a potential target for breeding for increased grain width and length.OsDA1 interacted with TCP gene-family proteins to regulate grain size and shape.Our findings deepen our understanding of the molecular mechanisms underlying grain size regulation and provide useful information for improving grain yield.

Fine mapping and characterization of a major QTL for grain length,QGl.cau-2D.1,that has pleiotropic effects in synthetic allohexaploid wheat

Grain size is one of the determinants of grain yield,and identifying the genetic loci that control grain size will be helpful for increasing grain yield.In our previous study,a quantitative trait locus(QTL)for grain length(GL),QGl.cau-2D.1,was identified from an F2 population developed from the cross between the natural(TAA10)and synthetic(XX329)allohexaploid wheat.In the present study,we mainly fine mapped and validated its genetic effects.To this end,multiple near-isogenic lines(NILs)were obtained through marker-assisted selection with TAA10 as the recurrent parent.The secondary populations derived from 25 heterozygous recombinants were used for fine mapping of QGl.cau-2D.1,and the allele from XX329 significantly increased GL,thousand-grain weight(TGW),total spikelet number per spike(TSN)and spike compactness(SC).Using NILs for XX329(2D+)and TAA10(2D−),we determined the genetic and pleiotropic effects of QGl.cau-2D.1.The target sequences were aligned with the wheat reference genome RefSeq v2.1 and spanned an~0.9 Mb genomic region.TraesCS2D03G0114900(ortholog of Os03g0594700)was predicted as the candidate gene based on whole-genome re-sequencing and expression analyses.In summary,the map-based cloning of QGl.cau-2D.1 will be useful for improving grain weight with enhanced GL and TSN.

Poaceae Orthologs of Rice OsSGL,DUF1645 Domain-Containing Genes,Positively Regulate Drought Tolerance,Grain Length and Weight in Rice

Grain yield is a polygenic trait that can be influenced by environmental factors and genetic compositions at all plant growth stages.Currently,the molecular mechanisms behind the coordination of the interaction between grain yield-related traits remain unknown.In this study,we characterized the function of four STRESS_tolerance and GRAIN_LENGTH(Os SGL)Poaceae ortholog genes that are transcribed into DUF1645 domain-containing proteins in relation to the grain length,grain weight,and drought stress-tolerance of rice.The transgenic plants with overexpressing or heterologous high levels of Poaceae OsSGL ortholog genes exhibited longer grain size than the wild type plants.Larger cells were seen in panicles of the four transgenic lines with paraffin sectioning and scanning electron microscopy analyses.In addition,four Poaceae OsSGL ortholog genes positively affected the drought tolerance of rice.Four transgenic plants displayed higher resistance to drought stress at the seedling and vegetative stages.RNA-sequencing and qRT-PCR results indicated that over-or heterologous-expression of four Poaceae OsSGL ortholog genes also affected the transcriptome of rice plants.These genes may play a role in auxin and cytokinin biosynthesis and their transduction pathways.Taken together,these results suggested that the four OsSGL orthologs have a conserved function in the regulation of stress-tolerance and cell growth by modulating hormonal biosynthesis and signaling.

Fine mapping and candidate gene analysis of qGL10 affecting rice grain length

Grain size influences the yield and quality of rice(Oryza sativa L.),and grain length is one of the component traits of grain size.In this study,a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428,with short grain size,as the recipient parent and indica rice cultivar ZYX,with long grain size,as the donor parent,by multi-generation backcrossing and selfing.BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus.The major QTL,tentatively named qGL10,for grain length was located in a 128.45 kb region of chromosome 10.Combined with haplotype analysis of rice varieties,expression pattern analysis of candidate genes suggested LOC_Os10g39130(OsMADS56)as a candidate gene.Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region.Further haplotype analysis suggested that SNP9(G/A)located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3.These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties.

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci （QTLs）. We earlier identified a major QTL that controls rice grain width and weight, GW5, which was mapped to a recombination hotspot on rice chromosome 5. To gain a better understanding of how GW5 controls rice grain width, we conducted fine mapping of this locus and uncovered a 1 212-bp deletion associated with the increased grain width in the rice cultivar Asominori, in comparison with the slender grain rice IR24. In addition, genotyping analyses of 46 rice cultivars revealed that this deletion is highly correlated with the grain-width phenotype, suggesting that the GW5 deletion might have been selected during rice domestication. GW5 encodes a novel nuclear protein of 144 amino acids that is localized to the nucleus. Furthermore, we show that GW5 physically interacts with polyubiquitin in a yeast two-hybrid assay. Together, our results suggest that GW5 represents a major QTL underlying rice width and weight, and that it likely acts in the ubiquitin-proteasome pathway to regulate cell division during seed development. This study provides novel insights into the molecular mechanisms controlling rice grain development and suggests that GW5 could serve as a potential tool for high-yield breeding of crops.

QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F_2 Population

Mapping and isolation of quantitative trait loci(QTLs)or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding.To identify the QTLs controlling grain size and weight,we developed a near isogenic line F_2(NIL-F_2)population,which was derived from a residual heterozygous plant in an F_7 generation of recombinant inbred line(RIL).With the completion of more than 30×whole genome re-sequencing of the parents,two DNA bulks for large and small grains,a total of 58.94 Gb clean nucleotide data were generated.A total of455 262 single nucleotide polymorphisms(SNPs)between the parents were identified to perform bulked QTL-seq.A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5.We designated the major QTL in the candidate region as q TGW5.3.Then,q TGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F_2 population.Furthermore,recombinants and the progeny tests delimited the candidate region of q TGW5.3 to 1.13 Mb,flanked by HX5009(15.15 Mb)and HX5003(16.28 Mb).A set of NILs,selected from the F_2 population,was developed to evaluate the genetic effect of q TGW5.3.Significant QTL effects were detected on grain length,grain width and 1000-grain weight of H12-29 allele with 1.14 mm,-0.11 mm and 3.11 g,which explained 99.64%,95.51%and 97.32%of the phenotypic variations,respectively.

Mapping of qGL7-2, a grain length QTL on chromosome 7 of rice

A residual heterozygous line （RHL） carrying a heterozygous segment between two S SR loci RM 11 and RM134 on the rice chromo- some 7 was selected from a set of recombinant inbred lines from the cross D50 （javanica）/HB277 （indica）. The former parent produces much longer grains than the latter. Selfed progenies of this selection were analyzed genotypically （SSRs） and phenotypically （grain length）. Grain length was discontinuously variable in the mapping populations, allowing for the placement of this QTL qGL7-2 within a -4.8 cM interval defined by RM351 and RM234. A set of new markers within this region were developed, which narrowed the QTL to a 278 kb region defined by the markers Indell and RM21945. This region contains 49 predicted genes. The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.

A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice

Grain size is one of the most important factors that control rice yield,as it is associated with grain weight(GW).To date,dozens of rice genes that regulate grain size have been isolated;however,the regulatory mechanism underlying GW control is not fully understood.Here,the quantitative trait locus qGL5 for grain length(GL)and GW was identified in recombinant inbred lines of 9311 and Nipponbare(NPB)and fine mapped to a candidate gene,OsAUX3.Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW.RNA sequencing,gene expression quantification,dual-luciferase reporter assays,chromatin immunoprecipitation-quantitative PCR,and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3.OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter,covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung,and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells.Furthermore,we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing.Taken together,our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice,providing a potential target for the improvement of rice yield.

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

Grain size is an important determinant of grain weight and yield in rice.Although several genes related to grain size have been identified,natural variations in these genes that affect grain size are poorly characterized.Here,we describe the grain length QTL GL10,encoding MADS56,which positively regulates grain length and grain weight.A natural allelic variation of NIL-gl10,containing an~1.0-kb deletion in the first exon that abolishes its transcription,results in shorter grain length,lower grain weight and delayed flowering in gl10 plants.The knockout of GL10 in the HJX74 background leads to grain phenotypes similar to that of NIL-gl10,while overexpression of GL10 results in increased grain length and weight and earlier heading date.GL10 regulates grain length by promoting greater longitudinal cell growth in the grain glume.Additionally,GL10 participates in the regulation of gibberellic acid(GA)signaling pathway genes in young panicle tissues.Analysis of GL10 haplotypes shows obvious divergence between the japonica and indica lineages.Our findings reveal an allelic variation of GL10 that may explain differences in grain length among modern cultivars and could be used to breed rice varieties with optimized grain shape.

GRAIN LENGTH AND AWN 1 negatively regulates grain size in rice

Grain size is an important factor determining yield in rice. Here, we identified a recessive mutant gene, grain length and awn 1 (gla1), which caused a significant increase in grain length and weight, and was associated with long awns. The gla1 mutation was mapped to a single-nucleotide polymorphism in a gene encoding a cytoplasmically-localized mitogen-activated protein kinase (MAPK) phosphatase. Overexpression of GLA1 caused a decrease in grain length, and the GLA1 protein interacted with OsMAPK6. These results suggest that GLA1 may serve as a negative regulator of the OsMAPKK4-OsMAPK6 cascade, controlling grain size via the dephosphorylation of OsMAPK6.

A single nucleotide substitution at 5'-UTR of GSN1 represses its translation and leads to an increase of grain length in rice

Rice grain size is an important trait that affects rice yield and quality, and thus the identification of genes related to grain size is of great significance for improving rice yield and quality. Many genes related to grain size, such as DEP1(Huang et al., 2009),GW5(Liu et al., 2017).

Identification and validation of major QTL for grain size and weight in bread wheat(Triticum aestivum L.)

Grain size and weight are key components of wheat yield.Exploitation of major underlying quantitative trait loci(QTL)can improve yield potential in wheat breeding.A recombinant inbred line(RIL)population was constructed to detect QTL for thousand-grain weight(TGW),grain length(GL)and grain width(GW)across eight environments.Genomic regions associated with grain size and grain weight were identified on chromosomes 4A and 6A using bulked segregant exome sequencing(BSE-Seq)analysis.After constructing genetic maps,six major QTL detected in at least four individual environments and in best linear unbiased estimator(BLUE)datasets,explained 7.50%-23.45%of the phenotypic variation.Except for QGl.cib-4A,the other five QTL were co-located in two regions,namely QTgw/Gw.cib-4A and QTgw/Gw/Gl.cib-6A.Interactions of these QTL were analyzed.Unlike QTgw/Gw/Gl.cib-6A,QTgw/Gw.cib-4A and QGl.cib-4A had no effect on grain number per spike(GNS).The QTL were validated in a second cross using Kompetitive Allele Specific PCR(KASP)markers.Since QTgw/Gw.cib-4A was probably a novel locus,it and the KASP markers reported here can be used in wheat breeding.TraesCS4A03G0191200 was predicted to be potential candidate gene for QTgw/Gw.cib-4A based on the sequence differences,spatiotemporal expression patterns,gene annotation and haplotype analysis.Our findings will be useful for fine mapping and for marker-assisted selection in wheat grain yield improvement.

A gain-of-function mutation of OsMAPK6 leads to long grain in rice

Grain size is one of the most important agronomic traits controlling grain yield. Development of novel germplasm with large grains would be beneficial for crop improvement. We report the genetic identification and functional analysis of the LONG GRAIN 6(LOG6) gene, which is identical to MITOGENACTIVATED PROTEIN KINASE 6(OsMAPK6), affecting grain length of rice. Map-based cloning revealed that the long-grain phenotype of log6-D results from a glutamine(E) to lysine(K) mutation in the conserved TEY motif of OsMAPK6. In near-isogenic lines(NILs), the log6-D allele increased grain length and grain yield of Guichao 2(GC2), Teqing(TQ), and 93–11. Sequence analysis revealed 10 OsMAPK6 haplotypes,with xian(indica) and geng(japonica) harboring different haplotypes. Our findings shed light on the function of MAPKs and offer a novel dominant allele for improving the grain yield of rice.

Creation of Long-grain Fragrant Japonica Rice by Genome Editing

To create the japonica germplasm with long grain and fragrance,we edited GS3 and OsBADH2 of a japonica rice cultivar Chunjiang 151 by using CRISPR/Cas9 system for multiplex genome editing.10 long-grain fragrant japonica rice plants without transgenic components were obtained.Compared with those of Chunjiang 151,the grain length,thousand-grain weight,and yield per plant of the edited line increased 12.20%,18.45%,and 8.31%,respectively.We created the fragrant japonica rice line with improved grain length and yield,which enriched the germplasm resource of japonica rice and provided reference for the improvement of rice quality.

Fine-Mapping of qTGW1.2a, a Quantitative Trait Locus for 1000-Grain Weight in Rice

Thousand-grain weight (TGW) is a key component of grain yield in rice. This study was conducted to validate and fine-map qTGW1.2a, a quantitative trait locus for grain weight and grain size previously located in a 933.6-kb region on the long arm of rice chromosome 1. Firstly, three residual heterozygotes (RHs) were selected from a BC2F11 population of the indica rice cross Zhenshan 97 (ZS97)///ZS97//ZS97/Milyang 46. The heterozygous segments in these RHs were arranged successively in physical positions, forming one set of sequential residual heterozygotes (SeqRHs). In each of the populations derived, non-recombinant homozygotes were identified to produce near isogenic lines (NILs) comprising the two homozygous genotypes. The NILs were tested for grain weight, grain length and grain width. QTL analyses for the three traits were performed. Then, the updated QTL location was followed for a new run of SeqRHs identification-NIL development-QTL mapping. Altogether, 11 NIL populations derived from four sets of SeqRHs were developed and used. qTGW1.2a was finally delimitated into a 77.5-kb region containing 13 annotated genes. In the six populations segregating this QTL, which were in four generations and were tested across four years, the allelic direction of qTGW1.2a remained consistent and the genetic effects were stable. For TGW, the additive effects ranged from 0.23 to 0.38 g and the proportions of phenotypic variance explained ranged from 26.15% to 41.65%. These results provide a good foundation for the cloning and functional analysis of qTGW1.2a.

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

Grain weight is one of themost important determinants of grain yield in rice.In this study,QTL analysis for grain weight,grain length,and grainwidthwas 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 onewas 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,ofwhich 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.

Identification of long-grain chromosome segment substitution line Z744 and QTL analysis for agronomic traits in rice

Length of grain affects the appearance, quality, and yield of rice. A rice long-grain chromosome segment substitution line Z744, with Nipponbare as the recipient parent and Xihui 18 as the donor parent, was identified. Z744 contains a total of six substitution segments distributed on chromosomes(Chrs.) 1, 2, 6, 7, and 12, with an average substitution length of 2.72 Mb. The grain length, ratio of length to width, and 1 000-grain weight of Z744 were significantly higher than those in Nipponbare. The plant height, panicle number, and seed-set ratio in Z744 were significantly lower than those in Nipponbare, but they were still 78.7 cm, 13.5 per plant, and 86.49%, respectively. Furthermore, eight QTLs of different traits were identified in the secondary F2 population, constructed by Nipponbare and Z744 hybridization. The grain weight of Z744 was controlled by two synergistic QTLs(qGWT1 and q GWT7) and two subtractive QTLs(qGWT2 and qGWT6), respectively. The increase in the grain weight of Z744 was caused mainly by the increase in grain length. Two QTLs were detected, qGL1 and qGL7-3, which accounted for 25.54 and 15.58% of phenotypic variation, respectively. A Chi-square test showed that the long-grain number and the short-grain number were in accordance with the 3:1 separation ratio, which indicates that the long grain is dominant over the short-grain and Z744 was controlled mainly by the principal effect qGL1. These results offered a good basis for further fine mapping of qGL1 and further dissection of other QTLs into single-segment substitution lines.

Effects of Interface and Grain Boundary on the Electrical Resistivity of Cu/Ta Multilayers

The electrical resistivity of Cu/Ta multilayers deposited by radio-frequency magnetron sputtering on a polyimide substrate was investigated as a function of monolayer thickness. It is found that the resistivity of the multilayer increases with decreasing monolayer thickness from 500 nm to 10 nm. Two significant effects of layer interface scattering and grain boundary scattering were identified to dominate electronic transportation behavior in the Cu/Ta multilayers at different length scales. The electrical resistivity of the multilayer with monolayer thickness ranging from nanometer to submicron scales can be well described by a newly-proposed Fuchs-Sandheimair （F-S） and Mayadas-Shatzkes （M-S） combined model.

A natural allele of TAW1 contributes to high grain number and grain yield in rice

Grain number per panicle (GNP) is a complex trait controlled by quantitative trait loci (QTL),directly determining grain yield in rice.Identifying GNP-associated QTL is desirable for increasing rice yield.A rice chromosome segment substitution line (CSSL),F771,which showed increased panicle length and GNP,was identified in a set of CSSLs derived from a cross between two indica cultivars,R498 (recipient) and WY11327 (donor).Genetic analysis showed that the panicle traits in F771 were semidominant and controlled by multiple QTL.Six QTL were consistently identified by QTL-seq analysis.Among them,the major QTL q PLN10 for panicle length and GNP was localized to a 121-kb interval between markers N802 and N909 on chromosome 10.Based on quantitative real-time PCR and sequence analysis,TAWAWA1(TAW1),a known regulator of rice inflorescence architecture,was identified as the candidate gene for q PLN10.A near-isogenic line,NIL-TAW1,was developed to evaluate its effects.In comparison with the recurrent parent R498,NIL-TAW1 showed increased panicle length (14.0%),number of secondary branches (20.9%) and GNP (22.0%),and the final grain yield per plant of NIL-TAW1 was increased by18.6%.Transgenic experiments showed that an appropriate expression level of TAW1 was necessary for panicle development.Haplotype analysis suggested that the favorable F771-type (Hap 13) of TAW1was introduced from aus accessions and had great potential value in high-yield breeding both in indica and japonica varieties.Our results provide a promising genetic resource for rice grain yield improvement.

Relationship between the eating quality and the physico-chemical properties of high grain quality rice in China

Relationship between eating quality(EQ)andphysico-chemical properties of 78 high grainquality rice varieties,45 indica and 33 japoni-ca,were studied in 1995.The samples werecollected from different rice growing regions in20 provinces.The physico-chemical proper-ties,including grain length(GL),length towidth ratio(L/W),chalky grain rate(CG),chalkiness(CH),translucency(TR),gela-tinization temperature(GT,measured by alka-li spreading value),gel consistency(CA2),amylase content(AC),and protein content(PC)were measured according to the standard