Phenotype In Rice Research Articles

Melatonin-deficient rice plants show a common semidwarf phenotype either dependent or independent of brassinosteroid biosynthesis.

Melatonin-deficient rice with a semidwarf erect-leaf phenotype was created by suppressing serotonin N-acetyltransferase 2 (SNAT2). We generated an RNAi transgenic rice that suppressed tryptophan decarboxylase (TDC), which encodes the first TDC enzyme committed step for melatonin biosynthesis in plants catalyzing the conversion of tryptophan into tryptamine, to determine whether other transgenic rice with downregulated melatonin biosynthetic genes exhibited the same erect-leaf phenotype as the snat2 RNAi rice. The TDC RNAi rice produced significantly less melatonin than the wild type and exhibited a semidwarf phenotype, but no erect-leaf phenotype was observed. In contrast, tryptamine 5-hydroxylase (T5H) knockout Sekiguchi rice and caffeic acid O-methyltransferase (COMT) RNAi rice seedlings were semidwarf phenotypes with erect leaves, as was the snat2 RNAi rice due to a melatonin deficiency. All RNAi rice plants showing erect-leaf phenotypes had lower expression levels of the DWARF4 gene, which is a key enzyme for brassinosteroid (BR) biosynthesis, leading to lower BR levels than their respective wild types. Suppressing melatonin synthesis did not alter the contents of indole 3-acetic acid (IAA), suggesting the irrelevance of melatonin deficiency to IAA biosynthesis. These data indicate that a semidwarf seedling is a common rice phenotype by the lack of melatonin synthesis with or without BR suppression in a melatonin biosynthetic gene-specific manner.

Morphological acclimation to agronomic manipulation in leaf dispersion and orientation to promote “Ideotype” breeding: Evidence from 3D visual modeling of “super” rice (Oryza sativa L.)

Food security is confronted by major threats from crop yield stagnation and global climate change. The benefits of phenotypic plasticity across environments for given crop genotypes are thought to be imperative for high-yielding cropping systems. Given that 3D modeling is increasingly recognized for dissecting crop phenotypic plasticity, it requires an assessment of the potential benefits of architectural adaptation of super rice to different agronomic practices. In this study, we focused on a comprehensive evaluation of the phenotypic plasticity of super rice on the aspects of 3D architectural “reoptimization,” photosynthetic productivity, nitrogen economy, and grain yield. A super rice phenotype in superhigh-yielding practice (SH) displays a “reoptimized” morphogenesis in the leaf vertical dispersion and orientation in comparison to that in Farmer's practice (FP). Specifically, a super rice phenotype in SH is provided with a high cumulative rate and peaks of leaf area, increasing the distribution of high leaf inclination angles in comparison to that in FP, particularly in the upper parts of the canopy. These “reoptimizations” sustained profits in light environment within a canopy, leaf area duration, photosynthetic light harvest, and light utilization efficiency and were coordinated with improving nitrogen uptake and assimilation. The current literature indicates that the agronomic plasticity of super rice in architectural “reoptimization” is a promising perspective for high yield formation. Our results suggest that more emphasis should be placed upon agronomic adaptation strategies for super rice across diverse genotypes and environments to further improve crop establishment and photosynthetic productivity.

The Role of Standing Variation in the Evolution of Weedines Traits in South Asian Weedy Rice (Oryza spp.).

Weedy rice (Oryza spp.) is a problematic weed of cultivated rice (O. sativa) around the world. Recent studies have established multiple independent evolutionary origins of weedy rice, raising questions about the traits and genes that are essential for the evolution of this weed. Among world regions, South Asia stands out due to the heterogeneity of its weedy rice populations, which can be traced to at least three origins: two through de-domestication from distinct cultivated rice varieties, and one from local wild rice (O. rufipogon/O. nivara). Here we examine five traits considered typical of or advantageous to weedy rice in weedy, cultivated and wild rice samples from South Asia. We establish that convergence among all three weed groups occurs for easy seed shattering, red pericarp color, and compact plant architecture, suggesting that these traits are essential for weed success in the South Asian agricultural environment. A high degree of convergence for black hull color is also seen among weeds with wild ancestors and weeds evolved from the aus cultivated rice group. We also examine polymorphism in five known domestication candidate genes, and find that Rc and Bh4 are associated with weed seed pericarp color and hull color, respectively, and weedy alleles segregate in the ancestral populations, as do alleles for the seed dormancy-linked gene Sdr4. The presence of a domestication related allele at the seed shattering locus, sh4, in weedy rice populations with cultivated ancestry supports a de-domestication origin for these weedy groups, and raises questions about the reacquisition of the shattering trait in these weedy populations. Our characterization of weedy rice phenotypes in South Asia and their associated candidate genes contribute to the emerging understanding of the mechanisms by which weedy rice evolves worldwide, suggesting that standing ancestral variation is often the source of weedy traits in independently evolved groups, and highlighting the reservoir of genetic variation that is present in cultivated varieties as well as in wild rice, and its potential for phenotypic evolution.

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage.

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

A semi-dominant mutation in a CC-NB-LRR-type protein leads to a short-root phenotype in rice

The mechanisms of plant defense against pathogen attack in plant leaves have been extensively studied. However, our understanding of plant defense mechanisms in plant roots is still limited. In this study, a semi-dominant mutant nrtp1-D (necrotic root tip 1), with a short-root phenotype, was characterized in rice. Map-based cloning revealed that NRTP1 encoded a typical coiled-coil nucleotide binding leucine rich repeat (CC-NB-LRR) type protein and the mutation caused an amino acid substitution in the Nucleotide-Binding adaptor shared by Apaf1, certain R genes and CED4 (NB-ARC) domain, which may cause constitutive auto-activation of the NRTP1 protein. Gene expression analysis revealed that NRTP1 was preferentially expressed in rice roots. Expression of mutant nrtp1-D in tobacco leaves induced necrotic lesions, which indicated a common mechanism of plant defense response between leaves and roots. Transcriptome analysis revealed that many typical defense-response genes were differentially expressed in homozygous nrtp1-D. In addition, we also found differential expression of genes in pathways which had not previously been described as being associated with pathogen response. Histochemical analysis showed that the level of nitric oxide (NO), but not reactive oxygen species (ROS), was increased in homozygous nrtp1-D mutant roots. These results indicate that, in addition to the mechanism of defense response common to both roots and shoots, a novel pathway may also exist in rice roots, which does not operate in shoots.

OsABCG9 Is an Important ABC Transporter of Cuticular Wax Deposition in Rice.

The importance of the cuticular layer in regulating a plant’s water status and providing protection from environmental challenges has been recognized for a long time. The cuticular layer in plants restricts non-stomatal water loss and protects plants against damage from pathogen infection and UV radiation. Much genetic and biochemical research has been done about cutin and wax transportation in Arabidopsis thaliana, but little is known about it in rice. Here, we report that a rice ATP-binding cassette (ABC) transporter, OsABCG9, is essential for normal development during vegetative growth and could play a critical role in the transportation of epicuticular wax in rice. Rice phenotypes with mutated OsABCG9 exhibited growth retardation and sensitivity to low humidity. The total amount of cuticular wax on the leaves of the osabcg9-1 mutant diminished by 53% compared with the wild type, and wax crystals disappeared completely in osabcg9-2 mutant leaves. However, OsABCG9 does not seem to be involved in cutin transportation, even though its ortholog in Arabidopsis, AtABCG11, transports both wax and cutin. Furthermore, the osabcg9-1 mutant had increased leaf chlorophyll leaching and more severe drought susceptibility. This study provides new insights about differences between rice and A. thaliana in wax and cutin transportation associated with the ABCG family during evolution.

SAG12, a Major Cysteine Protease Involved in Nitrogen Allocation during Senescence for Seed Production in Arabidopsis thaliana.

SAG12 is the most widely used senescence-associated reference gene for characterizing leaf senescence, and the increase in SAG12 protein during leaf senescence is remarkable. However, the role of this cysteine protease in N remobilization and the leaf senescence process remains unclear. The role of SAG12 has been poorly investigated and the few reports dealing with this are somewhat controversial. Indeed, sag12 Arabidopsis mutants have not shown any phenotype, while OsSAG12-1 and OsSAG12-2 overexpression in rice moderates senescence progression. Therefore, this study aims at clarifying the role of the SAG12 cysteine protease during the entire plant life span and during leaf senescence. Arabidopsis thaliana plants knocked-out for the SAG12 gene (sag12) did not exhibit any special phenotypic traits when grown under optimal nitrogen supply (HN), suggesting that other cysteine proteases could provide compensatory effects. Moreover, for the first time, this study shows that aspartate protease activity is significantly increased in sag12. Among the putative aspartate proteases involved, a CND41-like aspartate protease has been identified. Under low nitrogen (LN) availability, when inducible proteolytic systems are not sufficient to cope with SAG12 depletion, a decrease in yield is observed. Altogether, these results show that SAG12 (and perhaps also aspartate proteases) could be involved in RuBisCO degradation during the leaf senescence associated with seed filling.

Sheathed Panicle Phenotype (cv. Sathi) Maintains Normal Spikelet Fertility and Grain Filling under Prolonged Heat Stress in Rice

The failure of panicle exertion or sheathed panicle (SP) phenotype in rice (Oryza sativa L.) has been associated with spikelet sterility and grain yield loss under both stress and nonstress conditions. A unique SP phenotype (cv. Sathi) having the potential to maintain normal seed‐set and grain weight (exposed to 38°C for 20 d) was identified. Despite the higher spikelet tissue temperatures (38–40°C) at anthesis, pollen count and germinated pollen grains on the stigma were greater in number than the threshold required for successful seed‐set. Panicle length, total spikelet number, and grain thickness in SP phenotype were not affected significantly by heat stress. In addition, lower lipid peroxidation in spikelets and nonsignificant reduction in carbohydrate metabolism enzymes (invertases and starch synthase) were recorded during grain filling, even after 10 d of heat stress exposure. Minimal impact on carbohydrate metabolism enzymes would support normal sucrose unloading and starch synthesis in the grain and normal grain size under prolonged heat stress exposure. Our findings open novel avenues for genetic and molecular dissection for inducing greater heat stress resilience during anthesis and grain filling in sensitive, popular rice cultivars to sustain global food security under future uncertain environmental conditions.

A Single Nucleotide Mutation of the IspE Gene Participating in the MEP Pathway for Isoprenoid Biosynthesis Causes a Green-Revertible Yellow Leaf Phenotype in Rice.

Plant isoprenoids are dependent on two independent pathways, the cytosolic mevalonate (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. IspE is one of seven known enzymes in the MEP pathway. Currently, no IspE gene has been identified in rice. In addition, no virescent mutants have been reported to result from a gene mutation affecting the MEP pathway. In this study, we isolated a green-revertible yellow leaf mutant gry340 in rice. The mutant exhibited a reduced level of photosynthetic pigments, and an arrested development of chloroplasts and mitochondria in its yellow leaves. Map-based cloning revealed a missense mutation in OsIspE (LOC_Os01g58790) in gry340 mutant plants. OsIspE is constitutively expressed in all tissues, and its encoded protein is targeted to the chloroplast. Further, the mutant phenotype of gry340 was rescued by introduction of the wild-type gene. Therefore, we have successfully identified an IspE gene in monocotyledons via map-based cloning, and confirmed that the green-revertible yellow leaf phenotype of gry340 does result from a single nucleotide mutation in the IspE gene. In addition, the ispE ispF double mutant displayed an etiolation lethal phenotype, indicating that the isoprenoid precursors from the cytosol cannot efficiently compensate for the deficiency of the MEP pathway in rice chloroplasts. Furthermore, real-time quantitative reverse transcription-PCR suggested that this functional defect in OsIspE affected the expression of not only other MEP pathway genes but also that of MVA pathway genes, photosynthetic genes and mitochondrial genes.

Ion beam genetic-technology for modification of rice phenotypes

Ion beam genetic-technology (IBGT) extends ion beam technology to genetic modification of biological living materials aiming at improving biological species properties by ion-beam-induced mutation breeding. In this work, ion beam implantation of rice seeds was operated using a home-developed vertical compact ion implanter which was featured with simple structure, easy operation, high beam intensity and broad beam irradiation, particularly for IBGT applications. Many ten thousands of seeds of two selected local rice varieties were bombarded with 30-kV and 50-kV accelerated mixed molecular and atomic nitrogen ions to fluences ranging from 1 × 1016 to 4 × 1016 ions/cm2. The ion bombardments in 34,000 rice seeds of the two famous Thai rice varieties resulted in broad-spectrum mutation induction found in 91 rice mutants with phenotypic modifications and grain qualities such as photoperiod insensitivity, short in stature and changes in size of rough seed and brown rice, color of brown rice, proximate compositions and antioxidant capacities. This paper reports details of the results and exhibits evidence of the rice developments.

Photosynthesis, cellulose contents and ultrastructure changes of mutant rice leading to screw flag leaf

Leaf rolling is one of the most commonly observed phenotypes in plants and recently more concentration has been paid by researchers on the rolling leaf mutants because of the abundance of rolling leaf phenotypes in rice. The photosynthesis efficiency, chlorophyll contents, cellulose contents, chlorophyll fluorescence and ultrastructure changes between screw flag leaf 1 (sfl1) mutant found in Zhenong 34 (Oryza sativa L. ssp. indica) and wild type (WT) were investigated in the present study. The results indicated that the net photosynthesis rate, stomata conductance, intercellular CO2 concentration and transpiration rate in sfl1 were significantly lower than those in WT. Compared with the WT plant, the chlorophyll a, chlorophyll a + b, Chl a/b and carotenoid contents in sfl1 were significantly decreased, however, the chlorophyll b was lower in WT. The results of chlorophyll fluorescence showed that the variations in maximal quantum yield of PSII (Fv/Fm), effective quantum yield of PSII (ΦPSII) and electron transfer rate (ETR) in sfl1 mutant flag leaves were visibly decreased but photochemical quenching coefficient (qP) and non photochemical quenching coefficient (NPQ) were increased compared with those in the WT. We demonstrated that the cellulose and hemicelluloses contents in sfl1 were significantly lower than those in the WT, while the lignin content was significantly increased in sfl1. Transmission electron micrographs (TEM) revealed that there were distinguishing differences in the chloroplast, mitochondria and starch grana between sfl1 and WT at vegetative stage. However, there was no observable thylakoid in sfl1 chloroplasts at the reproductive stage, indicating that the chloroplasts could be largely undifferentiated in this mutant. These results might provide the significant basis for further understanding the screw leaf development mechanism in rice.

Impairment of Lhca4, a subunit of LHCI, causes high accumulation of chlorophyll and the stay-green phenotype in rice.

Chlorophyll is an essential molecule for acquiring light energy during photosynthesis. Mutations that result in chlorophyll retention during leaf senescence are called 'stay-green' mutants. One of the several types of stay-green mutants, Type E, accumulates high levels of chlorophyll in the pre-senescent leaves, resulting in delayed yellowing. We isolated delayed yellowing1-1 (dye1-1), a rice mutant whose yellowing is delayed in the field. dye1-1 accumulated more chlorophyll than the wild-type in the pre-senescent and senescent leaves, but did not retain leaf functionality in the 'senescent green leaves', suggesting that dye1-1 is a Type E stay-green mutant. Positional cloning revealed that DYE1 encodes Lhca4, a subunit of the light-harvesting complex I (LHCI). In dye1-1, amino acid substitution occurs at the location of a highly conserved amino acid residue involved in pigment binding; indeed, a severely impaired structure of the PSI-LHCI super-complex in dye1-1 was observed in a blue native PAGE analysis. Nevertheless, the biomass and carbon assimilation rate of dye1-1 were comparable to those in the wild-type. Interestingly, Lhcb1, a trimeric LHCII protein, was highly accumulated in dye1-1, in the chlorophyll-protein complexes. The high accumulation of LHCII in the LHCI mutant dye1 suggests a novel functional interaction between LHCI and LHCII.

Statistical Analysis of Foreign Rice Phenotypes under Different Seasons of the Philippines

Korean rice is a foreign genetic resources in the Philippines that has to be characterized for its proper germplasm utility. Ten Korean phenotypes were analyzed using correlation, clustering and principal component analyses (PCA) based on the 13 traits viz., culm length (CL), days to 50% flowering (D50F), days to maturity (DM), filled grains per panicle (FGP), flag leaf length (FLL), flag leaf width (FLW), grain length (GL), grain width (GW), grain yield (GY), plant height (PH), productive tillers (PT), spikelet fertility SF) and thousand grain weight (TGW) under different seasons of the Philippines. It was found out that Korean phenotypes had earlier D50F and DM, shorter PH and CL, more PT, FGP and SF, and higher GY under dry than wet season. Each season had three groups based on the clustering analysis with a pattern of group 1 having phenotypes with heavy TGW, early D50F and DM, short PH and FLL; and more FGP, SF and GY; group 2 having long CL, wide FLW, light TGW; and late D50F and DM; and group 3 having short CL, narrow FLW and low PT. Correlation in FGP, PT and SF to GY was consistently high positive (r≥0.68) in two seasons. Also, PCA consistently showed that GY, PH and PT were the highest contributor of variation with an average of 21.42% in two seasons. Korean GY therefore was highly variable but attaining higher GY can be possible by utilizing grain-filling (FGP and SF) and productive tillering (PT) traits as selection indices in the breeding program.

Relationship between the Spreading-Stub Phenotype of Rice and Negative Gravitropism of Stems at Tillering Stage

Relationship between the Spreading-Stub Phenotype of Rice and Negative Gravitropism of Stems at Tillering Stage

Shortened Basal Internodes Encodes a Gibberellin 2-Oxidase and Contributes to Lodging Resistance in Rice

Breeding semi-dwarf varieties to improve lodging resistance has been proven to be enormously successful in increasing grain yield since the advent of the “green revolution.” However, the breeding of the majority of semi-dwarf rice varieties in Asia has been dependent mainly on genetic introduction of the mutant alleles of SD1, which encodes a gibberellin (GA) 20-oxidase, OsGA20ox2, for catalyzing GA biosynthesis. Here, we report a new rice lodging-resistance gene, Shortened Basal Internodes (SBI), which encodes a gibberellin 2-oxidase and specifically controls the elongation of culm basal internodes through deactivating GA activity. SBI is predominantly expressed in culm basal internodes. Genetic analyses indicate that SBI is a semi-dominant gene affecting rice height and lodging resistance. SBI allelic variants display different activities and are associated with the height of rice varieties. Breeding with higher activity of the SBI allele generates new rice varieties with improved lodging resistance and increased yield. The discovery of the SBI provides a desirable gene resource for producing semi-dwarf rice phenotypes and offers an effective strategy for breeding rice varieties with enhanced lodging resistance and high yield.

Regulation of plant height in rice by the Polycomb group genes OsEMF2b, OsFIE2 and OsCLF

An ideal plant height is essential for crop yield. Some Polycomb group (PcG) genes mutants exhibit a dwarf phenotype in rice. To determine how PcG genes regulate plant height, we investigated the phenotypes of the emf2b mutant and OsEMF2b, OsFIE2 and OsCLF RNAi transgenic plants; they all exhibited dwarf phenotype. Further analyses indicated that stem elongation at jointing stage was seriously inhibited in emf2b and RNAi transgenic plants. Reduced cell expansion and cell division of stem caused significant reduction of stem length during mature period of OsEMF2b, OsFIE2 and OsCLF RNAi transgenic plants. Transcription analysis revealed that cell division, cell expansion and plant hormones related genes differentially expressed between emf2b and WT. In addition, PcG genes mutants weakened GA signal and GA concentration and leaded to suppresseion of plant height. Analysis of differentially expressed genes revealed that 109 up-regulated and 19 down-regulated genes were identified in both emf2b and fie2. H3K27me3-modified sites were observed in 95 of the 109 up-regulated genes, and some of them were up-regulated in OsFIE2, OsCLF and OsEMF2b RNAi transgenic plants, and their H3K27me3 levels were reduced in emf2b. Moreover, OsEMF2b interacted with OsCLF. Therefore, we speculated that these PcG genes, OsFIE2, OsCLF and OsEMF2b, may work as a PRC2 to regulate rice height.

A single nucleotide mutation of IspF gene involved in the MEP pathway for isoprenoid biosynthesis causes yellow-green leaf phenotype in rice.

We identified IspF gene through yellow-green leaf mutant 505ys in rice. OsIspF was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. On expression levels of genes in this mutant, OsIspF itself and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase were all up-regulated, however, among eight genes associated with photosynthesis, only psaA, psaN and psbA genes for three reaction center subunits of photosystem obviously changed. Isoprenoids are the most abundant natural compounds in all organisms, which originate from the basic five-carbon units isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, IPP and DMAPP are synthesized through two independent pathways, the mevalonic acid pathway in cytoplasm and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway in plastids. The MEP pathway comprises seven enzymatic steps, in which IspF is the fifth enzyme. So far, no IspF gene has been identified in monocotyledonous plants. In this study, we isolated a leaf-color mutant, 505ys, in rice (Oryza sativa). The mutant displayed yellow-green leaf phenotype, reduced level of photosynthetic pigments, and arrested development of chloroplasts. By map-based cloning of this mutant, we identified OsIspF gene (LOC_Os02g45660) showing significant similarity to IspF gene of Arabidopsis, in which a missense mutation occurred in the mutant, resulting in an amino acid change in the encoded protein. OsIspF gene was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. Further, the mutant phenotype of 505ys was complemented by transformation with the wild-type OsIspF gene. Therefore, we successfully identified an IspF gene in monocotyledonous plants. In addition, real-time quantitative RT-PCR implied that a positive regulation could exist between the OsIspF gene and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase. At the same time, it also implied that the individual genes involved in the MEP pathway might differentially regulated expression levels of the genes associated with photosynthesis.

Shattering or not shattering: that is the question in domestication of rice (Oryza sativa L.)

The loss of shattering of rice has long been acknowledged as a crucial step sweeping the path of domestication. Here, we collated evidence from genetics, and anthropology to challenge this long-held view. Our discussion dwelt on arguments that (1) undermined the effect of a mutation in the key locus (sh4) which does not always confer non-shattering, (2) identified the involvement of other loci, (3) uncovered natural variation in shatterability still existing in domesticated landraces, and (4) relatively recent fixation of the mutation. Similarly, cultural attributes asserted a long tradition of naturally shattering wild rice cultivation and adaptive strategies of gathering which is still widely exercised in many parts of South and South-East Asia, Africa, and Australia. Altogether, it strongly suggests that primitive agriculture thrived largely relying on wild rice or semi-domesticated shattering phenotype but non-shattering emerged into conspicuity much later in the history.

Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage.

Salt is the major factor limiting crop productivity in saline soils and is controlled by various genes. The development of salt-tolerant rice through molecular breeding methods is important to meet the needs of rice breeding. We used 295 accessions to perform a genome-wide association study (GWAS) of salt tolerance-related phenotypes in rice at the seedling stage and obtained 93 candidate genes with high association peaks across six phenotypes. We constructed a protein interaction network using the candidate genes identified here, and 33 genes were associated. Based on the expression patterns, we found that most of these genes showed a different expression level under control and salt stress conditions. In addition, haplotype network and sequence analysis of one 'key' gene, a transcription factor (Os12g0176700) encoding a SWIRM domain-containing protein, in the interaction network was investigated to explore its possible role in the network. Our study revealed candidate salt tolerance-related genes in rice at the seedling stage, and demonstrated the feasibility of using GWAS to identify genetic architecture underlying salt tolerance. The data generated here may provide resources for molecular breeding and functional analysis of salt tolerance in rice seedlings.

Ectopic Expression of WINDING 1 Leads to Asymmetrical Distribution of Auxin and a Spiral Phenotype in Rice.

Ectopic expression of the rice WINDING 1 (WIN1) gene leads to a spiral phenotype only in shoots but not in roots. Rice WIN1 belongs to a specific class of proteins in cereal plants containing a Bric-a-Brac/Tramtrack/Broad (BTB) complex, a non-phototropic hypocotyl 3 (NPH3) domain and a coiled-coil motif. The WIN1 protein is predominantly localized to the plasma membrane, but is also co-localized to plasmodesmata, where it exhibits a punctate pattern. It is observed that WIN1 is normally expressed in roots and the shoot-root junction, but not in the rest of shoots. In roots, WIN1 is largely localized to the apical and basal sides of cells. However, upon ectopic expression, WIN1 appears on the longitudinal sides of leaf sheath cells, correlated with the appearance of a spiral phenotype in shoots. Despite the spiral phenotype, WIN1-overexpressing plants exhibit a normal phototropic response. Although treatments with exogenous auxins or a polar auxin transport inhibitor do not alter the spiral phenotype, the excurvature side has a higher auxin concentration than the incurvature side. Furthermore, actin filaments are more prominent in the excurvature side than in the incurvature side, which correlates with cell size differences between these two sides. Interestingly, ectopic expression of WIN1 does not cause either unequal auxin distribution or actin filament differences in roots, so a spiral phenotype is not observed in roots. The action of WIN1 appears to be different from that of other proteins causing a spiral phenotype, and it is likely that WIN1 is involved in 1-N-naphthylphthalamic acid-insensitive plasmodesmata-mediated auxin transport.