水稻穗型突变体cl的鉴定、保护与遗传分析

通过神州八号飞船搭载广东省常规优质稻主导品种粤农丝苗获得一个稳定遗传的穗型突变体cl,中文名为粤花占1号,2015年完成农业部植物新品种权的申请工作(申请号:20151728.8,公告号:CNA014491E)。该突变体农艺性状与野生型极为相似,熟色好,产量高,但表现出异常的花序结构,一次枝梗数增加,二次枝梗、小穗梗长度严重缩短,枝梗顶端小穗3粒簇生在一起。进一步的细胞学观测发现,差异主要源自幼穗分化的第3期到第4期发育异常所致。遗传分析表明该性状由非完全显性单基因控制,BSA性状定位法初步将该基因定位于染色体6,命名为CL-6。本研究的结果为进一步精细定位和克隆CL-6基因、找到控制水稻幼穗枝梗伸长缩短的功能基因或调控因子奠定基础,同时为培育理想穗型水稻和观赏农业提供优良种质。     

Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice

Panicle architecture is one of the most important agronomical traits that directly contribute to grain yield in rice (Oryza sativa L.). We report herein an in-depth characterization of two allelic larger panicle (lp) mutants that show significantly increased panicle size as well as improved plant architecture. Morphological analyses reveal that panicles of two mutants produced more inflorescence branches, especially the primary branches, and contained more grains. Moreover, mutant plants also display more lodging resistance than the wild type. The grain yield per plant in mutants is also increased, suggesting that mutant plants have useful potential for high grain yield in rice breeding. Map-based cloning reveals that LARGER PANICLE (LP) encodes a Kelch repeat-containing F-box protein. RNA in situ hybridization studies display that LP expression was enriched in the branch primordial region. Subcellular localization analyses demonstrate that LP is an endoplasmic reticulum (ER) localized protein, suggesting that LP might be involved in ER-associated protein degradation (ERAD). Using yeast two-hybrid assay and bimolecular fluorescence complementation analysis, we confirm that LP is an F-box protein and could interact with rice SKP1-like protein in an F-box domain-dependent manner. Quantitative real-time PCR results show that OsCKX2, which encodes cytokinin oxidase/dehydrogenase, is down-regulated evidently in mutants, implying that LP might be involved in modulating cytokinin level in plant tissues. These results suggest that LP plays an important role in regulating plant architecture, particularly in regulating panicle architecture, thereby representing promising targets for genetic improvement of grain production plants.     

panicle phytomer 1 mutations affect the panicle architecture of rice

 We have characterized three panicle phytomer 1 (pap1) mutations from the phytomer viewpoint. In pap1 mutants, rachis phytomers were strongly affected involving a severe reduction of rachis internode length and an increase in the number of rachis internodes (number of phytomers), resulting in a large number of primary branches. In addition, bracts were frequently over-developed. By contrast, pap1 differently affected primary branch phytomers resulting in a reduction in both the number and length of internodes. Spikelets were also modified. Rudimentary and empty glumes were frequently elongated. Floral organs were mostly normal. However, a double mutation between pap1 and fon1 markedly increased the number of floral organs compared with the single fon1 mutation, suggesting that PAP1 has a distinct role in the differentiation of floral organs. The functions of PAP1 on panicle architecture are: (1) the negative regulation of the number of phytomers on the rachis but a positive regulation of the number on primary branches, (2) an elongation of internodes, and (3) the negative regulation of bract development. Received: 5 October 1997 / Accepted: 27 January 1998     

Overexpression of RCN1 and RCN2, rice TERMINAL FLOWER 1/CENTRORADIALIS homologs,confers delay of phase transition and altered panicle morphology in rice

TERMINAL FLOWER 1 (TFL1)/CENTRORADIALIS (CEN)-like genes play important roles in determining plant architecture, mainly by controlling the timing of phase transition. To investigate the possibility of similar mechanisms operating in the control of inflorescence architecture in rice, we analysed the functions of RCN1 and RCN2, rice TFL1/CEN homologs. Constitutive overexpression of RCN1 or RCN2 in Arabidopsis caused a late-flowering and highly branching phenotype, indicating that they possess conserved biochemical functions as TFL1. In 35S::RCN1 and 35S::RCN2 transgenic rice plants, the delay of transition to the reproductive phase was observed. The transgenic rice plants exhibited a more branched, denser panicle morphology. Detailed observation of the panicle structure revealed that the phase change from the branch shoot to the floral meristem state was also delayed, leading to the generation of higher-order panicle branches. These results suggest rice has a pathway that can respond to the overexpressed TFL1/CEN-like functions, and the molecular mechanisms controlling the phase transition of meristems are conserved between grass and dicot species, at least to some extent.     

Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.)

Architecture of the rice inflorescence, which is determined mainly by the morphology, number and length of primary and secondary inflorescence branches, is an important agronomical trait. In the current study, we characterized a novel dense and erect panicle (EP) mutant, dep3, derived from the Oryza sativa ssp. japonica cultivar Hwacheong treated with N-methyl-N-nitrosourea. The panicle of the dep3 mutant remained erect from flowering to full maturation, whereas the panicle of the wild type plant began to droop after flowering. The dep3 mutation also regulated other panicle characteristics, including panicle length, grain shape and grain number per panicle. Anatomical observations revealed that the dep3 mutant had more small vascular bundles and a thicker culm than wild type plants, explaining the EP phenotype. Genetic analysis indicated that the phenotype with the dense and EP was controlled by a single recessive gene, termed dep3. The DEP3 gene was identified as the candidate via a map-based cloning approach and was predicted to encode a patatin-like phospholipase A2 (PLA2) superfamily domain-containing protein. The mutant allele gene carried a 408?bp genomic deletion within LOC_Os06g46350, which included the last 47?bp coding region of the third exon and the first 361?bp of the 3??-untranslated region. Taken together, our results indicated that the patatin-like PLA2 might play a significant role in the formation of vascular bundles, and that the dep3 mutant may provide another EP resource for rice breeding programs.     

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.     

直立密穗基因DEP2-1388的遗传分析及在杂交稻中的育种利用

通过EMS诱变籼型重穗恢复系蜀恢498,获得一个直立穗突变体R1338。与野生型相比,突变体表现为植株变矮、穗直立、穗长变短、一次枝梗变短、着粒密度增加、穗部抗弯曲力极显著增强、籽粒增宽增厚、粒长变短。组织细胞学分析发现,穗颈节直径、纤维素含量和木质素含量在穗部抗弯曲上发挥了重要的作用。遗传分析表明该直立穗表型受一对半显性核基因DEP2控制,通过重测序以及MutMap方法定位发现,在R1338突变体中,DEP2第7外显子有一个A到G的碱基置换,导致第928个精氨酸(AGG)被置换成甘氨酸(GGG),推测R1338直立穗性状可能由DEP2中该SNP导致。用R1338、野生型与不同穗型不育系分别配组,R1338与弯曲穗不育系所配组合穗部表现半直立,且保持较高的结实率和杂种优势,与DEP1直立穗不育系配组表现为基因累加效应的直立穗。本研究还讨论了直立穗突变体R1338在杂交水稻育种中的利用价值。     

Nitrogen fertilizer increases spikelet number per panicle by enhancing cytokinin synthesis in rice

Key message

Nitrogen fertilizer enhances local cytokinin synthesis to increase flower numbers in the panicles of rice. Localized cytokinin biosynthesis is an important response to nitrogen.

Abstract

Flower number per panicle is one of the most important traits in rice productivity determination. The number of flowers is established in the early stages of panicle development. Nitrogen fertilizer application before panicle initiation is well known to increase flower number. Nitrogen increases cytokinin (CKs) biosynthesis in plants, and CKs have very similar effects as nitrogen fertilizer on panicle branching. The effects of nitrogen fertilizer on panicle branching may be mediated by CKs, in which accumulation in the inflorescence meristem can regulate panicle development, resulting in increased numbers of flowers and branches. Adenosine phosphate-isopentenyltransferase (IPT) catalyzes the rate-limiting step of CKs biosynthesis. We analyzed the effect of nitrogen fertilizer (urea) on the expression of OsIPT genes (OsIPTs). The results showed that OsIPTs were markedly increased, and CKs accumulated in panicle when nitrogen fertilizer was applied. CKs biosynthesis in the roots and leaves was not up-regulated by nitrogen. These results suggest that nitrogen fertilizer enhances local CKs synthesis to increase flower numbers in the panicles of rice. Localized CKs biosynthesis is an important response to nitrogen.     

Improving panicle exsertion of rice cytoplasmic male sterile line by combination of artificial microRNA and artificial target mimic

The adoption of hybrid rice caused the second leap in rice yield after the ‘green revolution’ and contributes substantially to food security of China and the world. However, almost all cytoplasmic male sterile lines (A lines) as females of hybrid rice have a natural deficiency of ‘panicle enclosure’, which blocks pollination between the A line and the fertility restorer line as the male (R line) of hybrid rice and decreases seed yield. In hybrid rice seed production, exogenous ‘920’ (the active ingredient is gibberellin A₃) must be applied to eliminate or alleviate panicle enclosure of the A line; however, this not only increases production cost and pollutes the environment, it also decreases seed quality. In this study, we designed a transgenic approach to improve plant height and panicle exsertion of the A line to facilitate hybrid rice production and maintain the semi‐dwarf plant type of the hybrid. This approach comprising two components—artificial microRNA (amiRNA) and artificial target mimicry—can manipulate the differential expression of the endogenous Eui1 gene that is associated with rice internode elongation in the A line and the hybrid. amiRNA is a recently developed gene silencing method with high specificity, while target mimicry is a natural mechanism inhibiting the miRNA function that was also recently characterized. This approach provides a paradigm to tune the expression of endogenous genes to achieve the desired phenotype by combining amiRNA and artificial target mimicry technologies.     

OsARG encodes an arginase that plays critical roles in panicle development and grain production in rice

Nitrogen is a crucial nutrient for plant growth and development. Arginine is considered to be an important amino acid for nitrogen transport and storage, playing a crucial role during plant seedling development. However, little is known about the role of arginine in nitrogen remobilization at the reproductive stage. We isolated a rice mutant nglf‐1 with reduced plant height, small panicle and grain size, and low seed‐setting rate (10% in nglf‐1 compared to 93% in wild‐type). Map‐based cloning revealed that the mutant phenotype was caused by loss of function of a gene (OsARG) encoding an arginine hydrolysis enzyme, which is consistent with arginine accumulation in the mutant. The phenotype was partially corrected supplying exogenous nitrogen, and fully corrected by expression of a wild‐type OsARG transgene. Over‐expression of OsARG in rice (cv. Kitaake) increased grain number per plant under nitrogen‐limited conditions. OsARG was ubiquitously expressed in various organs, but most strongly in developing panicles. The OsARG protein was localized in the mitochondria, consistent with other arginases. Our results suggest that the arginase encoded by OsARG, a key enzyme in Arg catabolism, plays a critical role during panicle development, especially under conditions of insufficient exogenous nitrogen. OsARG is a potential target for crop improvement.     

籼型常规早稻穗分化期低温对颖花形成和籽粒充实的影响

以籼型常规早稻中嘉早17为材料,于盆栽条件下采用人工气候箱控温,在水稻穗分化一次枝梗原基分化期(Ⅱ)与花粉母细胞减数分裂期(Ⅵ)进行17和20 ℃的低温胁迫处理,研究不同低温对水稻枝梗、颖花分化与退化及籽粒充实的影响.结果表明： 与对照相比,不同低温处理均显著降低每穗枝梗及颖花分化数和现存数,颖花现存数降幅为7.2%～12.4%,同时增加了枝梗和颖花的退化数,影响了花粉活性、花药开裂等花器官发育,导致籽粒充实不良,以17 ℃低温胁迫效应更明显.穗分化Ⅵ期低温处理总枝梗和颖花分化数与现存数低于穗分化Ⅱ期,但二次枝梗和颖花退化数较多,颖花退化数较穗分化Ⅱ期高11.6%;穗分化Ⅱ期低温处理穗部籽粒结实率显著低于穗分化Ⅵ期,降幅达3.7%,主要与花粉粒活性、柱头花粉散落数、花药开裂系数和籽粒充实度受低温影响较大有关.另外,穗分化Ⅱ、Ⅵ两时期受17 ℃低温胁迫效应大于20 ℃.综合穗分化两时期低温胁迫效应的差异,生产中需加强相应栽培措施的调控.     

Novel pleiotropic loci controlling panicle architecture across environments in japonica rice （Oryza sativa L.）

To identify quantitative trait loci (QTLs) controlling panicle architecture in japonica rice, a genetic map was constructed based on simple sequence repeat (SSR) markers and 254 recombinant inbred lines (RILs) derived from a cross between cultivars Xiushui 79 and C Bao. Seven panicle traits were investigated under three environments. Single marker analysis indicated that a total of 27 SSR markers were highly associated with panicle traits in all the three environments. Percentage of phenotypic variation explained by single locus varied from 2% to 35%. Based on the mixed linear model, a total of 40 additive QTLs for seven panicle traits were detected by composite interval mapping, explaining 1.2%-35% of phenotypic variation. Among the 9 QTLs with more than 10% of explained phenotypic variation, two QTLs were for the number of primary branches per panicle (NPB), two for panicle length (PL), two for spikelet density (SD), one for the number of secondary branches per panicle (NSB), one for secondary branch distribution density (SBD), and one for the number of spikelets per panicle (NS), respectively. qPLSD-9-1 and qPLSD-9-2 were novel pleiotropic loci, showing effects on PL and SD simultaneously. qPLSD-9-1 explained 34.7% of the phenotypic variation for PL and 25.4% of the phenotypic variation for SD, respec- tively. qPLSD-9-2 explained 34.9% and 24.4% of the phenotypic variation for PL and SD, respectively. The C Bao alleles at the both QTLs showed positive effects on PL, and the Xiushui 79 alleles at the both QTLs showed positive effects on SD. Genetic variation of panicle traits are mainly attributed to additive effects. QTL × environment interactions were not significant for additive QTLs and additive × additive QTL pairs.     

<Emphasis Type="Italic">OsREL2</Emphasis>, a rice TOPLESS homolog functions in axillary meristem development in rice inflorescence

The morphology of the rice inflorescence, called the panicle, is determined mainly by the activities of axillary meristems including primary, secondary, and spikelet meristems. Recently, in maize, the RAMOSA1 ENHANCER LOCUS2 (REL2) gene, orthologous to the Arabidopsis shoot apical meristem fate-determining TOPLESS, was shown to be involved in the regulation of axillary meristem determinacy. In order to investigate the function of the rice REL2 homolog, we identified and characterized the rice REL2 gene (OsREL2). Compared to other rice TPL homologs, OsREL2 gene expression stayed relatively low throughout panicle development. We characterized a T-DNA insertion osrel2 mutant that showed pleiotropic phenotypic defects, such as defects in panicle heading, sterile lemma elongation, and panicle development, suggesting the OsREL2 functions in multiple developmental processes. In particular, osrel2 developed shorter axillary branches and reduced numbers of lateral organs on axillary branches in comparison to the wild-type, indicating that OsREL2 is important in axillary meristem maintenance. Interestingly, osrel2 produced more primary branches and fewer secondary branches than the wild-type. These results suggest that OsREL2 is involved in branch formation regulation, presumably by suppressing primary branch formation and promoting secondary branch formation.     

基因型×环境互作效应对水稻穗部性状杂种优势的影响

采用包括基因型×环境互作效应的加性显性加性×加性上位性遗传模型,分析了籼粳杂交穗部性状杂种优势的两年资料。结果表明,7个穗部性状的杂种优势既由基因型控制也受环境(年份)互作效应影响。主穗粒数、主穗长、一次和二次枝梗总长和着粒密度表现较强的正向群体平均优势,而一次和二次枝梗数则表现显着的负向优势。基因型×环境互作预测结果表明,主穗粒数、主穗长、一次枝梗总长在两年中的环境互作表现正效应,一次和二次枝梗数则为负效应,着粒密度和二次枝梗总长表现不同方向的效应。利用IR66158-37(P₁)、IR65600-85(P₂)、明恢63(P₄)和R669(P₆)进行杂交配组,其杂种后代易获得重穗型的穗部结构,可在超高产育种中加以利用。     

Flowering time genes Heading date 1 and Early heading date 1 together control panicle development in rice

Although flowering time is often associated with plant size, little is known about how flowering time genes affect plant architecture. We grew four rice lines having different flowering time genotypes (hd1 ehd1, hd1 Ehd1, Hd1 ehd1 and Hd1 Ehd1) under distinct photoperiod conditions. By using genotype-treatment combinations that resulted in similar flowering times, we were able to compare the effects of flowering time genes on traits related to plant architecture. The results revealed that the combination of Heading-date 1 (Hd1) and Early heading date 1 (Ehd1) can reduce the number of primary branches in a panicle, resulting in smaller spikelet numbers per panicle; this occurs independently of the control of flowering time. In addition, expression of the Hd3a and Rice Flowering-locus T 1 (RFT1) florigen genes was up-regulated in leaves of the Hd1 Ehd1 line at the time of the floral transition. We further revealed that Hd1 and/or Ehd1 caused up-regulation of Terminal Flower 1-like genes and precocious expression of panicle formation-related genes at shoot apical meristems during panicle development. Therefore, two key flowering time genes, Hd1 and Ehd1, can control panicle development in rice; this may affect crop yields in the field through florigen expression in leaf.     

Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.)

SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F₂ and F₃ generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F₂ plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F₃ families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle.Feng Tian and Zuo Feng Zhu contributed equally to this work.