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Rice B03S mutants with intermittent leaf discoloration were developed from the photoperiod- and thermosensitive genic male sterile (PTGMS) rice line Efeng 1S. After these plants were deeply transplanted, the new leaves manifested typical stripe patterns. In this study, deep and shallow transplantation of B03S was carried out, and aluminum shading was performed directly on the leaf sheath. It was determined that the reason for the appearance of the striped leaf trait was that the base of leaf sheath lacked light, at which time the sheath transformed from the source organ to the sink organ in rice. To elucidate the related metabolic changes in glycometabolism and abscisic acid (ABA) biosynthesis and transcriptional regulation in the leaf sheath, ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) combined with transcriptome and real-time quantitative PCR (qPCR) validation were used for analysis after deep and shallow transplantation. The result indicates that the leaf sheath may need to compete with the new leaves for sucrose produced by the photosynthesis of old leaves in response to lacking light at the base of sheath. Moreover, the ABA content increases in the leaf sheath when the gene expression of ABA2 and AAO1 is upregulated at the same time, enhancing the plant's resistance to the adverse condition of shading at the leaf sheath. Furthermore, exogenous spraying of B03S with ABA solution was carried out to help recovery under shading stress. The result indicates that the synthesis of endogenous ABA in the leaf sheath is reduced by spraying ABA. At the same time, ABA regulates sucrose metabolism by inhibiting the expression of the SUS gene. This allows for more sucrose synthesized by the old leaves to be transported to the new leaves, resulting an obvious recovery effect of the strip leaf character due to the re-balance of sugar supply and demand in B03S. These findings improve the understanding of the physiological function and metabolic mechanism of the rice leaf sheath, provide a theoretical basis for uneven leaf coloration in nature, and provide theoretical guidance for rice production via seedling transplantation or direct seeding.

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Carbohydrates, proteins, lipids, minerals and vitamins are nutrient substances commonly seen in rice grains, but anthocyanidin, with benefit for plant growth and animal health, exists mainly in the common wild rice but hardly in the cultivated rice. To screen the rice germplasm with high intensity of anthocyanidins and identify the variations, we used metabolomics technique and detected significant different accumulation of anthocyanidins in common wild rice (Oryza rufipogon, with purple leaf sheath) and cultivated rice (Oryza sativa, with green leaf sheath). In this study, we identified and characterized a well-known MYB transcription factor, OsC1, through phenotypic (leaf sheath color) and metabolic (metabolite profiling) genome-wide association studies (pGWAS and mGWAS) in 160 common wild rice (O. rufipogon) and 151 cultivated (O. sativa) rice varieties. Transgenic experiments demonstrated that biosynthesis and accumulation of cyanidin-3-Galc, cyanidin 3-O-rutinoside and cyanidin O-syringic acid, as well as purple pigmentation in leaf sheath were regulated by OsC1. A total of 25 sequence variations of OsC1 constructed 16 functional haplotypes (higher accumulation of the three anthocyanidin types within purple leaf sheath) and 9 non-functional haplotypes (less accumulation of anthocyanidins within green leaf sheath). Three haplotypes of OsC1 were newly identified in our germplasm, which have potential values in functional genomics and molecular breeding of rice. Gene-to-metabolite analysis by mGWAS and pGWAS provides a useful and efficient tool for functional gene identification and omics-based crop genetic improvement.

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OBJECTIVES: The objective of this data set was to identify transcriptional networks that control elongation of seedling leaf sheaths in the C4 grass Sorghum bicolor. One motivation was that leaf sheaths are a primary constituent of stems in grass seedlings; therefore, genes that control growth of this organ are important contributors to successful transition from the seedling stage to the mature plant stage and, ultimately, crop success. Since diurnal rhythms contribute to regulation of signaling networks responsible for growth, a time course representing the late afternoon and early evening was anticipated to pinpoint important control genes for stem growth. Ultimately, the expected outcome was discovery of transcript networks that integrate internal and external signals to fine tune leaf sheath growth and, consequently, plant height. DATA DESCRIPTION: The data set is RNAseq profiling of upper leaf sheaths collected from wild type Sorghum bicolor (BTx623 line) plants at four-hour intervals from 12.5 h after dawn to 20 h after dawn. Global transcript levels in leaves were determined by deep sequencing of mRNA from four individual seedlings at each time point. This data set contains sequences representing the spectrum of mRNAs from individual genes. This data set enables detection of significant changes in gene-level expression caused by the progression of the day from late afternoon to the middle of the night. This data set is useful to identify gene expression networks regulating growth in the leaf sheath, an organ that is a major contributor to the sorghum seedling stem and defines seedling height.

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To play essential roles of manganese (Mn) in plant growth and development, it needs to be transported to different organs and tissues after uptake. However, the molecular mechanisms underlying Mn distribution between different tissues are poorly understood. We functionally characterized a member of rice natural resistance-associated macrophage protein (NRAMP) family, OsNramp5 in terms of its tissue specificity of gene expression, cell-specificity of protein localization, phenotypic analysis of leaf growth and response to Mn fluctuations. OsNramp5 is highly expressed in the leaf sheath. Immunostaining revealed that OsNramp5 is polarly localized at the proximal side of xylem parenchyma cells of the leaf sheath. Both the gene expression and protein abundance of OsNramp5 are unaffected by different Mn concentrations. Knockout of OsNramp5 decreased the distribution of Mn to the leaf sheath, but increased the distribution to the leaf blade at both low and high Mn supplies, resulting in reduced growth of leaf sheath. Furthermore, expression of OsNramp5 under the control of root-specific promoter in osnramp5 mutant complemented Mn uptake, but could not complement Mn distribution to the leaf sheath. These results indicate that OsNramp5 expressed in the leaf sheath plays an important role in unloading Mn from the xylem for the local distribution in rice.

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Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10-30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease.

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The brown planthopper (BPH) (Nilaparvata lugens) sucks rice sap causing leaves to turn yellow and wither, often leading to reduced or zero yields. Rice co-evolved to resist damage by BPH. However, the molecular mechanisms, including the cells and tissues, involved in the resistance are still rarely reported. Single-cell sequencing technology allows us to analyze different cell types involved in BPH resistance. Here, using single-cell sequencing technology, we compared the response offered by the leaf sheaths of the susceptible (TN1) and resistant (YHY15) rice varieties to BPH (48 hours after infestation). We found that the 14,699 and 16,237 cells (identified via transcriptomics) in TN1 and YHY15 could be annotated using cell-specific marker genes into nine cell-type clusters. The two rice varieties showed significant differences in cell types (such as mestome sheath cells, guard cells, mesophyll cells, xylem cells, bulliform cells, and phloem cells) in the rice resistance mechanism to BPH. Further analysis revealed that although mesophyll, xylem, and phloem cells are involved in the BPH resistance response, the molecular mechanism used by each cell type is different. Mesophyll cell may regulate the expression of genes related to vanillin, capsaicin, and ROS production, phloem cell may regulate the cell wall extension related genes, and xylem cell may be involved in BPH resistance response by controlling the expression of chitin and pectin related genes. Thus, rice resistance to BPH is a complicated process involving multiple insect resistance factors. The results presented here will significantly promote the investigation of the molecular mechanisms underlying the resistance of rice to insects and accelerate the breeding of insect-resistant rice varieties.

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Although several regulators associated with purple traits in rice have been identified, the genetic basis of the purple sheath remains unclear. In the present study, F2-1 and F2-2 populations were constructed using purple sheath (H93S) and green sheath (R1173 and YHSM), respectively. In order to identify QTL loci in purple sheaths, BSA analyses were performed on the two F2 populations. A crucial QTL for purple sheath was identified, tentatively named qPLSr6, and was located in the 4.61 Mb to 6.03 Mb region of chromosome 6. Combined with expression pattern analysis of candidate genes, LOC_Os06g10350 (OsC1PLSr) was suggested as a candidate gene. The homozygous mutant KO-1 and KO-2 created through CRISPR/Cas9 editing, lost their purple leaf sheath. The RT-PCR revealed that OsC1PLSr, anthocyanin synthase (ANS), diflavonol-4-reductase (DFR), flavanone-3-hydroxylase (F3H), and flavanone-3'-hydroxylase (F3'H) expression levels were dramatically down-regulated in the mutants. The yeast report system indicated that the 145-272 aa region at the C-terminal of OsC1PLSr is a positive transcriptional activation domain. The results indicated that OsC1PLSr synthesized anthocyanins by regulating the expression of ANS, DFR, F3H, and F3'H. This study provides new insights into the genetic basis of the purple sheath.

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The AP2/ERF family is a large group of plant-specific transcription factors that play an important role in many biological processes, such as growth, development, and abiotic stress responses. OsDREB2B, a dehydration responsive factor (DRE/CRT) in the DREB subgroup of the AP2/ERF family, is associated with abiotic stress responses, such as cold, drought, salt, and heat stress, in Arabidopsis or rice. However, its role in regulating plant growth and development in rice is unclear. In this study, we reported a new function of OsDREB2B, which negatively regulates plant height in rice. Compared with wild type (WT), OsDREB2B-overexpressing (OE) rice exhibited dwarf phenotypes, such as reduction in plant height, internode length, and seed length, as well as grain yield, while the knockout mutants developed by CRISPR/Cas9 technology exhibited similar phenotypes. Spatial expression analysis revealed that OsDREB2B was highly expressed in the leaf sheaths. Under exogenous GA3 application, OsDREB2B expression was induced, and the length of the second leaf sheath of the OsDREB2B-OE lines recovered to that of the WT. OsDREB2B localized to the nucleus of the rice protoplast acted as a transcription activator and upregulated OsAP2-39 by directly binding to its promoter. OsDREB2B-OE lines reduced endogenous bioactive GA levels by downregulating seven GA biosynthesis genes and upregulating eight GA deactivation genes but not GA signaling genes. The yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that OsDREB2B interacted with OsWRKY21. In summary, our study suggests that OsDREB2B plays a negative role in rice growth and development by regulating GA metabolic gene expression, which is mediated by OsAP2-39 and OsWRKY21, thereby reducing GA content and rice plant height.

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Over-accumulation of salt in rice plants is an effect of salt stress which decreases growth and grain yield. Salt removal ability in leaf sheaths is a tolerance mechanism to decrease salt entry and accumulation in leaf blades and maintain photosynthesis under salinity. In this study, a QTL analysis of removal ability of sodium ions (Na+) in leaf sheaths and Na+ accumulation-related traits, was conducted using F2 population between two rice varieties, IR-44595 with superior Na+ removal ability, and 318 with contrasting Na+ removal ability in leaf sheaths under salinity. Suggestive QTLs for Na+ removal ability in leaf sheaths were found on chromosomes 4 and 11. The suggestive QTL on chromosome 11 overlapped with other significant QTLs for Na+ concentration in shoots, leaf blades and leaf sheaths, and Na+/K+ ratio in leaf blades. Correlation analysis indicated that Na+ removal ability in leaf sheaths is important in reducing Na+ accumulation in leaf blades. The varietal difference of Na+ removal ability in leaf sheaths at the whole plant level was greater at lower NaCl concentrations and became smaller as the treatment NaCl concentration increased. Although the Na+ removal ability in leaf sheath was comparable between IR-44595 and 318 under high salinity at the whole plant level, the younger leaves of IR-44595 still showed a higher Na+ sheath-blade ratio than 318, which implied the Na+ removal ability functions in the younger leaves in IR-44595 to reduce Na+ entry in young leaf blades even under high salinity.

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The rapid development of high-throughput phenotypic detection techniques makes it possible to obtain a large number of crop phenotypic information quickly, efficiently, and accurately. Among them, image-based phenotypic acquisition method has been widely used in crop phenotypic identification and characteristic research due to its characteristics of automation, non-invasive, non-destructive and high throughput. In this study, we proposed a method to define and analyze the traits related to leaf sheaths including morphology-related, color-related and biomass-related traits at V6 stage. Next, we analyzed the phenotypic variation of leaf sheaths of 418 maize inbred lines based on 87 leaf sheath-related phenotypic traits. In order to further analyze the mechanism of leaf sheath phenotype formation, 25 key traits (2 biomass-related, 19 morphology-related and 4 color-related traits) with heritability greater than 0.3 were analyzed by genome-wide association studies (GWAS). And 1816 candidate genes of 17 whole plant leaf sheath traits and 1,297 candidate genes of 8 sixth leaf sheath traits were obtained, respectively. Among them, 46 genes with clear functional descriptions were annotated by single nucleotide polymorphism (SNPs) that both Top1 and multi-method validated. Functional enrichment analysis results showed that candidate genes of leaf sheath traits were enriched into multiple pathways related to cellular component assembly and organization, cell proliferation and epidermal cell differentiation, and response to hunger, nutrition and extracellular stimulation. The results presented here are helpful to further understand phenotypic traits of maize leaf sheath and provide a reference for revealing the genetic mechanism of maize leaf sheath phenotype formation.

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Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.

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The biomechanical role of the clasping leaf sheath in stalk lodging events has been historically understudied. Results from this study indicate that in some instances the leaf sheath plays an even larger role in reinforcing wheat against stalk lodging than the stem itself. Interestingly, it appears the leaf sheath does not resist bending loads by merely adding more material to the stalk (i.e., increasing the effective diameter). The radial preload of the leaf sheath on the stem, the friction between the sheath and the stem and several other complex biomechanical factors may contribute to increasing the stalk bending strength and stalk flexural rigidity of wheat. Results demonstrated that removal of the leaf sheath induces alternate failure patterns in wheat stalks. In summary the biomechanical role of the leaf sheath is complex and has yet to be fully elucidated. Many future studies are needed to develop high throughput phenotyping methodologies and to determine the genetic underpinnings of the clasping leaf sheath and its relation to stalk lodging resistance. Research in this area is expected to improve the lodging resistance of wheat.

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In nature, plants have evolved a myriad of preformed and induced defenses to protect themselves from microbes. Upon microbial infection, the recognition of the microbe-associated molecular patterns (MAMPs) by the pattern recognition receptors (PRRs) triggers the first stage of defense response (Dodds and Rathjen, Nat Rev Genet 11:539-548, 2010). However, in order to develop microbial delivery, effectors target PRRs for deregulating immune responses and facilitating host colonization (Thomma et al., Plant Cell 23:4-15, 2011). Here, we contribute a protocol for the screening system of Magnaporthe oryzae effectors and construct a fluorescent system to trace secretory proteins in the sheath infection samples. Using the tobacco rattle virus (TRV) system, the proteins including LysM, Chitin, Cutinase, and CFEM domains were selected and divided into two kinds according to the results of cell death induced or inhibited test in Nicotiana benthamiana. Then, candidate effectors can be deleted or overexpressed in M. oryzae. The barley or rice infection with M. oryzae, rice leaf sheath inoculation, and subcellular localization during infection can be performed to explore the functions of these effectors.

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Phloem-feeding insects cause massive losses in agriculture and horticulture. Host plant resistance to phloem-feeding insects is often mediated by changes in phloem composition, which deter insect settling and feeding and decrease viability. Here, we report that rice plant resistance to the phloem-feeding brown planthopper (BPH) is associated with fortification of the sclerenchyma tissue, which is located just beneath the epidermis and a cell layer or two away from the vascular bundle in the rice leaf sheath. We found that BPHs prefer to feed on the smooth and soft region on the surface of rice leaf sheaths called the long-cell block. We identified Bph30 as a rice BPH resistance gene that prevents BPH stylets from reaching the phloem due to the fortified sclerenchyma. Bph30 is strongly expressed in sclerenchyma cells and enhances cellulose and hemicellulose synthesis, making the cell walls stiffer and sclerenchyma thicker. The structurally fortified sclerenchyma is a formidable barrier preventing BPH stylets from penetrating the leaf sheath tissues and arriving at the phloem to feed. Bph30 belongs to a novel gene family, encoding a protein with two leucine-rich domains. Another member of the family, Bph40, also conferred resistance to BPH. Collectively, the fortified sclerenchyma-mediated resistance mechanism revealed in this study expands our understanding of plant-insect interactions and opens a new path for controlling planthoppers in rice.

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BACKGROUND: Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. RESULTS: In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. CONCLUSIONS: Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

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Cryptochrome 1 and 2 (CRY1 and CRY2) are blue light receptors involved in the regulation of hypocotyl elongation, cotyledon expansion, and flowering time in Arabidopsisthaliana. Two cryptochrome-interacting proteins, Blue-light Inhibitor of Cryptochrome 1 and 2 (BIC1 and BIC2), have been found in Arabidopsis. BIC1 plays critical roles in suppressing the physiological activities of CRY2, which include the blue light-dependent dimerization, phosphorylation, photobody formation, and degradation process, but the functional characterization of BIC protein in other crops has not yet been performed. To investigate the function of BIC protein in rice (Oryza sativa), two homologous genes of Arabidopsis BIC1 and BIC2, namely OsBIC1 and OsBIC2 (OsBICs), were identified. The overexpression of OsBIC1 and OsBIC2 led to increased leaf sheath length, whereas mutations in OsBIC1 displayed shorter leaf sheath in a blue light intensity-dependent manner. OsBIC1 regulated blue light-induced leaf sheath elongation through direct interaction with OsCRY1a, OsCRY1b, and OsCRY2 (OsCRYs). Longitudinal sections of the second leaf sheath demonstrated that OsBIC1 and OsCRYs controlled leaf sheath length by influencing the ratio of epidermal cells with different lengths. RNA-sequencing (RNA-seq) and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) analysis further proved that OsBIC1 and OsCRYs regulated similar transcriptome changes in regulating Gibberellic Acids (GA)-responsive pathway. Taken together, these results suggested that OsBIC1 and OsCRYs worked together to regulate epidermal cell elongation and control blue light-induced leaf sheath elongation through the GA-responsive pathway.

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BACKGROUND: A significant mechanism of salt-tolerance in rice is the ability to remove Na+ and Cl- in the leaf sheath, which limits the entry of these toxic ions into the leaf blade. The leaf sheath removes Na+ mainly in the basal parts, and Cl- mainly in the apical parts. These ions are unloaded from the xylem vessels in the peripheral part and sequestered into the fundamental parenchyma cells at the central part of the leaf sheath. RESULTS: This study aimed to identify associated Na+ and Cl- transporter genes with this salt removal ability in the leaf sheath of rice variety FL 478. From 21 known candidate Na+ and Cl- transporter rice genes, we determined the salt responsiveness of the expression of these genes in the basal and apical parts, where Na+ or Cl- ions were highly accumulated under salinity. We also compared the expression levels of these transporter genes between the peripheral and central parts of leaf sheaths. The expression of 8 Na+ transporter genes and 3 Cl- transporter genes was up-regulated in the basal and apical parts of leaf sheaths under salinity. Within these genes, OsHKT1;5 and OsSLAH1 were expressed highly in the peripheral part, indicating the involvement of these genes in Na+ and Cl- unloading from xylem vessels. OsNHX2, OsNHX3, OsNPF2.4 were expressed highly in the central part, which suggests that these genes may function in sequestration of Na+ and Cl- in fundamental parenchyma cells in the central part of leaf sheaths under salinity. Furthermore, high expression levels of 4 candidate genes under salinity were associated with the genotypic variation of salt removal ability in the leaf sheath. CONCLUSIONS: These results indicate that the salt removal ability in rice leaf sheath may be regulated by expressing various Na+ or Cl- transporter genes tissue-specifically in peripheral and central parts. Moreover, some genes were identified as candidates whose expression levels were associated with the genotypic variation of salt removal ability in the leaf sheath. These findings will enhance the understanding of the molecular mechanism of salt removal ability in rice leaf sheath, which is useful for breeding salt-tolerant rice varieties.

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BACKGROUND AND AIMS: The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS: In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS: For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS: These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.

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