Brittle culm 25, which encodes an UDP-xylose synthase, affects cell wall properties in rice

Because plant mechanical strength influences plant growth and development,the regulatory mechanisms underlying cell-wall synthesis deserve investigation.Rice mutants are useful for such research.We have identified a novel brittle culm 25(bc25)mutant with reduced growth and partial sterility.BC25 encodes an UDP-glucuronic acid decarboxylase involved in cellulose synthesis and belongs to the UXS family.A single-nucleotide mutation in BC25 accounts for its altered cell morphology and cellwall composition.Transmission electron microscopy analysis showed that the thickness of the secondary cell wall was reduced in bc25.Monosaccharide analysis revealed significant increases in content of rhamnose and arabinose but not of other monosaccharides,indicating that BC25 was involved in xylose synthesis with some level of functional redundancy.Enzymatic assays suggested that BC25 functions with high activity to interconvert UDP-glucuronic acid(UDP-Glc A)and UDP-xylose.GUS staining showed that BC25 was ubiquitously expressed with higher expression in culm,root and sheath,in agreement with that shown by quantitative real-time(q RT)-PCR.RNA-seq further suggested that BC25 is involved in sugar metabolism.We conclude that BC25 strongly influences rice cell wall formation.

Genetic and environmental control of rice tillering

Increasing tiller number is a target of high-yield rice breeding. Identification of tiller-defect mutants and their corresponding genes is helpful for clarifying the molecular mechanism of rice tillering. Summarizing research progress on the two processes of rice tiller formation, namely the formation and growth of axillary meristem, this paper reviews the effects of genetic factors, endogenous hormones, and exogenous environment on rice tillering, finding that multiple molecular mechanisms and signal pathways regulating rice tillering cooperate rice tillering, and discusses future research objectives and application of its regulatory mechanism. Elucidation of theis mechanism will be helpful for breeding high-yielding rice cultivars with ideal plant type via molecular design breeding.

LAZY1 controls rice shoot gravitropism through regulating polar auxin transport

米饭(Oryza sativa L.) 的分蘖角度是贡献粮谷生产的一个重要农学的特点，并且长为完成理想的植物建筑学改进谷物产量吸引了品种 ers 的注意。尽管庞大的努力在过去的十年被作了与极其传播或协议到 ers 为止学习异种，位于谷物庄稼的分蘖角度的控制下面的分子的机制仍然保持未知。这里，我们报导克隆调整米饭分蘖角度被控制的射击 gravitropism 的 LAZY1 (LA1 ) 基因。我们显示出那 LA1，新奇草特定的基因，是速度集合并且空间地表示，并且在极的植物生长素运输起一个否定作用(轻拍) 。LA1 的 Loss-of-function PATgreatly 提高并且因此在射击改变内长的 IAA 分发，导致 reducedgravitropism，并且因此，米饭的分蘖,枝散布显型种。

Genetic analysis and fine-mapping of a dwarfing with withered leaf-tip mutant in rice

A dwarf mutant of rice （Oryza sativa L.） by mutagenesis of ethylene methylsulfonate （EMS） treatment from Nipponbare was identified. The mutant exhibited phenotypes of dwarfism and withered leaf tip （dwll）. Based on the intemode length of dwll, this mutant belongs to the dm type of dwarfing. Analysis of elongation of the second sheath and m-amylase activity in endosperm showed that the phenotype caused by dwll was insensitive to gibberellin acid treatment. Using a large F2 population derived from a cross between the dwll and an indica rice variety, TN1, the DWL1 gene was mapped to the terminal region of the long arm of chromosome 3. Fine-mapping delimited it into a 46 kb physical distance between two STS markers, HL921 and HL944, where 6 open reading frames were predicted. Cloning of DWL1 will contribute to dissecting molecular mechanism that regulates plant height in rice, which will be beneficial to molecular assisted selection of this important trait.

Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen-deficiency tolerance in rice

The development of rice cultivars with improved nitrogen use efficiency(NUE)is desirable for sustainable agriculture.Achieving this goal depends in part on understanding how rice responds to low soil nitrogen(N)and identifying causative genes underlying this trait.To identify quantitative trait loci(QTL)or genes associated with low N response,we conducted a genome-wide association study(GWAS)using a diverse panel of 230 rice accessions and performed a transcriptomic investigation of rice accessions with differential responses to low N stress at two N levels.We detected 411 GWAS-associated genes in 5 QTL and 2722 differentially expressed genes in response to low N,of which 24 were identified by both methods and ranked according to gene annotations,literature queries,gene expression,and genetic diversity analysis.The large-scale datasets obtained from this study reveal low N-responsive characteristics and provide insights towards understanding the regulatory mechanisms of N-deficiency tolerance in rice,and the candidate genes or QTL would be valuable resources for increasing rice NUE via molecular biotechnology.

Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway

Tillers are unique inflorescence-like branches in grasses,and their number determines the panicle number,plant architecture,and yield(Shang et al.,2021).Tiller formation mainly undergoes axillary meristem(AM)initiation and tiller bud outgrowth(Wang et al.,2018;Yan et al.,2023).The rice(Oryza sativa)KNOX gene OSH1 is expressed in AMs,and an osh1 mutant produces fewer tillers(Tanaka et al.,2015).

A Rare Allele of GS2 Enhances Grain Size anc Grain Yield in Rice

Grain size determines grain weight and affects grain quality. Several major quantitative trait loci （QTLs） regulating grain size have been cloned; however, our understanding of the underlying mechanism that regulates the size of rice grains remains fragmentary. Here, we report the cloning and characterization of a dominant QTL, GRAIN SIZE ON CHROMOSOME 2 （GS2）, which encodes Growth-Regulating Factor 4 （OsGRF4）, a transcriptional regulator. GS2 localizes to the nucleus and may act as a transcription activator. A rare mutation of GS2 affecting the binding site of a microRNA, OsmiR396c, causes elevated expression of GS2/OsGRF4. The increase in GS2 expression leads to larger cells and increased numbers of cells, which thus enhances grain weight and yield. The introduction of this rare allele of GS2/OsGRF4 into rice cultivars could significantly enhance grain weight and increase grain yield, with possible applications in breeding high-yield rice varieties.

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice

The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high- yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/ GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with ｜Q domains, which interacts with the rice calmodulin protein, OsCaMl-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 （GSE5, GSE5DELl＋IN1, and GSESDEL~ in cultivated rice were identified based on the deletion/insertion type in its pro- moter region. We demonstrated that a 950-bp deletion （DELl） in indica varieties carrying the GSE5DELl＋IN1 haplotype and a 1212-bp deletion （DEL2） in japonica varieties carrying the GSE5DEL2 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice acces- sions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice.

A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice

Plant architecture is a complex agronomic trait and a major factor of crop yield,which is affected by several important hormones.Strigolactones(SLs)are identified as a new class hormoneinhibiting branching in many plant species and have been shown to be involved in various developmental processes.Genetical and chemical modulation of the SL pathway is recognized as a promising approach to modify plant architecture.However,whether and how the genes involved in the SL pathway could be utilized in breeding still remain elusive.Here,we demonstrate that a partial loss-of-function allele of the SL biosynthesis gene,HIGH TILLERING AND DWARF 1/DWARF17(HTD1/D17),which encodes CAROTENOID CLEAVAGE DIOXYGENASE 7(CCD7),increases tiller number and improves grain yield in rice.We found that the HTD1 gene had been widely utilized and co-selected with Semidwarf 1(SD1),both contributing to the improvement of plant architecture in modern rice varieties since the Green Revolution in the 1960s.Understanding how phytohormone pathway genes regulate plant architecture and how they have been utilized and selected in breeding will lay the foundation for developing the rational approaches toward improving crop yield.

The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice

Regulation of seed size is a key strategy for improving crop yield and is also a basic biological question.However,the molecular mechanisms by which plants determine their seed size remain elusive.Here,we report that the GW2-WG1-OsbZIP47 regulatory module controls grain width and weight in rice.WG1,which encodes a glutaredoxin protein,promotes grain growth by increasing cell proliferation.Interestingly,WG1 interacts with the transcription factor OsbZIP47 and represses its transcriptional activity by associating with the transcriptional co-repressor ASP1,indicating that WG1 may act as an adaptor protein to recruit the transcriptional co-repressor.In contrary,OsbZIP47 restricts grain growth by decreasing cell proliferation.Further studies reveal that the E3 ubiquitin ligase GW2 ubiquitinates WG1 and targets it for degradation.Genetic analyses confirm that GW2,WG1,and OsbZIP47 function in a comm on pathway to control grain growth.Taken together,ourfindi ngs reveal a genetic and molecular framework for the control of grain size and weight by the GW2-WG1-OsbZIP47 regulatory module,providing new targets for improving seed size and weight in crops.

ABNORMAL FLOWER AND GRAIN 1 encodes OsMADS6 and determines palea identity and affects rice grain yield and quality

The palea and lemma are floral organ structures unique to grasses;these structures form the hull and directly affect grain size and quality. However, the molecular mechanisms controlling the development of the hull are not well understood. In this study, we characterized the rice(Oryza sativa) abnormal flower and grain1(afg1) mutant, a new allele of OsMADS6. Similar to previously characterized osmads6 alleles, in the afg1 floret, the palea lost its marginal region and acquired the lemma identity. However, in contrast to other osmads6 alleles, the afg1 mutant showed altered grain size and grain quality, with decreased total starch and amylose contents, and increased protein and soluble sugar contents. The analysis of transcriptional activity suggested that AFG1 is a transcriptional activator and may affect grain size by regulating the expression levels of several genes related to cell expansion and proliferation in the afg1 mutant. These results revealed that AFG1 plays an important role in determining palea identity and affecting grain yield and quality in rice.

Genetic Analysis and Fine Mapping of Two Genes for Grain Shape and Weight in Rice

To identify genetic loci controlling grain weight, an elite indica rice variety, Baodali, with large grains was identified and used in this study. Its derived F2, F3 and BC2 F2 with another japonica rice variety Zhonghua 11 were used as mapping populations. Linkage analyses demonstrated that two genes controlling grain weight, designated as GW3 and GW6, were mapped to chromosome 3 and chromosome 6, respectively. Fine mapping delimited GW3 to a 122 kb physical distance between two sequence tagged site markers （WGWt6 and WGW19） containing 16 open reading frames annotated by The Institute for Genomic Research （http：//www.tigr.org）. GW6 was further mapped between two simple sequence repeat markers （RM7179 and RM3187）. These results are useful for both marker assisted selection of grain weight, and for further cloning of GW genes, which will contribute to the dissection of the molecular mechanism underlying grain weight in rice.

ALK,the Key Gene for Gelatinization Temperature,is a Modifier Gene for Gel Consistency in Rice

Gelatinization temperature（GT） is an important parameter in evaluating the cooking and eating quality of rice.Indeed,the phenotype,biochemistry and inheritance of GT have been widely studied in recent times.Previous map-based cloning revealed that GT was controlled by ALK gene,which encodes a putative soluble starch synthase II-3.Complementation vector and RNAi vector were constructed and transformed into Nipponbare mediated by Agrobacterium.Phenotypic and molecular analyses of transgenic lines provided direct evidence for ALK as a key gene for GT.Meanwhile,amylose content,gel consistency and pasting properties were also affected in transgenic lines.Two of four nonsynonymous single nucleotide polymorphisms in coding sequence of ALK were identified as essential for GT.Based on the single nucleotide polymorphisms（SNPs）,two new sets of SNP markers combined with one cleaved amplified polymorphic sequence marker were developed for application in rice quality breeding.

Xiaowei, a New Rice Germplasm for Large-Scale Indoor Research

Dear Editor,Rice (Oryza sativa)is a model monocot plant for biological studies due to its relatively small genome,rich germplasm resources,and high-efficiency transformation methods.Although significant progress has been made in rice genomics and functional genomics research (Li et al.,2018),large-scale indoor research toward better understanding of rice biology is hampered by its long growth period and extreme dependence on the natural environment for cultivation.There are some rice germplasms that have a short growth period and short plant height,such as Kitaake.

Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid （DH） population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus （QTL） for three related traits of paniclelayer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniforrnity in two locations：Hangzhou （HZ） and Hainan （HN）. A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH-4 and qTPH-8 were co-located with the QTLs for qLPH-4 and qLPH-8, which were only significant in the HZ environment, whereas the qTPH-6 and qLPH-6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD-10.1 and qPLD-10.2, were closely linked to qTPH-10, and they might have been at the same locus. One QTL, qPLD-3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD-3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD-3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice.

Quantitative Trait Loci Mapping of Flag-leaf Ligule Length in Rice and Alignment with ZmLG1 Gene

A doubled haploid （DH） population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid‘CJ06＇/‘TNI＇, was used in this study. Ligule lengths of flag leaf were investigated for quantitative trait loci （QTL） mapping using the DH population. Five QTLs （qLL-2, qLL.4, qLL-6, qLL-IO and qLL-12） controlling the ligule length （LL） were detected on chromosomes 2, 4, 6, 10 and 12, with the variances explained 11.4%, 13.6%, 27.8%, 22.1% and 11.0%, respectively. Using four known genes of ZmGL1, ZmGL2, ZmGL3 and ZmGL4 in maize from the MaizeGDB, their homologs in rice were aligned and integrated into the existing simple sequence repeats linkage map by in silico mapping. A ZmLG1 homolog gene, OsLG1 encoding a squamosa promoter binding protein, was located between the markers RM255 and RM280, which is just identical to the interval of qLL.4 on the long arm of chromosome 4. The results are beneficial to dissection of the ligule molecular mechanism and the study of cereal evolution.

Genetic analysis of leaffolder resistance in rice

A double haploid （DH） population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid ‘CJ06＇/‘TNI＇, was used to investigate the genetic basis for rice leaffolder resistance. Using a constructed molecular linkage map, five QTLs for rolled leaves were detected on chromosomes 1, 2, 3, 4, and 8. The positive alleles from C J06 on chromosomes 3, 4, and 8 increased the resistance to rice leaffolder, and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolder. The interactions between QTLs were identified and tested, and four conditional interactions were acquired for resistance to rice leaffolder. These loci were located on chromosomes 2, 9, 10, and 11, respectively. QTL pyramiding indicated that the positive alleles affect resistance to leaffolder. The prospective application of this data in rice breeding was also discussed.

Xa7, a new executor R gene that confers durable and broad-spectrum resistance to bacterial blight disease in rice

Bacterial blight(BB)is a globally devastating rice disease caused by Xanthomonas oryzae pv.oryzae(Xoo).The use of disease resistance(R)genes in rice breeding is an effective and economical strategy for the control of this disease.Nevertheless,a majority of R genes lack durable resistance for long-term use under global warming conditions.Here,we report the isolation of a novel executor R gene,Xa7,that confers extremely durable,broad-spectrum,and heat-tolerant resistance to Xoo.The expression of Xa7 was induced by incompatible Xoo strains that secreted the transcription activator-like effector(TALE)AvrXa7 or PthXo3,which recognized effector binding elements(EBEs)in the Xa7 promoter.Furthermore,Xa7 induction was faster and stronger under high temperatures.Overexpression of Xa7 or co-transformation of Xa7 with avrXa7 triggered a hypersensitive response in plants.Constitutive expression of Xa7 activated a defense response in the absence of Xoo but inhibited the growth of transgenic rice plants.In addition,analysis of over 3000 rice varieties showed that the Xa7 locuswas found primarily in the indica and aus subgroups.A variation consisting of an 11-bp insertion and a base substitution(G to T)was found in EBEAvrXa7 in the tested varieties,resulting in a loss of Xa7 BB resistance.Through a decade of effort,we have identified an important BB resistance gene and characterized its distinctive interaction with Xoo strains;these findings will greatly facilitate research on the molecular mechanism of Xa7-mediated resistance and promote the use of this valuable gene in breeding.

Development of nutritious rice with high zinc/selenium and low cadmium in grains through QTL pyramiding

Enriching zinc(Zn) and selenium(Se) levels,while reducing cadmium(Cd) concentration in rice grains is of great benefit for human diet and health.Large natural variations in grain Zn, Se, and Cd concentrations in different rice accessions enable Zn/Sebiofortification and Cd-minimization through molecular breeding. Here, we report the development of new elite varieties by pyramiding major quantitative trait loci(QTLs) that significantly contribute to high Zn/Se and low Cd accumulation in grains. A chromosome segment substitution line CSSLGCC7 with the PA64s-derived GCC7 allele in the 93-11 background, exhibited steadily higher Mn and lower Cd concentrations in grains than those of 93-11. This elite chromosome segment substitution line(CSSL) was used as the core breeding material to cross with CSSLs harboring other major QTLs for essential mineral elements, especially CSSLGZC6 for grain Zn concentration and CSSLGSC5 for grain Se concentration. The CSSLGCC7+GZC6 and CSSLGCC7+GSC5 exhibited lower Cd concentration with higher Zn and Se concentrations in grains, respectively. Our study thus provides elite materials for rice breeding targeting high Zn/Se and low Cd concentrations in grains.

C2H2锌指蛋白LRG1调控水稻小穗的发育

水稻小穗是一种独特的花序结构,其发育直接决定种子的大小和产量.一个正常的水稻小穗包含一个可育小花(1个外稃、1个内稃、2个浆片、6个雄蕊和1个雌蕊)、一对护颖及一对副护颖.通过EMS诱变,本研究分离得到了一个新的隐性水稻小穗突变体lacking rudimentary glume 1(lrg1).lrg1的小穗仅仅只有一个副护颖,且其与护颖一起被同源转化为外稃状器官.细胞学和分子生物学研究发现,LRG1基因在水稻小穗副护颖中显著表达,证明了LRG1是副护颖的特征基因.此外,lrg1突变体谷粒表型异常是由颖壳细胞数目和大小决定的,说明LRG1还参与调控谷粒大小.进一步的实验发现,LRG1基因编码的ZOS4-06-C2H2锌指结构转录因子可能是与TPRs蛋白相互作用来抑制下游基因表达.本研究一方面证实了副护颖、护颖和外稃是同源器官,另一方面LRG1基因参与调控种子大小,为分子设计育种提供了新的基因资源.